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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
VSD413
Library VS
(Link to library)
Clone ID VSD413
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig -
Original site URL
Representative seq. ID VSD413P
(Link to Original site)
Representative DNA sequence 
>VSD413 (VSD413Q) /CSM/VS/VSD4-A/VSD413Q.Seq.d/
GACGTCAAGAAAAGTTAAACAAAGTTGAATAAATTATTTACCTTTAATAATAAACAGATT
AAATAATTAATAAAAAAAAAAXXXXXXXXXXATGACTCTTATAAATCAAATTCAAGACGT
CAAGAAAAGTTAAACAAAGTNGAATAAATTTTTACCTTTAATAATAAACAGTATT
sequence update 2001. 3.22
Translated Amino Acid sequence 
rqeklnkve*iiyl***td*IINKKK---

---DSYKSNSRRQEKLNKVE*iftfnnkqy
Translated Amino Acid sequence (All Frames) 
Frame A:
dvkks*tklnklftfnnkqik*likkk---

---mtlinqiqdvkks*tkxnkflpliinsi

Frame B:
tsrkvkqs*inylpliinrlnn**kk---

---*ll*ikfktsrkvkqsxinfyl***tv

Frame C:
rqeklnkve*iiyl***td*IINKKK---

---DSYKSNSRRQEKLNKVE*iftfnnkqy
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSD413 (VSD413Q) /CSM/VS/VSD4-A/VSD413Q.Seq.d/                        161   4e-39
VSB578 (VSB578Q) /CSM/VS/VSB5-D/VSB578Q.Seq.d/                        141   4e-33
SLB264 (SLB264Q) /CSM/SL/SLB2-C/SLB264Q.Seq.d/                        135   2e-31
VSI631 (VSI631Q) /CSM/VS/VSI6-B/VSI631Q.Seq.d/                        131   4e-30
VFI293 (VFI293Q) /CSM/VF/VFI2-D/VFI293Q.Seq.d/                        111   3e-24
VFA435 (VFA435Q) /CSM/VF/VFA4-B/VFA435Q.Seq.d/                        111   3e-24
VFA343 (VFA343Q) /CSM/VF/VFA3-B/VFA343Q.Seq.d/                         60   1e-08
VSH383 (VSH383Q) /CSM/VS/VSH3-D/VSH383Q.Seq.d/                         34   0.63
VSG376 (VSG376Q) /CSM/VS/VSG3-D/VSG376Q.Seq.d/                         34   0.63
VHQ475 (VHQ475Q) /CSM/VH/VHQ4-D/VHQ475Q.Seq.d/                         34   0.63
own update 2004.12.25
Homology vs DNA 

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

AF231699|AF231699.1 Carabus fabricii NADH dehydrogenase subunit 5 (ND5) gene, partial cds; mitochondrial gene for mitochondrial product.    46  0.13  1
AX346957|AX346957.1 Sequence 2028 from Patent WO0200928.          46  0.13  1
AB047199|AB047199.1 Carabus depressus mitochondrial ND5 gene for NADH dehydrogenase subunit 5, partial cds, isolate:Locality No.6, Andrate, Torino, Piemonte, Italy.    46  0.13  1
AB047198|AB047198.1 Carabus depressus mitochondrial ND5 gene for NADH dehydrogenas subunit 5, partial cds, isolate:Locality No.5, Val Sesia, Varallo, Piemonte, Italy.    46  0.13  1
L17343|L17343.1 Budworm mitochondrial partial transfer RNA-Met (tRNA-Met) gene, and partial 12S ribosomal RNA (12S rRNA) gene.    26  0.16  4
AX458490|AX458490.1 Sequence 36 from Patent WO0246454.            32  0.41  5
BB454826|BB454826.2 Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130034D11, 3' end partial sequence.    36  0.43  2
AY265417|AY265417.1 Cooperia oncophora mitochondrion, complete genome.    40  0.51  2
AB092789|AB092789.1 Carabus masuzoi ND5 gene for NADH dehydrogenase subunit 5, pratial cds, isolate:Locality No. 36.    44  0.52  1
AB109863|AB109863.1 Nebria lewisi mitochondrial ND5 gene for NADH dehydrogenase subunit 5, partial cds, isolae:No. 71.    44  0.52  1
dna update 2003. 8.21
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: 159,809,287
protein update 2009. 7.29
PSORT 

 psg: 0.24  gvh: 0.08  alm: 0.94  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.00
 nuc: 0.24  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: 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 

	 56.0 %: nuclear
	 24.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for VSD413 is nuc
5' end seq. ID VSD413F
5' end seq. 
>VSD413F.Seq
GACGTCAAGAAAAGTTAAACAAAGTTGAATAAATTATTTACCTTTAATAATAAACAGATT
AAATAATTAATAAAAAAAAAA----------
Length of 5' end seq. 81
3' end seq. ID VSD413Z
3' end seq. 
>VSD413Z.Seq
----------ATGACTCTTATAAATCAAATTCAAGACGTCAAGAAAAGTTAAACAAAGTN
GAATAAATTTTTACCTTTAATAATAAACAGTATT
Length of 3' end seq. 84
Connected seq. ID VSD413P
Connected seq. 
>VSD413P.Seq
GACGTCAAGAAAAGTTAAACAAAGTTGAATAAATTATTTACCTTTAATAATAAACAGATT
AAATAATTAATAAAAAAAAAA----------ATGACTCTTATAAATCAAATTCAAGACGT
CAAGAAAAGTTAAACAAAGTNGAATAAATTTTTACCTTTAATAATAAACAGTATT
Length of connected seq. 165
Full length Seq ID -
Full length Seq. -
Length of full length seq. -