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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
VSG408
Library VS
(Link to library)
Clone ID VSG408
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U02204-1
Original site URL
Representative seq. ID VSG408P
(Link to Original site)
Representative DNA sequence 
>VSG408 (VSG408Q) /CSM/VS/VSG4-A/VSG408Q.Seq.d/
ATAATATTAAAAAAATAAAAAAAAAAAACCATNTAATTTTTTTTTANTAAAAAAAAAAXX
XXXXXXXXTNGGGGNCGGGNCCCCCCCCGNGGGNGNNCCCCGGGGNCNGTTATNTTTAAA
AAAAAAAAAAAAAAAAACANANNATTTTTTTTTTATAAAAAAAAAAAAATAAAAGAATAA
ATTTATTTAACATTAAAAATTCTAATAATAATAATAAATAATAATAATAATAATAAATAA
TAATATATCAAAAGGATAATTTTTTTTTAAAAAAAAAAATAAAT
sequence update 2001. 3.22
Translated Amino Acid sequence 
*y*KNKKKKPXNFFLXKKK---

---XGRXPPRGXXPGXVXFKKKKKKNXXFFFYKKKKIKE*iyltlkiliiiinnnnnnk*
*yikriiff*kkk*
Translated Amino Acid sequence (All Frames) 
Frame A:
iilkk*kkktx*fffxkkk---

---xgxgpppxxxpgxxyx*kkkkkkxxiffl*kkknkrinlfniknsnnnnk******i
iiyqkdnfflkkkin

Frame B:
*y*KNKKKKPXNFFLXKKK---

---XGRXPPRGXXPGXVXFKKKKKKNXXFFFYKKKKIKE*iyltlkiliiiinnnnnnk*
*yikriiff*kkk*

Frame C:
nikkikkknhxiffx*kk---

---gxgxppxgxprgxlxlkkkkkktxxfffikkkk*knkfi*h*kf*****iiiiiinn
niskg*fffkkknk
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSG408 (VSG408Q) /CSM/VS/VSG4-A/VSG408Q.Seq.d/                         66   3e-10
VSD433 (VSD433Q) /CSM/VS/VSD4-B/VSD433Q.Seq.d/                         66   3e-10
AHI870 (AHI870Q) /CSM/AH/AHI8-C/AHI870Q.Seq.d/                         38   0.069
SLI143 (SLI143Q) /CSM/SL/SLI1-B/SLI143Q.Seq.d/                         36   0.27
SLG278 (SLG278Q) /CSM/SL/SLG2-D/SLG278Q.Seq.d/                         36   0.27
FC-AD03 (FC-AD03Q) /CSM/FC/FC-AD/FC-AD03Q.Seq.d/                       36   0.27
VSH189 (VSH189Q) /CSM/VS/VSH1-D/VSH189Q.Seq.d/                         34   1.1
VSF739 (VSF739Q) /CSM/VS/VSF7-B/VSF739Q.Seq.d/                         34   1.1
VSB584 (VSB584Q) /CSM/VS/VSB5-D/VSB584Q.Seq.d/                         34   1.1
SSK237 (SSK237Q) /CSM/SS/SSK2-B/SSK237Q.Seq.d/                         34   1.1
own update 2004.12.25
Homology vs DNA 

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

AZ545756|AZ545756.1 ENTFJ02TF Entamoeba histolytica Sheared DNA Entamoeba histolytica genomic, DNA sequence.    44  0.89  1
AL592308|AL592308.3 Human DNA sequence from clone RP13-610P22 on chromosome 1.    46  0.98  2
BH470548|BH470548.1 BOGMP59TF BOGM Brassica oleracea genomic clone BOGMP59, DNA sequence.    38  3.0  2
AC055805|AC055805.3 Homo sapiens chromosome 1 clone RP11-224D11 map 1, WORKING DRAFT SEQUENCE, 11 unordered pieces.    46  3.3  2
AC068308|AC068308.12 Homo sapiens 3 BAC RP11-275H4 (Roswell Park Cancer Institute Human BAC Library) complete sequence.    42  3.5  1
AC115030|AC115030.3 Mus musculus clone RP24-255E15, WORKING DRAFT SEQUENCE, 7 ordered pieces.    42  3.5  1
AL662955|AL662955.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0019J05.    42  3.5  1
BX539312|BX539312.5 Mouse DNA sequence *** SEQUENCING IN PROGRESS *** from clone  RP24-164C21.    42  3.5  1
BX537299|BX537299.8 Mouse DNA sequence from clone RP23-412I17 on chromosome 7.    42  3.5  1
BU624651|BU624651.1 UI-H-FG1-bgk-j-08-0-UI.s1 NCI_CGAP_FG1 Homo sapiens cDNA clone UI-H-FG1-bgk-j-08-0-UI 3', mRNA sequence.    42  3.5  1
dna update 2003. 8.25
Homology vs Protein 

 ***** No hits found ******

Lambda     K      H
   0.318    0.134    0.401

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3019103
Number of Hits to DB: 186,487,710
protein update 2009. 3.23
PSORT 

 psg: 0.72  gvh: 0.23  alm: 0.73  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.00
 nuc: 0.98  erl: 0.00  erm: 0.60  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 VSG408 is nuc
5' end seq. ID VSG408F
5' end seq. 
>VSG408F.Seq
ATAATATTAAAAAAATAAAAAAAAAAAACCATNTAATTTTTTTTTANTAAAAAAAAAA--
--------
Length of 5' end seq. 58
3' end seq. ID VSG408Z
3' end seq. 
>VSG408Z.Seq
----------TNGGGGNCGGGNCCCCCCCCGNGGGNGNNCCCCGGGGNCNGTTATNTTTA
AAAAAAAAAAAAAAAAAAACANANNATTTTTTTTTTATAAAAAAAAAAAAATAAAAGAAT
AAATTTATTTAACATTAAAAATTCTAATAATAATAATAAATAATAATAATAATAATAAAT
AATAATATATCAAAAGGATAATTTTTTTTTAAAAAAAAAAATAAAT
Length of 3' end seq. 216
Connected seq. ID VSG408P
Connected seq. 
>VSG408P.Seq
ATAATATTAAAAAAATAAAAAAAAAAAACCATNTAATTTTTTTTTANTAAAAAAAAAA--
--------TNGGGGNCGGGNCCCCCCCCGNGGGNGNNCCCCGGGGNCNGTTATNTTTAAA
AAAAAAAAAAAAAAAAACANANNATTTTTTTTTTATAAAAAAAAAAAAATAAAAGAATAA
ATTTATTTAACATTAAAAATTCTAATAATAATAATAAATAATAATAATAATAATAAATAA
TAATATATCAAAAGGATAATTTTTTTTTAAAAAAAAAAATAAAT
Length of connected seq. 274
Full length Seq ID -
Full length Seq. -
Length of full length seq. -