EXERCISE 90

EXERCISE 90-09

Programs used in this exercise:

(1) Sequence manipulation – reverse

(2) ORF Searching - frames, map, translate

(3) Mapping (restriction sites) – 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

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

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.

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| | | |

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

| | || | | | | | || | |

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

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 –minc=2 –maxc=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 ..