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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
SHC556
Library SH
(Link to library)
Clone ID SHC556
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U15666-1
Original site URL
Representative seq. ID SHC556P
(Link to Original site)
Representative DNA sequence 
>SHC556 (SHC556Q) /CSM/SH/SHC5-C/SHC556Q.Seq.d/
GTAAAGTGTTGTTCAACTATTAACCCAACATTTATGATAAATAAATAAAAAAGGAGGGAA
AAAAAAATGAATGTAAAGGAAATGGATTTTAATGATTTATCAAATAAATCCAATCAAATA
ATCAATAGAATATCATCATTTTCAAGTCCAATTGGGTTATCATCATTCAACATTGAAAGA
AATCTACAAGAGATTGGTGATACATCAAAACAATTGAATGATTTAACTTCATCAAAAACT
CCATTTTCAAATCCATTGGAACCAAATGTATTTCAAGATTCTAAAATTAATAGAAAATAT
GGATTAGATCCAAAAGTTTTAGCAAAGAATTTATCTAATATCAATACATCATCATTCACA
GATGTTCAATCAGTACCAACAGATATTGATGGTTATTTAAAGGTTCAATTTGANAATATC
ATTTTGAATACAATTTGTGACATTCAAAAAAAGACATCAAAAGAGTTTCAATCCCATTAT
GAACAAACATCAATTCATGATTGGAATAGAGATAAAAAATXXXXXXXXXXTCTGAACTTG
TAGTATCATCTCCAAATGGTTTTAAATTTGCTCATGAATTATCTTTATTTTCTGAATTTA
TAAATAAACAACAATGGAGAACTATTATAGAACAGTCAGCATTGGAATTAGAGAATAAGA
ATGAATATCAAAGTGCAATTGAATTTTGGATTATGATTGAAGAGTATCCAAGAGTTTTAG
AGATTTATAATAGTAGAATATCGGTATTATTAACCTCAATTTCAAGTGAAAGAGATCAAT
TATATCAATTTGGTAAGCAATTATTCAATGATTATCAAGGTAGATTAAAAACAACCTCAA
CAGCAAGAACCAGTTATTTAGCCTTTGAGCAATTATTGAAACTTTGCGATTTCTTTGACC
TATACAACAAAGAAAAGTATCAAGAGGCAATTCAAAAGATTGAAAATTTGGAAATCTTAC
CAATCTCTGAATCAGAAATCGATTCAAAGGTACAAGATTATCGTTTCCTTTCACCACATA
TCACTAGAAATTTCTCTTCTATCATTCAAGCATACGTTGACATCATTGTTAAACAATACC
ATTTACTAAATAACTTTGACGAATTTACTAATCGTAGTGCCTTATTTGCTGGTCGTAAAC
AAACCATTCAAGATCTTCAATCTAGAACTCAATGTATTGCTTTGTTTGCTGGTAAAATAG
ATTTCCCAATGTNCTGGTAATATCTTACCTCGTTTAAGAATTTATTT
sequence update 2002.10.25
Translated Amino Acid sequence 
vkccstinptfmink*KRREKKMNVKEMDFNDLSNKSNQIINRISSFSSPIGLSSFNIER
NLQEIGDTSKQLNDLTSSKTPFSNPLEPNVFQDSKINRKYGLDPKVLAKNLSNINTSSFT
DVQSVPTDIDGYLKVQFXNIILNTICDIQKKTSKEFQSHYEQTSIHDWNRDKK---

---SELVVSSPNGFKFAHELSLFSEFINKQQWRTIIEQSALELENKNEYQSAIEFWIMIE
EYPRVLEIYNSRISVLLTSISSERDQLYQFGKQLFNDYQGRLKTTSTARTSYLAFEQLLK
LCDFFDLYNKEKYQEAIQKIENLEILPISESEIDSKVQDYRFLSPHITRNFSSIIQAYVD
IIVKQYHLLNNFDEFTNRSALFAGRKQTIQDLQSRTQCIALFAGKIDFPMXW*yltsfkn
lf
Translated Amino Acid sequence (All Frames) 
Frame A:
vkccstinptfmink*KRREKKMNVKEMDFNDLSNKSNQIINRISSFSSPIGLSSFNIER
NLQEIGDTSKQLNDLTSSKTPFSNPLEPNVFQDSKINRKYGLDPKVLAKNLSNINTSSFT
DVQSVPTDIDGYLKVQFXNIILNTICDIQKKTSKEFQSHYEQTSIHDWNRDKK---

---SELVVSSPNGFKFAHELSLFSEFINKQQWRTIIEQSALELENKNEYQSAIEFWIMIE
EYPRVLEIYNSRISVLLTSISSERDQLYQFGKQLFNDYQGRLKTTSTARTSYLAFEQLLK
LCDFFDLYNKEKYQEAIQKIENLEILPISESEIDSKVQDYRFLSPHITRNFSSIIQAYVD
IIVKQYHLLNNFDEFTNRSALFAGRKQTIQDLQSRTQCIALFAGKIDFPMXW*yltsfkn
lf

Frame B:
*svvqlltqhl**inkkggkkk*m*rkwilmiyqinpik*sieyhhfqvqlgyhhstlke
iykrlvihqnn*mi*lhqklhfqihwnqmyfkilklienmd*iqkf*qriylisihhhsq
mfnqyqqilmvi*rfnlxisf*iqfvtfkkrhqksfnpimnkhqfmigieikn---

---lnl*yhlqmvlnllmnylyflnl*innngell*nsqhwn*rirmnikvqlnfgl*lk
siqef*rfiiveyryy*pqfqvkeinyinlvsnysmiikvd*kqpqqqepvi*plsny*n
faisltyttkksikrqfkrlkiwksyqslnqksiqrykiivsfhhisleisllsfkhtlt
sllnntiy*itltnllivvpyllvvnkpfkifnlelnvllcllvk*isqcxgnilprlri
y

Frame C:
kvlfny*pniydk*ikkegkkneckgngf**fik*iqsnnq*niiifksnwviiiqh*kk
strdw*yiktie*fnfiknsifksigtkcisrf*n**kiwirsksfskefi*yqyiiihr
csistnry*wlfkgsi*xyhfeynl*hskkdikrvsipl*tnins*le*r*k---

---*tcsiiskwf*ics*iifif*iyk*ttmenyyrtvsigire*e*iskcn*ildyd*r
vsksfrdl***nigiinlnfk*krsiisiw*aiiq*lsr*iknnlnsknqlfsl*aiiet
lrfl*piqqrkvsrgnskd*kfgnltnl*irnrfkgtrlsfpfttyh*kflfyhssir*h
hc*tipftk*l*riy*s*clicws*tnhsrssi*nsmycfvcw*nrfpnvlvisylv*ef
i
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SHC556 (SHC556Q) /CSM/SH/SHC5-C/SHC556Q.Seq.d/                       2226   0.0
SHC447 (SHC447Q) /CSM/SH/SHC4-B/SHC447Q.Seq.d/                       1390   0.0
AHN719 (AHN719Q) /CSM/AH/AHN7-A/AHN719Q.Seq.d/                       1388   0.0
VHI450 (VHI450Q) /CSM/VH/VHI4-C/VHI450Q.Seq.d/                       1386   0.0
SHJ831 (SHJ831Q) /CSM/SH/SHJ8-B/SHJ831Q.Seq.d/                       1384   0.0
VHC228 (VHC228Q) /CSM/VH/VHC2-B/VHC228Q.Seq.d/                       1378   0.0
VHA241 (VHA241Q) /CSM/VH/VHA2-B/VHA241Q.Seq.d/                       1378   0.0
AHD783 (AHD783Q) /CSM/AH/AHD7-D/AHD783Q.Seq.d/                       1378   0.0
AHD282 (AHD282Q) /CSM/AH/AHD2-D/AHD282Q.Seq.d/                       1378   0.0
AHK332 (AHK332Q) /CSM/AH/AHK3-B/AHK332Q.Seq.d/                       1376   0.0
own update 2004.12.25
Homology vs DNA 

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

CV410734|CV410734.1 RC1-TN0152-200900-011-e05 TN0152 Homo sapiens cDNA, mRNA sequence.    48   0.45   1
AC093890|AC093890.3 Homo sapiens BAC clone RP11-673E1 from 4, complete sequence.    36   0.45   6
AY653733|AY653733.1 Acanthamoeba polyphaga mimivirus, complete genome.    42   0.58   15
AC116986|AC116986.2 Dictyostelium discoideum chromosome 2 map 2234041-2567370 strain AX4, complete sequence.    34   0.70   10
AC116471|AC116471.8 Mus musculus chromosome 12, clone RP23-384N3, complete sequence.    36   0.89   2
AC141479|AC141479.3 Mus musculus BAC clone RP23-281N15 from chromosome 12, complete sequence.    36   0.90   2
BU548665|BU548665.1 GM880023A10B05 Gm-r1088 Glycine max cDNA clone Gm-r1088-8505 3', mRNA sequence.    44   1.5    2
DT465988|DT465988.1 GH_CHX18D20.f GH_CHX Gossypium hirsutum cDNA clone GH_CHX18D20 5', mRNA sequence.    42   1.7    2
AC162677|AC162677.2 Bos taurus clone CH240-111D19, WORKING DRAFT SEQUENCE, 26 unordered pieces.    46   1.8    1
AC158838|AC158838.1 Bos taurus clone CH240-297N14, WORKING DRAFT SEQUENCE, 32 unordered pieces.    46   1.8    1
dna update 2006. 1. 6
Homology vs Protein 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q7ZX96) RecName: Full=Nuclear pore complex protein Nup93; AltNa...    78   7e-13
U63919_1(U63919|pid:none) Xenopus laevis An4a mRNA, complete cds.      78   7e-13
BX470170_7(BX470170|pid:none) Zebrafish DNA sequence from clone ...    76   3e-12
(Q7ZU29) RecName: Full=Nuclear pore complex protein Nup93; AltNa...    76   3e-12
DQ156149_2(DQ156149|pid:none) Salmo salar clone BAC S0085O16, pa...    75   6e-12
U77595_1(U77595|pid:none) Danio rerio dye mRNA, complete cds.          74   8e-12
BT045693_1(BT045693|pid:none) Salmo salar clone ssal-rgf-528-376...    74   1e-11
(A5PJZ5) RecName: Full=Nuclear pore complex protein Nup93; AltNa...    67   1e-09
(Q5R822) RecName: Full=Nuclear pore complex protein Nup93; AltNa...    67   1e-09
CR859933_1(CR859933|pid:none) Pongo abelii mRNA; cDNA DKFZp469K1...    67   1e-09
protein update 2009. 4.16
PSORT 

 psg: 0.57  gvh: 0.44  alm: 0.45  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.02
 nuc: 0.00  erl: 0.00  erm: 0.40  pox: 0.00  px2: 0.00  vac: 0.33  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 40.0 %: cytoplasmic
	 32.0 %: mitochondrial
	 28.0 %: nuclear

>> prediction for SHC556 is cyt
5' end seq. ID SHC556F
5' end seq. 
>SHC556F.Seq
GTAAAGTGTTGTTCAACTATTAACCCAACATTTATGATAAATAAATAAAAAAGGAGGGAA
AAAAAAATGAATGTAAAGGAAATGGATTTTAATGATTTATCAAATAAATCCAATCAAATA
ATCAATAGAATATCATCATTTTCAAGTCCAATTGGGTTATCATCATTCAACATTGAAAGA
AATCTACAAGAGATTGGTGATACATCAAAACAATTGAATGATTTAACTTCATCAAAAACT
CCATTTTCAAATCCATTGGAACCAAATGTATTTCAAGATTCTAAAATTAATAGAAAATAT
GGATTAGATCCAAAAGTTTTAGCAAAGAATTTATCTAATATCAATACATCATCATTCACA
GATGTTCAATCAGTACCAACAGATATTGATGGTTATTTAAAGGTTCAATTTGANAATATC
ATTTTGAATACAATTTGTGACATTCAAAAAAAGACATCAAAAGAGTTTCAATCCCATTAT
GAACAAACATCAATTCATGATTGGAATAGAGATAAAAAATNNNNNNNNNN
Length of 5' end seq. 530
3' end seq. ID SHC556Z
3' end seq. 
>SHC556Z.Seq
NNNNNNNNNNTCTGAACTTGTAGTATCATCTCCAAATGGTTTTAAATTTGCTCATGAATT
ATCTTTATTTTCTGAATTTATAAATAAACAACAATGGAGAACTATTATAGAACAGTCAGC
ATTGGAATTAGAGAATAAGAATGAATATCAAAGTGCAATTGAATTTTGGATTATGATTGA
AGAGTATCCAAGAGTTTTAGAGATTTATAATAGTAGAATATCGGTATTATTAACCTCAAT
TTCAAGTGAAAGAGATCAATTATATCAATTTGGTAAGCAATTATTCAATGATTATCAAGG
TAGATTAAAAACAACCTCAACAGCAAGAACCAGTTATTTAGCCTTTGAGCAATTATTGAA
ACTTTGCGATTTCTTTGACCTATACAACAAAGAAAAGTATCAAGAGGCAATTCAAAAGAT
TGAAAATTTGGAAATCTTACCAATCTCTGAATCAGAAATCGATTCAAAGGTACAAGATTA
TCGTTTCCTTTCACCACATATCACTAGAAATTTCTCTTCTATCATTCAAGCATACGTTGA
CATCATTGTTAAACAATACCATTTACTAAATAACTTTGACGAATTTACTAATCGTAGTGC
CTTATTTGCTGGTCGTAAACAAACCATTCAAGATCTTCAATCTAGAACTCAATGTATTGC
TTTGTTTGCTGGTAAAATAGATTTCCCAATGTNCTGGTAATATCTTACCTCGTTTAAGAA
TTTATTT
Length of 3' end seq. 727
Connected seq. ID SHC556P
Connected seq. 
>SHC556P.Seq
GTAAAGTGTTGTTCAACTATTAACCCAACATTTATGATAAATAAATAAAAAAGGAGGGAA
AAAAAAATGAATGTAAAGGAAATGGATTTTAATGATTTATCAAATAAATCCAATCAAATA
ATCAATAGAATATCATCATTTTCAAGTCCAATTGGGTTATCATCATTCAACATTGAAAGA
AATCTACAAGAGATTGGTGATACATCAAAACAATTGAATGATTTAACTTCATCAAAAACT
CCATTTTCAAATCCATTGGAACCAAATGTATTTCAAGATTCTAAAATTAATAGAAAATAT
GGATTAGATCCAAAAGTTTTAGCAAAGAATTTATCTAATATCAATACATCATCATTCACA
GATGTTCAATCAGTACCAACAGATATTGATGGTTATTTAAAGGTTCAATTTGANAATATC
ATTTTGAATACAATTTGTGACATTCAAAAAAAGACATCAAAAGAGTTTCAATCCCATTAT
GAACAAACATCAATTCATGATTGGAATAGAGATAAAAAAT----------TCTGAACTTG
TAGTATCATCTCCAAATGGTTTTAAATTTGCTCATGAATTATCTTTATTTTCTGAATTTA
TAAATAAACAACAATGGAGAACTATTATAGAACAGTCAGCATTGGAATTAGAGAATAAGA
ATGAATATCAAAGTGCAATTGAATTTTGGATTATGATTGAAGAGTATCCAAGAGTTTTAG
AGATTTATAATAGTAGAATATCGGTATTATTAACCTCAATTTCAAGTGAAAGAGATCAAT
TATATCAATTTGGTAAGCAATTATTCAATGATTATCAAGGTAGATTAAAAACAACCTCAA
CAGCAAGAACCAGTTATTTAGCCTTTGAGCAATTATTGAAACTTTGCGATTTCTTTGACC
TATACAACAAAGAAAAGTATCAAGAGGCAATTCAAAAGATTGAAAATTTGGAAATCTTAC
CAATCTCTGAATCAGAAATCGATTCAAAGGTACAAGATTATCGTTTCCTTTCACCACATA
TCACTAGAAATTTCTCTTCTATCATTCAAGCATACGTTGACATCATTGTTAAACAATACC
ATTTACTAAATAACTTTGACGAATTTACTAATCGTAGTGCCTTATTTGCTGGTCGTAAAC
AAACCATTCAAGATCTTCAATCTAGAACTCAATGTATTGCTTTGTTTGCTGGTAAAATAG
ATTTCCCAATGTNCTGGTAATATCTTACCTCGTTTAAGAATTTATTT
Length of connected seq. 1237
Full length Seq ID -
Full length Seq. -
Length of full length seq. -