EXERCISE 92-07
Programs used in this exercise:
(1) Sequence manipulation ¡V reverse
(2) ORF Searching - frames, map, translate
(3) Mapping (restriction sites) ¡V map (-minc, -maxc), mapsort(-exclude, -digest), mapplot, plasmidmap
(4) Mapping (transcription factor) - map(tfsites).
Sequences used in this exercise:
gb:z18853 (C.elegans mRNA for capping protein alpha subunit.)
cds:10-858
gb:x03795 (Human mRNA for platelet derived growth factor A-chain, PDGF-A) cds:388-1020.
-------------------------------------------------------------------------------
gcg2 1% go
gcg2 3% fetch gb:z18853
Fetch copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
z18853.gb_in1
gcg2 5% ls
z18853.gb_in1
gcg2 13% reverse z18853.gb_in1
Reverse reverses and/or complements a sequence.
Begin (* 1 *) ?
End (* 1144 *) ?
Do you want to:
1) reverse only
2) complement only
3) reverse and complement
Please choose one (* 3 *) ? Try options 1, 2 and 3 one by one
What should I call the output file (* z18853.rev *) ?
Use file extensions r for option 1 (z18853.r)
c for option 2 (z18853.c)
rc for option 3 (z18853.rc)
gcg2 5% ls
z18853.gb_in1 z18853.r z18853.c z18853.rc
*****Use cat to view and compare the files z18853.gb_in1 and z18853.r-c-rc.
Observe the differences among them
-------------------------------------------------------------------------------------------------------
gcg2 6% map gb:z18853
Map maps a DNA sequence and displays both strands of the mapped sequence
with restriction enzyme cut points above the sequence and protein
translations below. Map can also create a peptide map of an amino acid
sequence.
Begin (* 1 *) ?
End (* 1144 *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):HELP
What protein translations do you want:
a) frame 1 b) frame 2 c) frame 3
a) frame 1 b) frame 2 c) frame 3
d) frame 4 e) frame 5 f) frame 6
t)hree forward frames s)ix frames o)pen frames only
n)o protein translation q)uit
Please select (capitalize for 3-letter) (* t *):
What should I call the output file (* z18853.map *) ?
Mapping .
Writing ....................
MAP complete with:
Sequence Length: 1,144
Enzymes Chosen: 0
Cutsites found: 0
CPU time: 00.50
Output file: z18853.map
gcg2 7% cat z18853.map
(Linear) MAP of: gb_in1:z18853 check: 4598 from: 1 to: 1144
LOCUS CECPASMR 1144 bp mRNA INV 10-MAR-1994
DEFINITION C.elegans mRNA for capping protein alpha subunit.
ACCESSION Z18853
VERSION Z18853.1 GI:6687
KEYWORDS capping protein alpha subunit.
SOURCE Caenorhabditis elegans. . . .
April 28, 2000 11:16 ..
AGTTTGAGAATGTCGGAGATCAGTGACGCCGAAAAGGTCCGCATTGCTTCGGATTTCATT
1 ---------+---------+---------+---------+---------+---------+ 60
TCAAACTCTTACAGCCTCTAGTCACTGCGGCTTTTCCAGGCGTAACGAAGCCTAAAGTAA
a S L R M S E I S D A E K V R I A S D F I -
b V * E C R R S V T P K R S A L L R I S L -
c F E N V G D Q * R R K G P H C F G F H * -
AAACACGCGCCACCCGGCGAGTTCAACGAGGTATTCAATTCGGTTCGGATGCTTTTGGAA
61 ---------+---------+---------+---------+---------+---------+ 120
TTTGTGCGCGGTGGGCCGCTCAAGTTGCTCCATAAGTTAAGCCAAGCCTACGAAAACCTT
a K H A P P G E F N E V F N S V R M L L E -
b N T R H P A S S T R Y S I R F G C F W K -
c T R A T R R V Q R G I Q F G S D A F G K -
AATGATGATCTTCTGAAGAACAAATGTGTTAATGCTATCGCTCAATATAACGTTGGACAA
121 ---------+---------+---------+---------+---------+---------+ 180
TTACTACTAGAAGACTTCTTGTTTACACAATTACGATAGCGAGTTATATTGCAACCTGTT
a N D D L L K N K C V N A I A Q Y N V G Q -
b M M I F * R T N V L M L S L N I T L D N -
c * * S S E E Q M C * C Y R S I * R W T I -
TTTGTGCCAGTAAAGTTGGATGGTGTTGCCAAGCAGACTCTGATCACTCCATACAATGAT
181 ---------+---------+---------+---------+---------+---------+ 240
AAACACGGTCATTTCAACCTACCACAACGGTTCGTCTGAGACTAGTGAGGTATGTTACTA
a F V P V K L D G V A K Q T L I T P Y N D -
b L C Q * S W M V L P S R L * S L H T M I -
c C A S K V G W C C Q A D S D H S I Q * F -
TTGGGTAATGGACGTTTCTACGATGAAGTTTCAAAGAAAAGTTTCAAATACGATCACGTC
241 ---------+---------+---------+---------+---------+---------+ 300
AACCCATTACCTGCAAAGATGCTACTTCAAAGTTTCTTTTCAAAGTTTATGCTAGTGCAG
a L G N G R F Y D E V S K K S F K Y D H V -
b W V M D V S T M K F Q R K V S N T I T S -
c G * W T F L R * S F K E K F Q I R S R P -
CGTAAAGAGGCCGCAGATCTTCAACCACATCCAGCCGAGTCTGGAATAACCGAACAATGG
301 ---------+---------+---------+---------+---------+---------+ 360
GCATTTCTCCGGCGTCTAGAAGTTGGTGTAGGTCGGCTCAGACCTTATTGGCTTGTTACC
a R K E A A D L Q P H P A E S G I T E Q W -
b V K R P Q I F N H I Q P S L E * P N N G -
c * R G R R S S T T S S R V W N N R T M A -
CGTCAAGCTCTTCAAACTCAACTCGATATATATATTGATGATCATTACGCGAAAAGTGGA
361 ---------+---------+---------+---------+---------+---------+ 420
GCAGTTCGAGAAGTTTGAGTTGAGCTATATATATAACTACTAGTAATGCGCTTTTCACCT
a R Q A L Q T Q L D I Y I D D H Y A K S G -
b V K L F K L N S I Y I L M I I T R K V E -
c S S S S N S T R Y I Y * * S L R E K W N -
ACGGGAGTGGTTTTTGCTCGAAACGGAGTTTTCACGATTTGCATCGAATCTCATCAATTC
421 ---------+---------+---------+---------+---------+---------+ 480
TGCCCTCACCAAAAACGAGCTTTGCCTCAAAAGTGCTAAACGTAGCTTAGAGTAGTTAAG
a T G V V F A R N G V F T I C I E S H Q F -
b R E W F L L E T E F S R F A S N L I N S -
c G S G F C S K R S F H D L H R I S S I P -
CAGCCAAAAAATTTCTGTAACGGAAGATGGCGTTCGGAGTGGAATGTGCCGGTTGGCGAT
481 ---------+---------+---------+---------+---------+---------+ 540
GTCGGTTTTTTAAAGACATTGCCTTCTACCGCAAGCCTCACCTTACACGGCCAACCGCTA
a Q P K N F C N G R W R S E W N V P V G D -
b S Q K I S V T E D G V R S G M C R L A M -
c A K K F L * R K M A F G V E C A G W R W -
GGTAAATCAGGATCTCAGGAGATGAAAGGAAAAATTTTGTCGCAAGTTCATTATTACGAA
541 ---------+---------+---------+---------+---------+---------+ 600
CCATTTAGTCCTAGAGTCCTCTACTTTCCTTTTTAAAACAGCGTTCAAGTAATAATGCTT
a G K S G S Q E M K G K I L S Q V H Y Y E -
b V N Q D L R R * K E K F C R K F I I T K -
c * I R I S G D E R K N F V A S S L L R R -
GACGGAAACGTGCAGTTGTTCTCTGAGAAAGAGCCGGTTCTTAAAGTCAATGTTTCGGCT
601 ---------+---------+---------+---------+---------+---------+ 660
CTGCCTTTGCACGTCAACAAGAGACTCTTTCTCGGCCAAGAATTTCAGTTACAAAGCCGA
a D G N V Q L F S E K E P V L K V N V S A -
b T E T C S C S L R K S R F L K S M F R L -
c R K R A V V L * E R A G S * S Q C F G * -
GACTTCGACAAAACCGCCAAAGAAATAATTCATGCCATTTCCGAGGAAGAGACTATATAT
661 ---------+---------+---------+---------+---------+---------+ 720
CTGAAGCTGTTTTGGCGGTTTCTTTATTAAGTACGGTAAAGGCTCCTTCTCTGATATATA
a D F D K T A K E I I H A I S E E E T I Y -
b T S T K P P K K * F M P F P R K R L Y I -
c L R Q N R Q R N N S C H F R G R D Y I S -
CAGAATGCTGTACAAGAGAATTACGCTAATATGTCTGATACCACATTCAAAGCACTTCGT
721 ---------+---------+---------+---------+---------+---------+ 780
GTCTTACGACATGTTCTCTTAATGCGATTATACAGACTATGGTGTAAGTTTCGTGAAGCA
a Q N A V Q E N Y A N M S D T T F K A L R -
b R M L Y K R I T L I C L I P H S K H F V -
c E C C T R E L R * Y V * Y H I Q S T S S -
CGCCAATTGCCAGTTACTCGCGCTAAGATGGACTGGAATAAGGCTCAAACCTACCGAATT
781 ---------+---------+---------+---------+---------+---------+ 840
GCGGTTAACGGTCAATGAGCGCGATTCTACCTGACCTTATTCCGAGTTTGGATGGCTTAA
a R Q L P V T R A K M D W N K A Q T Y R I -
b A N C Q L L A L R W T G I R L K P T E L -
c P I A S Y S R * D G L E * G S N L P N W -
GGTCAGGAAATGAAGTAATCACAAAATCGTTATCACATCGCTTTGCTTCAAGTTCGTCTG
841 ---------+---------+---------+---------+---------+---------+ 900
CCAGTCCTTTACTTCATTAGTGTTTTAGCAATAGTGTAGCGAAACGAAGTTCAAGCAGAC
a G Q E M K * S Q N R Y H I A L L Q V R L -
b V R K * S N H K I V I T S L C F K F V C -
c S G N E V I T K S L S H R F A S S S S A -
CTGGTCTTCATCATCTTCCTAATCCTCTCCAAAAACCAAAAAATCCTCCAATTTCGACCT
901 ---------+---------+---------+---------+---------+---------+ 960
GACCAGAAGTAGTAGAAGGATTAGGAGAGGTTTTTGGTTTTTTAGGAGGTTAAAGCTGGA
a L V F I I F L I L S K N Q K I L Q F R P -
b W S S S S S * S S P K T K K S S N F D L -
c G L H H L P N P L Q K P K N P P I S T F -
TTATTTCTCCCACTTTCCTTTATCCTTTGGCCGGACACTAGACGTGCTTTACAACATAAT
961 ---------+---------+---------+---------+---------+---------+ 1020
AATAAAGAGGGTGAAAGGAAATAGGAAACCGGCCTGTGATCTGCACGAAATGTTGTATTA
a L F L P L S F I L W P D T R R A L Q H N -
b Y F S H F P L S F G R T L D V L Y N I I -
c I S P T F L Y P L A G H * T C F T T * Y -
ACCCTTCGTTTGCTCCGCTGCTTCTTTTTTCATGATTTGATAATTTGTATCATCTATGTA
ACCCTTCGTTTGCTCCGCTGCTTCTTTTTTCATGATTTGATAATTTGTATCATCTATGTA
1021 ---------+---------+---------+---------+---------+---------+ 1080
TGGGAAGCAAACGAGGCGACGAAGAAAAAAGTACTAAACTATTAAACATAGTAGATACAT
a T L R L L R C F F F H D L I I C I I Y V -
b P F V C S A A S F F M I * * F V S S M Y -
c P S F A P L L L F S * F D N L Y H L C I -
TCTAATTTTATTGTATGGTATGATTCATTTTTCAATTATATATTATTTGTGTGTGTGTGA
1081 ---------+---------+---------+---------+---------+---------+ 1140
AGATTAAAATAACATACCATACTAAGTAAAAAGTTAATATATAATAAACACACACACACT
a S N F I V W Y D S F F N Y I L F V C V * -
b L I L L Y G M I H F S I I Y Y L C V C D -
c * F Y C M V * F I F Q L Y I I C V C V I -
TTAA
1141 ---- 1144
AATT
a L -
b * -
c -
-------------------------------------------------------------------------------------------------------
gcg2 8% translate gb:z18853
Translate translates nucleotide sequences into peptide sequences.
Begin (* 1 *) ? 10
End (* 1144 *) ? 858
Reverse (* No *) ?
Range begins ATGTC and ends AGTAA. Is this correct (* Yes *) ?
That is done, now would you like to:
A) Add another exon from this sequence
B) Add another exon from a new sequence
C) Translate and then add more genes from this sequence
D) Translate and then add more genes from a new sequence
W) Translate assembly and write everything into a file
Please choose one (* W *):
What should I call the output file (* z18853.pep *) ?
gcg2 9% cat z18853.pep
!!AA_SEQUENCE 1.0
TRANSLATE of: z18853 check: 4598 from: 10 to: 858
generated symbols 1 to: 283.
generated symbols 1 to: 283.
LOCUS CECPASMR 1144 bp mRNA INV 10-MAR-1994
DEFINITION C.elegans mRNA for capping protein alpha subunit.
ACCESSION Z18853
VERSION Z18853.1 GI:6687
KEYWORDS capping protein alpha subunit.
SOURCE Caenorhabditis elegans. . . .
z18853.pep Length: 283 April 28, 2000 11:21 Type: P Check: 8944 ..
1 MSEISDAEKV RIASDFIKHA PPGEFNEVFN SVRMLLENDD LLKNKCVNAI
51 AQYNVGQFVP VKLDGVAKQT LITPYNDLGN GRFYDEVSKK SFKYDHVRKE
101 AADLQPHPAE SGITEQWRQA LQTQLDIYID DHYAKSGTGV VFARNGVFTI
151 CIESHQFQPK NFCNGRWRSE WNVPVGDGKS GSQEMKGKIL SQVHYYEDGN
201 VQLFSEKEPV LKVNVSADFD KTAKEIIHAI SEEETIYQNA VQENYANMSD
251 TTFKALRRQL PVTRAKMDWN KAQTYRIGQE MK*
-------------------------------------------------------------------------------------------------------
gcg2 16% fetch gb:x03795
Fetch copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
x03795.gb_pr2
gcg2 17% map gb:x03795
Map maps a DNA sequence and displays both strands of the mapped sequence
with restriction enzyme cut points above the sequence and protein
translations below. Map can also create a peptide map of an amino acid
sequence.
Begin (* 1 *) ?
End (* 1308 *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):***Press return to select all the enzymes in the list
What protein translations do you want:
a) frame 1 b) frame 2 c) frame 3
d) frame 4 e) frame 5 f) frame 6
t)hree forward frames s)ix frames o)pen frames only
n)o protein translation q)uit
Please select (capitalize for 3-letter) (* t *):
What should I call the output file (* x03795.map *) ?
Mapping .............................
Writing ........... ..
MAP complete with:
Sequence Length: 1,308
Enzymes Chosen: 209
Cutsites found: 531
CPU time: 00.85
Output file: x03795.map
gcg2 18% cat x03795.map
(Linear) MAP of: gb_pr2:x03795 check: 5107 from: 1 to: 1308
LOCUS HSPDGFAR 1308 bp mRNA PRI 21-MAR-1995
DEFINITION Human mRNA for platelet derived growth factor A-chain (PDGF-A).
ACCESSION X03795
VERSION X03795.1 GI:35365
KEYWORDS glycoprotein; platelet-derived growth factor 1; signal peptide.
SOURCE human. . . .
With 209 enzymes: *
April 28, 2000 14:13 ..
NciI
ScrFI BslI
BsiEI| AciI|
HpaII| BstUI|
BssKI|| HhaI| AciI
CviJI|| HinP1I || BstUI
HaeIII|| MnlI || HhaI
EaeI ||| Cac8I | || HinP1I |
EagI ||| CviJI | | || Eco57I| |
Tsp509I HpaII| ||| FauI| | | || Fnu4HI|| |
AciI HpyCH4V |BsrFI|| ||| MwoI || | | || TseI||| |
| | | ||| ||| | || | | || |||| |
TCCGCAAATATGCAGAATTACCGGCCGGGTCGCTCCTGAAGCCAGCGCGGGGAGGCAGCG
1 ---------+---------+---------+---------+---------+---------+ 60
AGGCGTTTATACGTCTTAATGGCCGGCCCAGCGAGGACTTCGGTCGCGCCCCTCCGTCGC
a S A N M Q N Y R P G R S * S Q R G E A A -
b P Q I C R I T G R V A P E A S A G R Q R -
c R K Y A E L P A G S L L K P A R G G S A -
NciI
ScrFI
BslI|
HpaII|
BssKI||
Cac8I |||
CviJI | |||
HaeIII | |||
BbvI | | |||
EaeI | | |||
Fnu4HI | | |||
AciI| | | ||| BsmFI
MwoI| | | ||| AciI |
Fnu4HI || | | ||| MboII | |
AciI| || | | ||| BsaJI CviJI| | |AciI
Fnu4HI || || | | ||| MnlI | CviJI EciI| | |FauI
| || || | | ||| | | | || | | |
CGGCGGCGGCCAGCACCGGGAACGCACCGAGGAAGAAGCCCAGCCCCCGCCCTCCGCCCC
61 ---------+---------+---------+---------+---------+---------+ 120
GCCGCCGCCGGTCGTGGCCCTTGCGTGGCTCCTTCTTCGGGTCGGGGGCGGGAGGCGGGG
a R R R P A P G T H R G R S P A P A L R P -
b G G G Q H R E R T E E E A Q P P P S A P -
c A A A S T G N A P R K K P S P R P P P L -
NlaIV
CviJI|
BglI ||
MwoI ||
BstNI | || BseRI
ScrFI | || BseRI |
BsaJI | | || HhaI | |
BssKI | | || BstUI | | |
PspGI | | || Cac8I | | |
CviJI| | | || HhaI | | |
HaeIII| | | || HinP1I | | |
MnlI|| | | || BssHII | | | |
Sau96I|| | | || HinP1I | | | |
Fnu4HI||| | | || FauI| | | | |
AciI|||| | | || Cac8I|| | | | |
HpaII ||||| | | || BslI ||| | | | |
NciI ||||| | | || HhaI ||| | | | |
ScrFI ||||| | | || BstUI | ||| | | | |
BslI| ||||| | | ||HinP1I | ||| | | | |
FokI BssKI|| ||||| | | || MwoI| | ||| | | | |
MnlI| BstF5I ||| ||||| | | ||AciI|| | ||| | | | |
|| | ||| ||||| | | || ||| | ||| | | | |
TTCCGTCCCCACCCCCATCCCGGCGGCCCAGGAGGCTCCCCGCGCTGGCGCGCACTCCCT
121 ---------+---------+---------+---------+---------+---------+ 180
AAGGCAGGGGTGGGGGTAGGGCCGCCGGGTCCTCCGAGGGGCGCGACCGCGCGTGAGGGA
a F R P H P H P G G P G G S P R W R A L P -
b S V P T P I P A A Q E A P R A G A H S L -
c P S P P P S R R P R R L P A L A R T P C -
Cac8I BbeI
MwoI| HaeII
Fnu4HI || HhaI|
HaeII || NlaIV||
HhaI| || SfoI||
MwoI| || BsaHI|||
TseI| || HinP1I|||
HinP1I || || NarI|||
MnlI| || || BanI||||
Cac8I|| || || KasI||||
CviJI ||| || || MwoI |||||
MnlI ||| || || NciI |||||
BstNI | ||| || || ScrFI |||||
ScrFI | ||| || || EciI| |||||
BslI| | ||| || || BstAPI HpaII| |||||
BssKI|| | ||| || || MwoI BssKI|| |||||
PspGI|| | ||| || || BtsI |Cac8I ||| |||||
BbvI ||| | ||| || || AciI MnlI| |TspRI ||| |||||
| ||| | ||| || || | || | | ||| |||||
GTTTCTCCTCCTCCTGGCTGGCGCTGCCTGCCTCTCCGCACTCACTGCTCGCCGGGCGCC
181 ---------+---------+---------+---------+---------+---------+ 240
CAAAGAGGAGGAGGACCGACCGCGACGGACGGAGAGGCGTGAGTGACGAGCGGCCCGCGG
a V S P P P G W R C L P L R T H C S P G A -
b F L L L L A G A A C L S A L T A R R A P -
c F S S S W L A L P A S P H S L L A G R R -
Bsu36I
HhaI |
BstUI | |
HinP1I | |
MnlI | |
AciI | | |
Fnu4HI | | |
CviJI| | | |
FauI HaeIII| | | |
HhaI | MnlI| | | |
BstUI | | Sau96I || | | |
HinP1I | | NciI| || | | |
AluI BseRI| | | ScrFI| || | | |
CviJI MwoI| | | BslI|| || | | |
Cac8I | AciI|| | | HpaII|| || | | |
AciI | | BsiHKAI ||| | | BslI||| || | | |
MwoI| | | Bsp1286I ||| | | BssKI||| || | | DdeI Csp6I
|| | | | ||| | | |||| || | | | |
GTCCGCCAGCTCCGTGCTCCCCGCGCCACCCTCCTCCGGGCCGCGCTCCCTAAGGGATGG
241 ---------+---------+---------+---------+---------+---------+ 300
CAGGCGGTCGAGGCACGAGGGGCGCGGTGGGAGGAGGCCCGGCGCGAGGGATTCCCTACC
a V R Q L R A P R A T L L R A A L P K G W -
b S A S S V L P A P P S S G P R S L R D G -
c P P A P C S P R H P P P G R A P * G M V -
BpmI
FauI|
BseRI ||
CviJI ||
HaeIII ||
Fnu4HI | ||
SacII | ||
AciI| | ||
BstUI| | ||
BsaI AciI MspA1I| | ||
BsmAI Fnu4HI BslI|| | ||
AciI | CviJI HaeII AciI||| | ||
BstF5I Fnu4HI | HpaII | HhaI|BsaJI||| | ||
RsaI FokI | | BsrFI| |HinP1I || BtgI||| | || MnlI
| | | | || | | || |||| | || |
TACTGATTTTCGCCGCCACAGGAGACCGGCTGGAGCGCCGCCCCGCGGCCTCGCCTCTCC
301 ---------+---------+---------+---------+---------+---------+ 360
ATGACTAAAAGCGGCGGTGTCCTCTGGCCGACCTCGCGGCGGGGCGCCGGAGCGGAGAGG
a Y * F S P P Q E T G W S A A P R P R L S -
b T D F R R H R R P A G A P P R G L A S P -
c L I F A A T G D R L E R R P A A S P L L -
BbvI
AvaI|
BsaJI||
HaeII||
HhaI|||
HinP1I |||| BbvI
MwoI| |||| BsaJI
Cac8I|| |||| StyI Fnu4HI
CviJI ||| |||| BsmFI| TseI|
MnlI ||| |||| AvaII || BbvI || Fnu4HI
Fnu4HI | ||| |||| EcoO109I || Cac8I || CviJI|
TseI| | ||| |||| MnlI PpuMI || BseRI | || TseI|
MnlI || | ||| |||| BstUI|Sau96I || Cac8I| | || BciVI||
Hpy188I| || | ||| |||| MnlI || HgaI| ||CviJI || | ||BsaJI |||
|| || | ||| |||| | || || || | || | || | |||
TCCGAGCAGCCAGCGCCTCGGGACGCGATGAGGACCTTGGCTTGCCTGCTGCTCCTCGGC
361 ---------+---------+---------+---------+---------+---------+ 420
AGGCTCGTCGGTCGCGGAGCCCTGCGCTACTCCTGGAACCGAACGGACGACGAGGAGCCG
a S E Q P A P R D A M R T L A C L L L L G -
b P S S Q R L G T R * G P W L A C C S S A -
c R A A S A S G R D E D L G L P A A P R L -
BsaJI BslI
CviJI| BstUI|
HaeIII| AciI ||
EaeI || MnlI | ||
BslI | || DpnI | | || TaqI
MnlI | || BstYI | | | || DpnI|
PflMI | || CviJI | | | | || MboI ||
MnlI MnlI | | || AlwI| | | | | || MnlI ||
AciI | NlaIII | | || MwoI ||MboI | | | ||FauI| ||
| | | | | || | || | | | | || || ||
TGCGGATACCTCGCCCATGTTCTGGCCGAGGAAGCCGAGATCCCCCGCGAGGTGATCGAG
421 ---------+---------+---------+---------+---------+---------+ 480
ACGCCTATGGAGCGGGTACAAGACCGGCTCCTTCGGCTCTAGGGGGCGCTCCACTAGCTC
a C G Y L A H V L A E E A E I P R E V I E -
b A D T S P M F W P R K P R S P A R * S R -
c R I P R P C S G R G S R D P P R G D R E -
MlyI
PleI
SfaNI |
NlaIV| |
AvaII|| |
EcoO109I|| |
PpuMI|| |
Sau96I|| |
NciI ||| |
ScrFI ||| |
HpaII| ||| |
BssKI|| ||| |
BstF5I ||| ||| |
BpmI | ||| ||| |
DpnI | | ||| ||| |
BstYI | | | ||| ||| |
Hpy188I | | | ||| ||| |
MboI | | | ||| ||| |
FauI| | | | ||| ||| |
FokI || | | | ||| ||| |
AlwI| || | | | ||| ||| | MlyI
AciI || || | | | ||| ||| | PleI
Cac8I || || | | | ||| ||| | BstNI |
CviJI | || || | | | ||| ||| | ScrFI |
HaeIII | || || | | | ||| ||| | BssKI | |
Sau96I| | || || | | | ||| ||| | PspGI | |
Cac8I|| | || || | | | ||| ||| | BsmFI| | |
CviJI ||| | || || | | | ||| ||| | MnlI| | |
HphI ||| | || || | | | ||| ||| | HinfI || | | HinfI
| ||| | || || | | | ||| ||| | | || | | |
AGGCTGGCCCGCAGTCAGATCCACAGCATCCGGGACCTCCAGCGACTCCTGGAGATAGAC
481 ---------+---------+---------+---------+---------+---------+ 540
TCCGACCGGGCGTCAGTCTAGGTGTCGTAGGCCCTGGAGGTCGCTGAGGACCTCTATCTG
a R L A R S Q I H S I R D L Q R L L E I D -
b G W P A V R S T A S G T S S D S W R * T -
c A G P Q S D P Q H P G P P A T P G D R L -
BanII
BsiHKAI
Bsp1286I
SacI
AluI |
CviJI |
HinfI Ecl136II | NlaIV
BpmI TfiI DdeI | | AvaII| DdeI
MnlI | BplI| BseMII CviJI | | |Sau96I|NlaIII |
| | || | | | | | || | |
TCCGTAGGGAGTGAGGATTCTTTGGACACCAGCCTGAGAGCTCACGGGGTCCATGCCACT
541 ---------+---------+---------+---------+---------+---------+ 600
AGGCATCCCTCACTCCTAAGAAACCTGTGGTCGGACTCTCGAGTGCCCCAGGTACGGTGA
a S V G S E D S L D T S L R A H G V H A T -
b P * G V R I L W T P A * E L T G S M P L -
c R R E * G F F G H Q P E S S R G P C H * -
MwoI
NlaIV |
CviJI| |
HaeIII| |
BseSI Sau96I|| |
Bsp1286I Fnu4HI||| |
AvaI| AciI|||| | BslI MboII AluI
NlaIII || BslI||||| | Hpy188I BsmFI | CviJI
NspI ||MwoI |||||| | MnlI EarI| MnlI|TaqI|SfaNI |
| || | |||||| | | || || || | |
AAGCATGTGCCCGAGAAGCGGCCCCTGCCCATTCGGAGGAAGAGAAGCATCGAGGAAGCT
601 ---------+---------+---------+---------+---------+---------+ 660
TTCGTACACGGGCTCTTCGCCGGGGACGGGTAAGCCTCCTTCTCTTCGTAGCTCCTTCGA
a K H V P E K R P L P I R R K R S I E E A -
b S M C P R S G P C P F G G R E A S R K L -
c A C A R E A A P A H S E E E K H R G S C -
EciI
HincII
MlyI
BstNI HinfI AccI|
ScrFI Hpy188I| PleI|
MspA1I BssKI | BsaJI || TaqI|
AciI |HpyCH4V | | HinfI | || SalI||
MwoI| | FauI |PspGI |Bst4CI TfiI | || MnlI |||
|| | | | | | | | | || | |||
GTCCCCGCTGTCTGCAAGACCAGGACGGTCATTTACGAGATTCCTCGGAGTCAGGTCGAC
661 ---------+---------+---------+---------+---------+---------+ 720
CAGGGGCGACAGACGTTCTGGTCCTGCCAGTAAATGCTCTAAGGAGCCTCAGTCCAGCTG
a V P A V C K T R T V I Y E I P R S Q V D -
b S P L S A R P G R S F T R F L G V R S T -
c P R C L Q D Q D G H L R D S S E S G R P -
Fnu4HI
BstAPI|
CviJI|
MwoI|
TseI|
HpaII ||
MwoI ||
BsrFI| ||
NlaIV HphI|| ||
AciI CviJI| HpyCH4V||| ||
TaiI| HaeIII| BbvI Fnu4HI |||| ||
BtrI || Sau96I|| BsgI| TseI| |||| ||
MaeII| || DpnI ||| BslI| BbvI|| |||| ||
AhdI|| || MboI | ||| MnlI || BbvI ||| |||| ||
||| || | | ||| | || | ||| |||| ||
CCCACGTCCGCCAACTTCCTGATCTGGCCCCCGTGCGTGGAGGTGAAACGCTGCACCGGC
721 ---------+---------+---------+---------+---------+---------+ 780
GGGTGCAGGCGGTTGAAGGACTAGACCGGGGGCACGCACCTCCACTTTGCGACGTGGCCG
a P T S A N F L I W P P C V E V K R C T G -
b P R P P T S * S G P R A W R * N A A P A -
c H V R Q L P D L A P V R G G E T L H R L -
MwoI
BssSI | FauI
HpyCH4V | | CviJI HgaI| Fnu4HI
Fnu4HI | | | BtsI Cac8I | BstUI || TseI|
TseI| | | | TspRI HgaI| | AciI |MnlI| AciI ||
|| | | | | || | | | || | ||
TGCTGCAACACGAGCAGTGTCAAGTGCCAGCCCTCCCGCGTCCACCACCGCAGCGTCAAG
781 ---------+---------+---------+---------+---------+---------+ 840
ACGACGTTGTGCTCGTCACAGTTCACGGTCGGGAGGGCGCAGGTGGTGGCGTCGCAGTTC
a C C N T S S V K C Q P S R V H H R S V K -
b A A T R A V S S A S P P A S T T A A S R -
c L Q H E Q C Q V P A L P R P P P Q R Q G -
BsaJI
StyI
CviJI| BstNI
HaeIII| MseI ScrFI
MscI| MboII| BssKI |
BbvI || TaiI Tsp509I || MnlI |
EaeI || MaeII | CviJI | || PspGI | MnlI
| || | | | | || | | |
GTGGCCAAGGTGGAATACGTCAGGAAGAAGCCAAAATTAAAAGAAGTCCAGGTGAGGTTA
841 ---------+---------+---------+---------+---------+---------+ 900
CACCGGTTCCACCTTATGCAGTCCTTCTTCGGTTTTAATTTTCTTCAGGTCCACTCCAAT
a V A K V E Y V R K K P K L K E V Q V R L -
b W P R W N T S G R S Q N * K K S R * G * -
c G Q G G I R Q E E A K I K R S P G E V R -
BstUI HpaII
HhaI BsaWI|
HinP1I | BslI|
Cac8I | | BspEI|
HhaI | | | HinfI ||
HinP1I | | | | TfiI || MnlI
HphI BseRI| | | | | CviJI | || EarI|
| || | | | | | | || ||
GAGGAGCATTTGGAGTGCGCCTGCGCGACCACAAGCCTGAATCCGGATTATCGGGAAGAG
901 ---------+---------+---------+---------+---------+---------+ 960
CTCCTCGTAAACCTCACGCGGACGCGCTGGTGTTCGGACTTAGGCCTAATAGCCCTTCTC
a E E H L E C A C A T T S L N P D Y R E E -
b R S I W S A P A R P Q A * I R I I G K R -
c G A F G V R L R D H K P E S G L S G R G -
BfaI
AvrII|
BsaJI|
StyI|
CviJI||
HaeIII|| MlyI
MboII StuI||HinfI PleI| MseI
| ||| | || |
GACACGGGAAGGCCTAGGGAGTCAGGTAAAAAACGGAAAAGAAAAAGGTTAAAACCCACC
961 ---------+---------+---------+---------+---------+---------+ 1020
CTGTGCCCTTCCGGATCCCTCAGTCCATTTTTTGCCTTTTCTTTTTCCAATTTTGGGTGG
a D T G R P R E S G K K R K R K R L K P T -
b T R E G L G S Q V K N G K E K G * N P P -
c H G K A * G V R * K T E K K K V K T H L -
FokI
CviJI| BbvI
Fnu4HI || BslI|
TseI| || BstNI|
AciI || || ScrFI|
Fnu4HI || || BsaJI||
CviJI MnlI HphI || || BslI|| BsrGI
Fnu4HI | BbvI | BstF5I| || ||BssKI||| TatI
TseI| | MnlI | | CviJI| || ||PspGI||| NlaIII |
|| | | | | || || || |||| | |
TAAAGCAGCCAACCAGATGTGAGGTGAGGATGAGCCGCAGCCCTTTCCTGGGACATGGAT
1021 ---------+---------+---------+---------+---------+---------+ 1080
ATTTCGTCGGTTGGTCTACACTCCACTCCTACTCGGCGTCGGGAAAGGACCCTGTACCTA
a * S S Q P D V R * G * A A A L S W D M D -
b K A A N Q M * G E D E P Q P F P G T W M -
c K Q P T R C E V R M S R S P F L G H G C -
MaeIII
FokI|
NlaIII ||
BsmFI | || BseRI
BstF5I| | || Bst4CI AciI |
RsaI|| | || RsaI | TspRI |
Csp6I||| | || Csp6I| | BsrI BslI| |
|||| | || || | | || |
GTACATGGCGTGTTACATTCCTGAACCTACTATGTACGGTGCTTTATTGCCAGTGTGCGG
1081 ---------+---------+---------+---------+---------+---------+ 1140
CATGTACCGCACAATGTAAGGACTTGGATGATACATGCCACGAAATAACGGTCACACGCC
a V H G V L H S * T Y Y V R C F I A S V R -
b Y M A C Y I P E P T M Y G A L L P V C G -
c T W R V T F L N L L C T V L Y C Q C A V -
Hpy188I
Bst4CI | ApaLI
MnlI | | AvaI BsmAI Bst4CI|
| | | | | ||
TCTTTGTTCTCCTCCGTGAAAAACTGTGTCCGAGAACACTCGGGAGAACAAAGAGACAGT
1141 ---------+---------+---------+---------+---------+---------+ 1200
AGAAACAAGAGGAGGCACTTTTTGACACAGGCTCTTGTGAGCCCTCTTGTTTCTCTGTCA
a S L F S S V K N C V R E H S G E Q R D S -
b L C S P P * K T V S E N T R E N K E T V -
c F V L L R E K L C P R T L G R T K R Q C -
BseSI
BsiHKAI
Bsp1286I MaeIII
TspRI Tsp45I HindIII
HpyCH4V | MseI | DraIII HphI |
| | | | | | |
GCACATTTGTTTAATGTGACATCAAAGCAAGTATTGTAGCACTCGGTGAAGCAGTAAGAA
1201 ---------+---------+---------+---------+---------+---------+ 1260
CGTGTAAACAAATTACACTGTAGTTTCGTTCATAACATCGTGAGCCACTTCGTCATTCTT
a A H L F N V T S K Q V L * H S V K Q * E -
b H I C L M * H Q S K Y C S T R * S S K K -
c T F V * C D I K A S I V A L G E A V R S -
ApoI
AluI EcoRI
CviJI Tsp509I
| |
GCTTCCTTGTCAAAAAGAGAGAGAGAGAAAAGAAAAAAAAAGGAATTC
1261 ---------+---------+---------+---------+-------- 1308
CGAAGGAACAGTTTTTCTCTCTCTCTCTTTTCTTTTTTTTTCCTTAAG
a A S L S K R E R E K R K K K E F -
b L P C Q K E R E R K E K K R N -
c F L V K K R E R E K K K K G I -
Enzymes that do cut:
AccI AciI AhdI AluI AlwI ApaLI ApoI AvaI
AvaII AvrII BanI BanII BbeI BbvI BciVI BfaI
BglI BplI BpmI BsaI BsaHI BsaJI BsaWI BseMII
BseRI BseSI BsgI BsiEI BsiHKAI BslI BsmAI BsmFI
Bsp1286I BspEI BsrI BsrFI BsrGI BssHII BssKI BssSI
BstAPI Bst4CI BstF5I BstNI BstUI BstYI Bsu36I BtgI
BtrI BtsI Cac8I Csp6I CviJI DdeI DpnI DraIII
EaeI EagI EarI EciI Ecl136II Eco57I EcoO109I EcoRI
EaeI EagI EarI EciI Ecl136II Eco57I EcoO109I EcoRI
FauI Fnu4HI FokI HaeII HaeIII HgaI HhaI HinP1I
HincII HindIII HinfI HpaII HphI Hpy188I HpyCH4V KasI
MaeII MaeIII MboI MboII MlyI MnlI MscI MseI
MspA1I MwoI NarI NciI NlaIII NlaIV NspI PflMI
PleI PpuMI PspGI RsaI SacI SacII SalI Sau96I
ScrFI SfaNI SfoI StuI StyI TaiI TaqI TatI
TfiI TseI Tsp45I Tsp509I TspRI
Enzymes that do not cut:
AatII Acc65I AclI AfeI AflII AflIII AgeI AlwNI
ApaI AscI AseI BaeI BamHI BbsI BbvCI BcgI
BclI BglII BlpI BmrI Bpu10I BsaAI BsaBI BsiWI
BsmI BsmBI BspHI BspMI BsrBI BsrDI BstBI BstEII
BstXI BstZ17I ClaI DraI DrdI EcoNI EcoRV FseI
FspI HpaI Hpy99I KpnI MfeI MluI MslI NaeI
NcoI NdeI NgoMIV NheI NotI NruI NsiI PacI
PciI PmeI PmlI Ppu10I PshAI PsiI PspOMI PstI
PvuI PvuII RsrII SanDI SapI SbfI ScaI SexAI
SfcI SfiI SgfI SgrAI SmaI SmlI SnaBI SpeI
SphI SrfI SspI SwaI Tth111I XbaI XcmI XhoI
XmaI XmnI
-------------------------------------------------------------------------------------------------------
gcg2 19% map ¡Vminc=2 ¡Vmaxc=2
*****To show the restriction sites of enzymes that cut ONLY twice.
Map maps a DNA sequence and displays both strands of the mapped sequence
with restriction enzyme cut points above the sequence and protein
translations below. Map can also create a peptide map of an amino acid
sequence.
(Linear) MAP of what sequence ? x03795.gb_pr2
Begin (* 1 *) ?
End (* 1308 *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):
What protein translations do you want:
a) frame 1 b) frame 2 c) frame 3
d) frame 4 e) frame 5 f) frame 6
t)hree forward frames s)ix frames o)pen frames only
n)o protein translation q)uit
Please select (capitalize for 3-letter) (* t *): n
What should I call the output file (* x03795.map *) ? x03795-1.map
Mapping ...............
Writing ........... ..
MAP complete with:
Sequence Length: 1,308
Enzymes Chosen: 209
Cutsites found: 28
CPU time: 00.39
Output file: x03795-1.map
gcg2 10% cat x03795-1.map
(Linear) MAP of: x03795.gb_pr2 check: 5107 from: 1 to: 1308
LOCUS HSPDGFAR 1308 bp mRNA PRI 21-MAR-1995
DEFINITION Human mRNA for platelet derived growth factor A-chain (PDGF-A).
ACCESSION X03795
VERSION X03795.1 GI:35365
KEYWORDS glycoprotein; platelet-derived growth factor 1; signal peptide.
SOURCE human. . . .
With 209 enzymes: *
MinCuts: 2 MaxCuts: 2
April 28, 2000 15:00 ..
TCCGCAAATATGCAGAATTACCGGCCGGGTCGCTCCTGAAGCCAGCGCGGGGAGGCAGCG
1 ---------+---------+---------+---------+---------+---------+ 60
AGGCGTTTATACGTCTTAATGGCCGGCCCAGCGAGGACTTCGGTCGCGCCCCTCCGTCGC
CGGCGGCGGCCAGCACCGGGAACGCACCGAGGAAGAAGCCCAGCCCCCGCCCTCCGCCCC
61 ---------+---------+---------+---------+---------+---------+ 120
GCCGCCGCCGGTCGTGGCCCTTGCGTGGCTCCTTCTTCGGGTCGGGGGCGGGAGGCGGGG
TTCCGTCCCCACCCCCATCCCGGCGGCCCAGGAGGCTCCCCGCGCTGGCGCGCACTCCCT
121 ---------+---------+---------+---------+---------+---------+ 180
AAGGCAGGGGTGGGGGTAGGGCCGCCGGGTCCTCCGAGGGGCGCGACCGCGCGTGAGGGA
BstAPI
BtsI |
| |
GTTTCTCCTCCTCCTGGCTGGCGCTGCCTGCCTCTCCGCACTCACTGCTCGCCGGGCGCC
181 ---------+---------+---------+---------+---------+---------+ 240
CAAAGAGGAGGAGGACCGACCGCGACGGACGGAGAGGCGTGAGTGACGAGCGGCCCGCGG
GTCCGCCAGCTCCGTGCTCCCCGCGCCACCCTCCTCCGGGCCGCGCTCCCTAAGGGATGG
241 ---------+---------+---------+---------+---------+---------+ 300
CAGGCGGTCGAGGCACGAGGGGCGCGGTGGGAGGAGGCCCGGCGCGAGGGATTCCCTACC
BsmAI MspA1I
| |
TACTGATTTTCGCCGCCACAGGAGACCGGCTGGAGCGCCGCCCCGCGGCCTCGCCTCTCC
301 ---------+---------+---------+---------+---------+---------+ 360
ATGACTAAAAGCGGCGGTGTCCTCTGGCCGACCTCGCGGCGGGGCGCCGGAGCGGAGAGG
EcoO109I
PpuMI
|
TCCGAGCAGCCAGCGCCTCGGGACGCGATGAGGACCTTGGCTTGCCTGCTGCTCCTCGGC
361 ---------+---------+---------+---------+---------+---------+ 420
AGGCTCGTCGGTCGCGGAGCCCTGCGCTACTCCTGGAACCGAACGGACGACGAGGAGCCG
BstYI
AlwI |
| |
TGCGGATACCTCGCCCATGTTCTGGCCGAGGAAGCCGAGATCCCCCGCGAGGTGATCGAG
421 ---------+---------+---------+---------+---------+---------+ 480
ACGCCTATGGAGCGGGTACAAGACCGGCTCCTTCGGCTCTAGGGGGCGCTCCACTAGCTC
SfaNI
BstYI EcoO109I |
AlwI | PpuMI |
| | | |
AGGCTGGCCCGCAGTCAGATCCACAGCATCCGGGACCTCCAGCGACTCCTGGAGATAGAC
481 ---------+---------+---------+---------+---------+---------+ 540
TCCGACCGGGCGTCAGTCTAGGTGTCGTAGGCCCTGGAGGTCGCTGAGGACCTCTATCTG
TCCGTAGGGAGTGAGGATTCTTTGGACACCAGCCTGAGAGCTCACGGGGTCCATGCCACT
541 ---------+---------+---------+---------+---------+---------+ 600
AGGCATCCCTCACTCCTAAGAAACCTGTGGTCGGACTCTCGAGTGCCCCAGGTACGGTGA
BseSI EarI SfaNI
| | |
AAGCATGTGCCCGAGAAGCGGCCCCTGCCCATTCGGAGGAAGAGAAGCATCGAGGAAGCT
601 ---------+---------+---------+---------+---------+---------+ 660
TTCGTACACGGGCTCTTCGCCGGGGACGGGTAAGCCTCCTTCTCTTCGTAGCTCCTTCGA
MspA1I
|
GTCCCCGCTGTCTGCAAGACCAGGACGGTCATTTACGAGATTCCTCGGAGTCAGGTCGAC
661 ---------+---------+---------+---------+---------+---------+ 720
CAGGGGCGACAGACGTTCTGGTCCTGCCAGTAAATGCTCTAAGGAGCCTCAGTCCAGCTG
TaiI
MaeII | BstAPI
| | |
CCCACGTCCGCCAACTTCCTGATCTGGCCCCCGTGCGTGGAGGTGAAACGCTGCACCGGC
721 ---------+---------+---------+---------+---------+---------+ 780
GGGTGCAGGCGGTTGAAGGACTAGACCGGGGGCACGCACCTCCACTTTGCGACGTGGCCG
BtsI
|
TGCTGCAACACGAGCAGTGTCAAGTGCCAGCCCTCCCGCGTCCACCACCGCAGCGTCAAG
781 ---------+---------+---------+---------+---------+---------+ 840
ACGACGTTGTGCTCGTCACAGTTCACGGTCGGGAGGGCGCAGGTGGTGGCGTCGCAGTTC
TaiI
MaeII |
| |
GTGGCCAAGGTGGAATACGTCAGGAAGAAGCCAAAATTAAAAGAAGTCCAGGTGAGGTTA
841 ---------+---------+---------+---------+---------+---------+ 900
CACCGGTTCCACCTTATGCAGTCCTTCTTCGGTTTTAATTTTCTTCAGGTCCACTCCAAT
EarI
|
GAGGAGCATTTGGAGTGCGCCTGCGCGACCACAAGCCTGAATCCGGATTATCGGGAAGAG
901 ---------+---------+---------+---------+---------+---------+ 960
CTCCTCGTAAACCTCACGCGGACGCGCTGGTGTTCGGACTTAGGCCTAATAGCCCTTCTC
GACACGGGAAGGCCTAGGGAGTCAGGTAAAAAACGGAAAAGAAAAAGGTTAAAACCCACC
961 ---------+---------+---------+---------+---------+---------+ 1020
CTGTGCCCTTCCGGATCCCTCAGTCCATTTTTTGCCTTTTCTTTTTCCAATTTTGGGTGG
TAAAGCAGCCAACCAGATGTGAGGTGAGGATGAGCCGCAGCCCTTTCCTGGGACATGGAT
1021 ---------+---------+---------+---------+---------+---------+ 1080
ATTTCGTCGGTTGGTCTACACTCCACTCCTACTCGGCGTCGGGAAAGGACCCTGTACCTA
MaeIII
|
GTACATGGCGTGTTACATTCCTGAACCTACTATGTACGGTGCTTTATTGCCAGTGTGCGG
1081 ---------+---------+---------+---------+---------+---------+ 1140
CATGTACCGCACAATGTAAGGACTTGGATGATACATGCCACGAAATAACGGTCACACGCC
BsmAI
|
TCTTTGTTCTCCTCCGTGAAAAACTGTGTCCGAGAACACTCGGGAGAACAAAGAGACAGT
1141 ---------+---------+---------+---------+---------+---------+ 1200
AGAAACAAGAGGAGGCACTTTTTGACACAGGCTCTTGTGAGCCCTCTTGTTTCTCTGTCA
BseSI MaeIII
| |
GCACATTTGTTTAATGTGACATCAAAGCAAGTATTGTAGCACTCGGTGAAGCAGTAAGAA
1201 ---------+---------+---------+---------+---------+---------+ 1260
CGTGTAAACAAATTACACTGTAGTTTCGTTCATAACATCGTGAGCCACTTCGTCATTCTT
GCTTCCTTGTCAAAAAGAGAGAGAGAGAAAAGAAAAAAAAAGGAATTC
1261 ---------+---------+---------+---------+-------- 1308
CGAAGGAACAGTTTTTCTCTCTCTCTCTTTTCTTTTTTTTTCCTTAAG
Enzymes that do cut and were not excluded:
AlwI BseSI BsmAI BstAPI BstYI BtsI EarI EcoO109I
MaeII MaeIII MspA1I PpuMI SfaNI TaiI
Enzymes that do not cut:
AatII Acc65I AclI AfeI AflII AflIII AgeI AlwNI
ApaI AscI AseI BaeI BamHI BbsI BbvCI BcgI
BclI BglII BlpI BmrI Bpu10I BsaAI BsaBI BsiWI
BsmI BsmBI BspHI BspMI BsrBI BsrDI BstBI BstEII
BstXI BstZ17I ClaI DraI DrdI EcoNI EcoRV FseI
FspI HpaI Hpy99I KpnI MfeI MluI MslI NaeI
NcoI NdeI NgoMIV NheI NotI NruI NsiI PacI
PciI PmeI PmlI Ppu10I PshAI PsiI PspOMI PstI
PvuI PvuII RsrII SanDI SapI SbfI ScaI SexAI
SfcI SfiI SgfI SgrAI SmaI SmlI SnaBI SpeI
SphI SrfI SspI SwaI Tth111I XbaI XcmI XhoI
XmaI XmnI
Enzymes excluded; MinCuts: 2 MaxCuts: 2
AccI AciI AhdI AluI ApaLI ApoI AvaI AvaII
AvrII BanI BanII BbeI BbvI BciVI BfaI BglI
BplI BpmI BsaI BsaHI BsaJI BsaWI BseMII BseRI
BsgI BsiEI BsiHKAI BslI BsmFI Bsp1286I BspEI BsrI
BsrFI BsrGI BssHII BssKI BssSI Bst4CI BstF5I BstNI
BstUI Bsu36I BtgI BtrI Cac8I Csp6I CviJI DdeI
DpnI DraIII EaeI EagI EciI Ecl136II Eco57I EcoRI
FauI Fnu4HI FokI HaeII HaeIII HgaI HhaI HinP1I
HincII HindIII HinfI HpaII HphI Hpy188I HpyCH4V KasI
MboI MboII MlyI MnlI MscI MseI MwoI NarI
NciI NlaIII NlaIV NspI PflMI PleI PspGI RsaI
SacI SacII SalI Sau96I ScrFI SfoI StuI StyI
TaqI TatI TfiI TseI Tsp45I Tsp509I TspRI
-------------------------------------------------------------------------------------------------------
gcg2 11% mapsort -exclude=388,1020
*****Identify restriction sites that DO NOT OCCUR in the excluded region (388-1020)
MapSort finds the coordinates of the restriction enzyme cuts in a
DNA sequence and sorts the fragments of the resulting digest by size.
MapSort can sort the fragments from single or multiple enzyme
digests.
(Linear) MAPSORT of what sequence ? x03795.gb_pr2
Begin (* 1 *) ?
End (* 1308 *) ?
Is this sequence circular (* No *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):
What should I call the output file (* x03795.mapsort *) ?
Mapping ......
gcg2 12% cat x03795.mapsort
(Linear) MAPSORT of: x03795.gb_pr2 Check: 5107 from: 1 to: 1308
LOCUS HSPDGFAR 1308 bp mRNA PRI 21-MAR-1995
DEFINITION Human mRNA for platelet derived growth factor A-chain (PDGF-A).
ACCESSION X03795
VERSION X03795.1 GI:35365
KEYWORDS glycoprotein; platelet-derived growth factor 1; signal peptide.
SOURCE human. . . .
With 209 enzymes: *
April 28, 2000 15:07 ..
ApaLI G'TGCA_C
Cuts at: 0 1199 1308
Size: 1199 109
ApoI r'AATT_y
Cuts at: 0 1303 1308
Size: 1303 5
BanI G'GyrC_C
Cuts at: 0 235 1308
Size: 235 1073
BbeI G_GCGC'C
Cuts at: 0 239 1308
Size: 239 1069
BglI GCCn_nnn'nGGC
Cuts at: 0 152 1308
Size: 152 1156
BsaI GGTCTCn'nnnn_
Cuts at: 0 316 1308
Size: 316 992
BsaHI Gr'CG_yC
Cuts at: 0 236 1308
Size: 236 1072
BsiEI CG_ry'CG
Cuts at: 0 25 1308
Size: 25 1283
BsmAI GTCTCn'nnnn_
Cuts at: 0 316 1187 1308
Size: 316 871 121
Fragments arranged by size:
871 316 121
BsrI ACTG_Gn'
Cuts at: 0 1130 1308
Size: 1130 178
BsrGI T'GTAC_A
Cuts at: 0 1080 1308
Size: 1080 228
BssHII G'CGCG_C
Cuts at: 0 168 1308
Size: 168 1140
Bsu36I CC'TnA_GG
Cuts at: 0 290 1308
Size: 290 1018
BtgI C'CryG_G
Cuts at: 0 343 1308
Size: 343 965
Csp6I G'TA_C
Cuts at: 0 300 1081 1114 1308
Size: 300 781 33 194
Fragments arranged by size:
781 300 194 33
DraIII CAC_nnn'GTG
Cuts at: 0 1245 1308
Size: 1245 63
EagI C'GGCC_G
Cuts at: 0 22 1308
Size: 22 1286
Eco57I CTGAAGnnnnnnnnnnnnnn_nn'
Cuts at: 0 57 1308
Size: 57 1251
EcoRI G'AATT_C
Cuts at: 0 1303 1308
Size: 1303 5
HaeII r_GCGC'y
Cuts at: 0 204 239 338 376 1308
Size: 204 35 99 38 932
Fragments arranged by size:
932 204 99 38 35
HindIII A'AGCT_T
Cuts at: 0 1259 1308
Size: 1259 49
KasI G'GCGC_C
Cuts at: 0 235 1308
Size: 235 1073
MaeIII 'GTnAC_
Cuts at: 0 1091 1215 1308
Size: 1091 124 93
Fragments arranged by size:
1091 124 93
NarI GG'CG_CC
Cuts at: 0 236 1308
Size: 236 1072
RsaI GT'AC
Cuts at: 0 301 1082 1115 1308
Size: 301 781 33 193
Fragments arranged by size:
781 301 193 33
SacII CC_GC'GG
Cuts at: 0 346 1308
Size: 346 962
SfoI GGC'GCC
Cuts at: 0 237 1308
Size: 237 1071
TatI w'GTAC_w
Cuts at: 0 1080 1308
Size: 1080 228
Tsp45I 'GTsAC_
Cuts at: 0 1215 1308
Size: 1215 93
Enzymes that do cut and were not excluded:
ApaLI ApoI BanI BbeI BglI BsaI BsaHI BsiEI
BsmAI BsrI BsrGI BssHII Bsu36I BtgI Csp6I DraIII
EagI Eco57I EcoRI HaeII HindIII KasI MaeIII NarI
RsaI SacII SfoI TatI Tsp45I
Enzymes that do not cut:
AatII Acc65I AclI AfeI AflII AflIII AgeI AlwNI
ApaI AscI AseI BaeI BamHI BbsI BbvCI BcgI
BclI BglII BlpI BmrI Bpu10I BsaAI BsaBI BsiWI
BsmI BsmBI BspHI BspMI BsrBI BsrDI BstBI BstEII
BsmI BsmBI BspHI BspMI BsrBI BsrDI BstBI BstEII
BstXI BstZ17I ClaI DraI DrdI EcoNI EcoRV FseI
FspI HpaI Hpy99I KpnI MfeI MluI MslI NaeI
NcoI NdeI NgoMIV NheI NotI NruI NsiI PacI
PciI PmeI PmlI Ppu10I PshAI PsiI PspOMI PstI
PvuI PvuII RsrII SanDI SapI SbfI ScaI SexAI
SfcI SfiI SgfI SgrAI SmaI SmlI SnaBI SpeI
SphI SrfI SspI SwaI Tth111I XbaI XcmI XhoI
XmaI XmnI
Enzymes excluded; MinCuts: 1 MaxCuts: 350000 Excluded ranges: 388,1020
AccI AciI AhdI AluI AlwI AvaI AvaII AvrII
BanII BbvI BciVI BfaI BplI BpmI BsaJI BsaWI
BseMII BseRI BseSI BsgI BsiHKAI BslI BsmFI Bsp1286I
BspEI BsrFI BssKI BssSI BstAPI Bst4CI BstF5I BstNI
BstUI BstYI BtrI BtsI Cac8I CviJI DdeI DpnI
EaeI EarI EciI Ecl136II EcoO109I FauI Fnu4HI FokI
HaeIII HgaI HhaI HinP1I HincII HinfI HpaII HphI
Hpy188I HpyCH4V MaeII MboI MboII MlyI MnlI MscI
MseI MspA1I MwoI NciI NlaIII NlaIV NspI PflMI
PleI PpuMI PspGI SacI SalI Sau96I ScrFI SfaNI
StuI StyI TaiI TaqI TfiI TseI Tsp509I TspRI
-------------------------------------------------------------------------------------------------------
gcg2 2% mapsort ¡Vdig
*****Restriction fragments generated by selected enzymes
MapSort finds the coordinates of the restriction enzyme cuts in a
DNA sequence and sorts the fragments of the resulting digest by size.
MapSort can sort the fragments from single or multiple enzyme
digests.
(Linear) (Digest) MAPSORT of what sequence ? x03795.gb_pr2
Begin (* 1 *) ?
End (* 1308 *) ?
Is this sequence circular (* No *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):
No enzymes named "TAGI". Try "?T*"! Enzyme: alui
AluI
"ALUI" selected 1 enzyme, new total: 1. Enzyme: mae*
MaeI MaeII MaeIII
"MAE*" selected 3 enzymes, new total: 4. Enzyme:
What should I call the output file (* x03795.mapsort *) ? x03795-1.mapsort
Mapping .
gcg2 3% cat x03795-1.mapsort
(Linear) (Digest) MAPSORT of: x03795.gb_pr2 Check: 5107 from: 1 to: 1308
LOCUS HSPDGFAR 1308 bp mRNA PRI 21-MAR-1995
DEFINITION Human mRNA for platelet derived growth factor A-chain (PDGF-A).
ACCESSION X03795
VERSION X03795.1 GI:35365
KEYWORDS glycoprotein; platelet-derived growth factor 1; signal peptide.
SOURCE human. . . .
With 4 enzymes: ALUI MAE*
April 28, 2000 15:20 ..
A: AluI AG'CT B: MaeI C'TA_G C: MaeII A'CG_T D: MaeIII 'GTnAC_
Cuts at: 0 249A 580A 658A 724C 857C 974B 1091D 1215D
Size: 249 331 78 66 133 117 117 124
Cuts at: 1215D 1261A 1308
Size: 46 47
Fragments arranged by size:
331 249 133 124 117 117 78 66
47 46
Enzymes that do cut:
AluI MaeI MaeII MaeIII
Enzymes that do not cut:
NONE
-------------------------------------------------------------------------------------------------------
gcg2 8% fetch tfsites.dat
Fetch copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
tfsites.dat
gcg2 9% mv tfsites.dat enzymes.dat
gcg2 10% map gb:z18853
Map maps a DNA sequence and displays both strands of the mapped sequence
with restriction enzyme cut points above the sequence and protein
translations below. Map can also create a peptide map of an amino acid
sequence.
Begin (* 1 *) ?
End (* 1144 *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):
What protein translations do you want:
a) frame 1 b) frame 2 c) frame 3
d) frame 4 e) frame 5 f) frame 6
t)hree forward frames s)ix frames o)pen frames only
n)o protein translation q)uit
Please select (capitalize for 3-letter) (* t *): n
What should I call the output file (* z18853.map *) ? z18853-tfsites.map
Mapping ..............................
Writing .................... ..
MAP complete with:
Sequence Length: 1,144
Enzymes Chosen: 209
Cutsites found: 185
CPU time: 00.77
Output file: z18853-tfsites.map
gcg2 11% cat z18853-tfsites.map
gcg2 11% cat z18853-tfsites.map
(Linear) MAP of: z18853.gb_in check: 4598 from: 1 to: 1144
LOCUS CECPASMR 1144 bp mRNA linear INV 10-MAR-1994
DEFINITION C.elegans mRNA for capping protein alpha subunit.
ACCESSION Z18853
VERSION Z18853.1 GI:6687
KEYWORDS capping protein alpha subunit.
SOURCE Caenorhabditis elegans. . . .
Using Enzyme data from: enzyme.dat FileCheck: 2714
Note that some entries in this file are prefixed by ;. These entries
have recognition sites which are very common and therefore by default
these entries are not included in the search (according to David Ghosh these
are entries for which N_PROB > 5.0e-04). If you wish your search
to include these entries, specify /ENZ=** (VMS) or -enz=** (UNIX) on
the command line of any of the mapping programs (MAP, MAPLOT, or . . .
With 4920 enzymes: *
April 26, 2002 07:40 ..
GRE_CS8 GRE_CS7 EcR-consensus_(2)
abaA-consensus |ATF_CS2| H4TF-1hist | D9
| | || | | |
AGTTTGAGAATGTCGGAGATCAGTGACGCCGAAAAGGTCCGCATTGCTTCGGATTTCATT
1 ---------+---------+---------+---------+---------+---------+ 60
TCAAACTCTTACAGCCTCTAGTCACTGCGGCTTTTCCAGGCGTAACGAAGCCTAAAGTAA
CNBP-SRE
c-fos.5 |
HSVIE | | CAP-box
TAATGARAT | | HSF-consensus |
pha-TIF_CS | | c-Myb-c-myb | |
| | | | | |
AAACACGCGCCACCCGGCGAGTTCAACGAGGTATTCAATTCGGTTCGGATGCTTTTGGAA
61 ---------+---------+---------+---------+---------+---------+ 120
TTTGTGCGCGGTGGGCCGCTCAAGTTGCTCCATAAGTTAAGCCAAGCCTACGAAAACCTT
GR-uteroglobin.1
GR-uteroglobin.2
CAP-box |
-undefined-site | | GAL1-TATA
ned_site_2 | | |EcR-consensus_(2) |
| | | | | |
AATGATGATCTTCTGAAGAACAAATGTGTTAATGCTATCGCTCAATATAACGTTGGACAA
121 ---------+---------+---------+---------+---------+---------+ 180
TTACTACTAGAAGACTTCTTGTTTACACAATTACGATAGCGAGTTATATTGCAACCTGTT
OMP-undefined-site DTF-1_RS2
tron-site-2 | box_5 C/EBP_CS1
| | | |
TTTGTGCCAGTAAAGTTGGATGGTGTTGCCAAGCAGACTCTGATCACTCCATACAATGAT
181 ---------+---------+---------+---------+---------+---------+ 240
AAACACGGTCATTTCAACCTACCACAACGGTTCGTCTGAGACTAGTGAGGTATGTTACTA
AntP_CS
E1A-F_CS | TFIID-MBP TFIID-MBP UCE.1
| | | | |
TTGGGTAATGGACGTTTCTACGATGAAGTTTCAAAGAAAAGTTTCAAATACGATCACGTC
241 ---------+---------+---------+---------+---------+---------+ 300
AACCCATTACCTGCAAAGATGCTACTTCAAAGTTTCTTTTCAAAGTTTATGCTAGTGCAG
T-antigen_RS c-mos_DS2
E1A-F_CS | MSP_CS | E1A-F_CS
| | | | |
CGTAAAGAGGCCGCAGATCTTCAACCACATCCAGCCGAGTCTGGAATAACCGAACAATGG
301 ---------+---------+---------+---------+---------+---------+ 360
GCATTTCTCCGGCGTCTAGAAGTTGGTGTAGGTCGGCTCAGACCTTATTGGCTTGTTACC
AntP_CS
TATA-box-CS |
TATA-box-CS | |
TATA-box-CS | | | element_II_rs-4
TFIID-MBP TATA-box-CS | | | | CCBF-CLN2 |
ATF_CS2 | F5 | | | | |D2 | |
| | | | | | | | | | |
CGTCAAGCTCTTCAAACTCAACTCGATATATATATTGATGATCATTACGCGAAAAGTGGA
361 ---------+---------+---------+---------+---------+---------+ 420
GCAGTTCGAGAAGTTTGAGTTGAGCTATATATATAACTACTAGTAATGCGCTTTTCACCT