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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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
VSD542
Library VS
(Link to library)
Clone ID VSD542
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U13793-1
Original site URL
Representative seq. ID VSD542P
(Link to Original site)
Representative DNA sequence 
>VSD542 (VSD542Q) /CSM/VS/VSD5-B/VSD542Q.Seq.d/
GTTTTCGTTGTATACATAAATAATGTCAAAAGCACAAGCCGTCGGTAGTAACTACAGAGT
ATCACTCGGTCTTCCTGTTGGTGCTGTCATGAACAGTGCTGATAATTCTGGTGCCAAAAA
TTTATACGTCATTGCCGTCAAAGGTATCAAAGGTCGTTTAAATAGATTACCATCCGCAGG
TGTTGGTTATATGGTCATGGCTACCGTCAAAAAGGGTAAACCAGAATTAAGAAAGAAAGT
TTGCACTGGTTTAGTTGTCAGACAAAGAAAACACTGGAAGAGAAAGGATGGTGTTTACAT
CTATTTCGAAGATAACGCTGGTGTTATGTGTAATCCAAAAGGTGAAGTCAAAGGTAACAT
TCTCGGACCAGTCGCCAAGGAATGCTCCGATTTATGGCCAAAGGTTGCCACCAATGCCGG
TACCATTGTTTAAATAAATACACATAAAGTTAAAACAATATAAAAAAAAAAAAAAANTTA
AAACTTTAAAAAAAAAAXXXXXXXXXXGTTTTCGTTGTATACATAAATAATGTCAAAAGC
ACAAGCCGTCGGTAGTAACTACAGAGTATCACTCGGTCTTCCTGTTGGTGCTGTCATGAA
CAGTGCTGATAATTCTGGTGCCAAAAATTTATACGTCATTGCCGTCAAAGGTATCAAAGG
TCGTTTAAATAGATTACCATCCGCAGGTGTTGGTTATATGGTCATGGCTACCGTCAAAAA
GGGTAAACCAGAATTAAGAAAGAAAGTTTGCACTGGTTTAGTTGTCAGACAAAGAAAACA
CTGGAAGAGAAAGGATGGTGTTTACATCTATTTCGAAGATAACGCTGGTGTTATGTGTAA
TCCAAAAGGTGAAGTCAAAGGTAACATTCTCGGACCAGTCGCCAAGGAATGCTCCGATTT
AGGCCAAAGGTTGCCACCAATGCCGGTACCATTGTTTAAATAAATACACATAAAGT
sequence update 2001. 3.22
Translated Amino Acid sequence 
frcihk*cqkhkpsvvtteyhsvfllvls*tvliilvpkiytslpskvskvv*idyhpqv
lviwswlpskrvnqn*erkfalv*lsdkentgrermvftsiskitlvlcviqkvkskvtf
sdqsprnapiygqrlppmpvplfk*IHIKLKQYKKKKKXKTLKKK---

---VFVVYINNVKSTSRR**lqsitrsscwccheqc**fwcqkfirhcrqryqrsfk*it
irrcwlyghgyrqkg*trikkeslhwfscqtkktleekgwclhlfrr*rwcyv*skr*sq
r*hsrtsrqgmlrfrpkvatnagtiv*inthk
Translated Amino Acid sequence (All Frames) 
Frame A:
vfvvyinnvkstsrr**lqsitrsscwccheqc**fwcqkfirhcrqryqrsfk*itirr
cwlyghgyrqkg*trikkeslhwfscqtkktleekgwclhlfrr*rwcyv*skr*sqr*h
srtsrqgmlrfmakgchqcryhclnkyt*s*nnikkkkxlkl*kk---

---VFVVYINNVKSTSRR**lqsitrsscwccheqc**fwcqkfirhcrqryqrsfk*it
irrcwlyghgyrqkg*trikkeslhwfscqtkktleekgwclhlfrr*rwcyv*skr*sq
r*hsrtsrqgmlrfrpkvatnagtiv*inthk

Frame B:
fslyt*imskaqavgsnyrvslglpvgavmnsadnsgaknlyviavkgikgrlnrlpsag
vgymvmatvkkgkpelrkkvctglvvrqrkhwkrkdgvyiyfednagvmcnpkgevkgni
lgpvakecsdlwpkvatnagtiv*inthkvkti*kkkkx*nfkkk---

---fslyt*imskaqavgsnyrvslglpvgavmnsadnsgaknlyviavkgikgrlnrlp
sagvgymvmatvkkgkpelrkkvctglvvrqrkhwkrkdgvyiyfednagvmcnpkgevk
gnilgpvakecsdlgqrlppmpvplfk*ihik

Frame C:
frcihk*cqkhkpsvvtteyhsvfllvls*tvliilvpkiytslpskvskvv*idyhpqv
lviwswlpskrvnqn*erkfalv*lsdkentgrermvftsiskitlvlcviqkvkskvtf
sdqsprnapiygqrlppmpvplfk*IHIKLKQYKKKKKXKTLKKK---

---frcihk*cqkhkpsvvtteyhsvfllvls*tvliilvpkiytslpskvskvv*idyh
pqvlviwswlpskrvnqn*erkfalv*lsdkentgrermvftsiskitlvlcviqkvksk
vtfsdqsprnapi*akgchqcryhclnkyt*s
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSD542 (VSD542Q) /CSM/VS/VSD5-B/VSD542Q.Seq.d/                        914   0.0
VSJ186 (VSJ186Q) /CSM/VS/VSJ1-D/VSJ186Q.Seq.d/                        898   0.0
VSF856 (VSF856Q) /CSM/VS/VSF8-C/VSF856Q.Seq.d/                        898   0.0
VSF463 (VSF463Q) /CSM/VS/VSF4-C/VSF463Q.Seq.d/                        898   0.0
VSF104 (VSF104Q) /CSM/VS/VSF1-A/VSF104Q.Seq.d/                        898   0.0
VSE769 (VSE769Q) /CSM/VS/VSE7-C/VSE769Q.Seq.d/                        898   0.0
VSB365 (VSB365Q) /CSM/VS/VSB3-C/VSB365Q.Seq.d/                        898   0.0
VHP304 (VHP304Q) /CSM/VH/VHP3-A/VHP304Q.Seq.d/                        898   0.0
VSD585 (VSD585Q) /CSM/VS/VSD5-D/VSD585Q.Seq.d/                        894   0.0
VSB254 (VSB254Q) /CSM/VS/VSB2-C/VSB254Q.Seq.d/                        892   0.0
own update 2003. 1. 9
Homology vs DNA 

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

BG661762|BG661762.1 kx06a08.y1 Parastrongyloides trichosuri IL SL1 TOPO v2 Parastrongyloides trichosuri cDNA similar to SW:RL23_CAEEL P48158 PROBABLE 60S RIBOSOMAL PROTEIN L23. [1] ;, mRNA sequence.    56  3e-27  5
BG301372|BG301372.1 kt04f05.y1 Strongyloides ratti L1 SL1 Topo1 Chiapelli McCarter Strongyloides ratti cDNA 5' similar to SW:RL23_CAEEL P48158 PROBABLE 60S RIBOSOMAL PROTEIN L23. [1] ;, mRNA sequence.    58  2e-18  4
BG301543|BG301543.1 kt02d05.y1 Strongyloides ratti L1 SL1 Topo1 Chiapelli McCarter Strongyloides ratti cDNA 5' similar to SW:RL23_CAEEL P48158 PROBABLE 60S RIBOSOMAL PROTEIN L23. [1] ;, mRNA sequence.    58  2e-18  4
BG301842|BG301842.1 kt06b05.y1 Strongyloides ratti L3 adult SL1 Topo1 Chiapelli McCarter Strongyloides ratti cDNA 5' similar to SW:RL23_CAEEL P48158 PROBABLE 60S RIBOSOMAL PROTEIN L23. [1] ;, mRNA sequence.    58  2e-18  4
BG661420|BG661420.1 kx01f05.y1 Parastrongyloides trichosuri IL SL1 TOPO v2 Parastrongyloides trichosuri cDNA similar to SW:RL23_CAEEL P48158 PROBABLE 60S RIBOSOMAL PROTEIN L23. [1] ;, mRNA sequence.    50  1e-16  4
AV536650|AV536650.1 Arabidopsis thaliana cDNA clone:pAZNII0387R, 5' end.    52  3e-16  3
Z47587|Z47587.1 A. thaliana transcribed sequence; clone FAI235; 5' end; Similar to 60S ribosomal protein L1 ; Nicotiana tabacum.    48  7e-15  3
AY081677|AY081677.1 Arabidopsis thaliana similar to 60S ribosomal protein L17 (At1g04480) mRNA, complete cds.    48  2e-14  3
AX507764|AX507764.1 Sequence 2459 from Patent WO0216655.          48  2e-14  3
AV535717|AV535717.1 Arabidopsis thaliana cDNA clone:FB101a09F, 3' end.    48  2e-14  3
dna update 2003. 8.21
Homology vs Protein 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q6PC14) RecName: Full=60S ribosomal protein L23;  &AY684289_1(A...   202   1e-50
AK012694_1(AK012694|pid:none) Mus musculus 10, 11 days embryo wh...   202   1e-50
BC102556_1(BC102556|pid:none) Bos taurus ribosomal protein L23, ...   202   2e-50
BT058333_1(BT058333|pid:none) Salmo salar clone Contig3997 60S r...   201   2e-50
BT073700_1(BT073700|pid:none) Oncorhynchus mykiss clone omyk-evo...   201   2e-50
EU042114_1(EU042114|pid:none) Epinephelus coioides ribosomal pro...   201   2e-50
BC003518_1(BC003518|pid:none) Homo sapiens, Similar to ribosomal...   201   2e-50
BC073541_1(BC073541|pid:none) Xenopus laevis MGC82808 protein, m...   200   7e-50
CP000498_170(CP000498|pid:none) Pichia stipitis CBS 6054 chromos...   200   7e-50
(Q5REU2) RecName: Full=60S ribosomal protein L23;  &CR857424_1(C...   200   7e-50
protein update 2009. 7.29
PSORT 

 psg: 0.34  gvh: 0.23  alm: 0.59  top: 0.53  tms: 0.00  mit: 0.46  mip: 0.00
 nuc: 0.45  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  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 

	 76.0 %: nuclear
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for VSD542 is nuc
5' end seq. ID VSD542F
5' end seq. 
>VSD542F.Seq
GTTTTCGTTGTATACATAAATAATGTCAAAAGCACAAGCCGTCGGTAGTAACTACAGAGT
ATCACTCGGTCTTCCTGTTGGTGCTGTCATGAACAGTGCTGATAATTCTGGTGCCAAAAA
TTTATACGTCATTGCCGTCAAAGGTATCAAAGGTCGTTTAAATAGATTACCATCCGCAGG
TGTTGGTTATATGGTCATGGCTACCGTCAAAAAGGGTAAACCAGAATTAAGAAAGAAAGT
TTGCACTGGTTTAGTTGTCAGACAAAGAAAACACTGGAAGAGAAAGGATGGTGTTTACAT
CTATTTCGAAGATAACGCTGGTGTTATGTGTAATCCAAAAGGTGAAGTCAAAGGTAACAT
TCTCGGACCAGTCGCCAAGGAATGCTCCGATTTATGGCCAAAGGTTGCCACCAATGCCGG
TACCATTGTTTAAATAAATACACATAAAGTTAAAACAATATAAAAAAAAAAAAAAANTTA
AAACTTTAAAAAAAAAA----------
Length of 5' end seq. 497
3' end seq. ID VSD542Z
3' end seq. 
>VSD542Z.Seq
----------GTTTTCGTTGTATACATAAATAATGTCAAAAGCACAAGCCGTCGGTAGTA
ACTACAGAGTATCACTCGGTCTTCCTGTTGGTGCTGTCATGAACAGTGCTGATAATTCTG
GTGCCAAAAATTTATACGTCATTGCCGTCAAAGGTATCAAAGGTCGTTTAAATAGATTAC
CATCCGCAGGTGTTGGTTATATGGTCATGGCTACCGTCAAAAAGGGTAAACCAGAATTAA
GAAAGAAAGTTTGCACTGGTTTAGTTGTCAGACAAAGAAAACACTGGAAGAGAAAGGATG
GTGTTTACATCTATTTCGAAGATAACGCTGGTGTTATGTGTAATCCAAAAGGTGAAGTCA
AAGGTAACATTCTCGGACCAGTCGCCAAGGAATGCTCCGATTTAGGCCAAAGGTTGCCAC
CAATGCCGGTACCATTGTTTAAATAAATACACATAAAGT
Length of 3' end seq. 449
Connected seq. ID VSD542P
Connected seq. 
>VSD542P.Seq
GTTTTCGTTGTATACATAAATAATGTCAAAAGCACAAGCCGTCGGTAGTAACTACAGAGT
ATCACTCGGTCTTCCTGTTGGTGCTGTCATGAACAGTGCTGATAATTCTGGTGCCAAAAA
TTTATACGTCATTGCCGTCAAAGGTATCAAAGGTCGTTTAAATAGATTACCATCCGCAGG
TGTTGGTTATATGGTCATGGCTACCGTCAAAAAGGGTAAACCAGAATTAAGAAAGAAAGT
TTGCACTGGTTTAGTTGTCAGACAAAGAAAACACTGGAAGAGAAAGGATGGTGTTTACAT
CTATTTCGAAGATAACGCTGGTGTTATGTGTAATCCAAAAGGTGAAGTCAAAGGTAACAT
TCTCGGACCAGTCGCCAAGGAATGCTCCGATTTATGGCCAAAGGTTGCCACCAATGCCGG
TACCATTGTTTAAATAAATACACATAAAGTTAAAACAATATAAAAAAAAAAAAAAANTTA
AAACTTTAAAAAAAAAA----------GTTTTCGTTGTATACATAAATAATGTCAAAAGC
ACAAGCCGTCGGTAGTAACTACAGAGTATCACTCGGTCTTCCTGTTGGTGCTGTCATGAA
CAGTGCTGATAATTCTGGTGCCAAAAATTTATACGTCATTGCCGTCAAAGGTATCAAAGG
TCGTTTAAATAGATTACCATCCGCAGGTGTTGGTTATATGGTCATGGCTACCGTCAAAAA
GGGTAAACCAGAATTAAGAAAGAAAGTTTGCACTGGTTTAGTTGTCAGACAAAGAAAACA
CTGGAAGAGAAAGGATGGTGTTTACATCTATTTCGAAGATAACGCTGGTGTTATGTGTAA
TCCAAAAGGTGAAGTCAAAGGTAACATTCTCGGACCAGTCGCCAAGGAATGCTCCGATTT
AGGCCAAAGGTTGCCACCAATGCCGGTACCATTGTTTAAATAAATACACATAAAGT
Length of connected seq. 946
Full length Seq ID -
Full length Seq. -
Length of full length seq. -