NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
VSD568
Library VS
(Link to library)
Clone ID VSD568
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U02244-1
Original site URL
Representative seq. ID VSD568P
(Link to Original site)
Representative DNA sequence 
>VSD568 (VSD568Q) /CSM/VS/VSD5-C/VSD568Q.Seq.d/
GACTAGTTCTAGATCGCGAGCGGCTGCCCTTTTTTTTTTTTTTNATTTTTTNATTTTTTT
TTTTTTNANANTTTTTTNGNTTTTTTTTTNGAAAAAAAAAAXXXXXXXXXXTGNATAAAT
AAATCACCACTTNTANTATTATACTATANATAAATNNTANTAATATATATATATATATAT
TAATTTATATNGTAAATAGATATTA
sequence update 2001. 3.22
Translated Amino Acid sequence 
TSSRSRAAALFFFFXFXIFFFXXXFXXFFXKKK---

---XINKSPLXXLYYX*xxxiyiyiy*fix*idi
Translated Amino Acid sequence (All Frames) 
Frame A:
d*f*iasgcpffffxffxffffxxfxxffxekk---

---XINKSPLXXLYYX*xxxiyiyiy*fix*idi

Frame B:
TSSRSRAAALFFFFXFXIFFFXXXFXXFFXKKK---

---x*inhhxxyytixkxx*yiyiyinlyxk*il

Frame C:
lvldrerlpffffxifxffffxxffxfffxkkk---

---xk*ittxxiilxinxxniyiyiliyxvnry
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSD568 (VSD568Q) /CSM/VS/VSD5-C/VSD568Q.Seq.d/                         58   5e-08
SSC822 (SSC822Q) /CSM/SS/SSC8-A/SSC822Q.Seq.d/                         50   1e-05
SLI833 (SLI833Q) /CSM/SL/SLI8-B/SLI833Q.Seq.d/                         50   1e-05
FC-BF13 (FC-BF13Q) /CSM/FC/FC-BF/FC-BF13Q.Seq.d/                       50   1e-05
FC-044 (FC-044Q) /CSM/CG/CG-FC/FC-044Q.Seq.d/                          50   1e-05
SSM380 (SSM380Q) /CSM/SS/SSM3-D/SSM380Q.Seq.d/                         48   5e-05
SSM332 (SSM332Q) /CSM/SS/SSM3-B/SSM332Q.Seq.d/                         48   5e-05
SSK277 (SSK277Q) /CSM/SS/SSK2-D/SSK277Q.Seq.d/                         48   5e-05
SSC426 (SSC426Q) /CSM/SS/SSC4-B/SSC426Q.Seq.d/                         48   5e-05
FC-AP11 (FC-AP11Q) /CSM/FC/FC-AP/FC-AP11Q.Seq.d/                       48   5e-05
own update 2004. 8. 5
Homology vs DNA 

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

BU095841|BU095841.1 tca-326 tca Trypanosoma carassii cDNA clone 02i6 5', mRNA sequence.    58  4e-05  1
BQ428271|BQ428271.1 AGENCOURT_7887825 NIH_MGC_71 Homo sapiens cDNA clone IMAGE:6176332 5', mRNA sequence.    58  4e-05  1
BM451892|BM451892.1 AGENCOURT_6397259 NIH_MGC_67 Homo sapiens cDNA clone IMAGE:5492749 5', mRNA sequence.    58  4e-05  1
BM611355|BM611355.1 17000687114723 A.Gam.ad.cDNA.blood1 Anopheles gambiae cDNA clone 19600449726382 5', mRNA sequence.    58  4e-05  1
BG574988|BG574988.1 602598078F1 NIH_MGC_87 Homo sapiens cDNA clone IMAGE:4706851 5', mRNA sequence.    58  4e-05  1
BG169144|BG169144.1 602320604F1 NIH_MGC_89 Homo sapiens cDNA clone IMAGE:4423728 5', mRNA sequence.    58  4e-05  1
BM617899|BM617899.1 17000687160107 A.Gam.ad.cDNA.blood1 Anopheles gambiae cDNA clone 19600449701204 5', mRNA sequence.    58  4e-05  1
BQ399486|BQ399486.1 NISC_mp03g12.y1 NICHD XGC Sp1 Xenopus laevis cDNA clone IMAGE:4965718 5', mRNA sequence.    58  4e-05  1
AW337394|AW337394.1 xx56a08.x1 NCI_CGAP_Lym12 Homo sapiens cDNA clone IMAGE:2847638 3' similar to contains element MSR1 MSR1 repetitive element ;, mRNA sequence.    58  4e-05  1
BF786690|BF786690.1 602111451F1 NCI_CGAP_Kid14 Mus musculus cDNA clone IMAGE:4239732 5', mRNA sequence.    58  4e-05  1
dna update 2003. 8.22
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: 3268448
Number of Hits to DB: 98,594,874
protein update 2009. 7.29
PSORT 

 psg: 0.99  gvh: 0.62  alm: 0.29  top: 0.60  tms: 0.07  mit: 0.48  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  tyr: 0.25  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 36.0 %: cytoplasmic
	 36.0 %: nuclear
	 12.0 %: mitochondrial
	  4.0 %: Golgi
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for VSD568 is cyt
5' end seq. ID VSD568F
5' end seq. 
>VSD568F.Seq
GACTAGTTCTAGATCGCGAGCGGCTGCCCTTTTTTTTTTTTTTNATTTTTTNATTTTTTT
TTTTTTNANANTTTTTTNGNTTTTTTTTTNGAAAAAAAAAA----------
Length of 5' end seq. 101
3' end seq. ID VSD568Z
3' end seq. 
>VSD568Z.Seq
----------TGNATAAATAAATCACCACTTNTANTATTATACTATANATAAATNNTANT
AATATATATATATATATATTAATTTATATNGTAAATAGATATTA
Length of 3' end seq. 94
Connected seq. ID VSD568P
Connected seq. 
>VSD568P.Seq
GACTAGTTCTAGATCGCGAGCGGCTGCCCTTTTTTTTTTTTTTNATTTTTTNATTTTTTT
TTTTTTNANANTTTTTTNGNTTTTTTTTTNGAAAAAAAAAA----------TGNATAAAT
AAATCACCACTTNTANTATTATACTATANATAAATNNTANTAATATATATATATATATAT
TAATTTATATNGTAAATAGATATTA
Length of connected seq. 195
Full length Seq ID -
Full length Seq. -
Length of full length seq. -