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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
VSD860
Library VS
(Link to library)
Clone ID VSD860
Atlas ID -
NBRP ID -
dictyBase ID -
Link to Contig Contig-U06606-1
Original site URL
Representative seq. ID VSD860P
(Link to Original site)
Representative DNA sequence 
>VSD860 (VSD860Q) /CSM/VS/VSD8-C/VSD860Q.Seq.d/
GAAACAAATAGAACAACCAATTGAACAATCAATTGAAAAACAAAATGAAGAACAAATAAT
AGAACAAATAATAGAACAAACAATAGAACAAAAAGAATTAGTTTTTGATAATGAAAATAA
TAATAGTAACATTCAAGCCAATGAAGATGATGAAGAGTTAGGTTGGGATTAAAAAACAAA
AACATAACCAAAAATAAAATTAAAAATAAAAAAAACATAACCAAAAACAAAAAATTTTTG
GAAATTGGGAAATAAAAAAAAAAXXXXXXXXXXGAAACAAATAGAACAACCAATTGAACA
ATCAATTGAAAAACAAAATGAAGAACAAATAATAGAACAAATAATAGAACAAACAATAGA
ACAAAAAGAATTAGTTTTTGATAATGAAAATAATAATAGTAACATTCAAGCCAATGAAGA
TGATGAAGAGTTAGGTTGGGATTAAAAAACAAAAACATAACCAAAAATAAAATTAAAAAT
AAAAAAAACATAACCAAAAACAAAAAATTTT
sequence update 2001. 3.22
Translated Amino Acid sequence 
nk*nnqlnnqlknkmknk**nk**nkq*nkkn*flimkiiivtfkpmkmmks*vgikkqk
hnqk*n*k*KKHNQKQKIFGNWEIKKK---

---KQIEQPIEQSIEKQNEEQIIEQIIEQTIEQKELVFDNENNNSNIQANEDDEELGWD*
ktkt*pkiklkikkt*pktknf
Translated Amino Acid sequence (All Frames) 
Frame A:
etnrttn*tin*ktk*rtnnrtnnrtnnrtkrisf***k****hssq*r**rvrlglknk
nitknkiknkknitknkkfleigk*kk---

---etnrttn*tin*ktk*rtnnrtnnrtnnrtkrisf***k****hssq*r**rvrlgl
knknitknkiknkknitknkkf

Frame B:
kqieqpieqsiekqneeqiieqiieqtieqkelvfdnennnsniqaneddeelgwd*ktk
t*pkiklkikkt*pktknfwklgnkkk---

---KQIEQPIEQSIEKQNEEQIIEQIIEQTIEQKELVFDNENNNSNIQANEDDEELGWD*
ktkt*pkiklkikkt*pktknf

Frame C:
nk*nnqlnnqlknkmknk**nk**nkq*nkkn*flimkiiivtfkpmkmmks*vgikkqk
hnqk*n*k*KKHNQKQKIFGNWEIKKK---

---nk*nnqlnnqlknkmknk**nk**nkq*nkkn*flimkiiivtfkpmkmmks*vgik
kqkhnqk*n*k*kkhnqkqki
Homology vs CSM-cDNA 

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VSE532 (VSE532Q) /CSM/VS/VSE5-B/VSE532Q.Seq.d/                        168   5e-41
VSD860 (VSD860Q) /CSM/VS/VSD8-C/VSD860Q.Seq.d/                        168   5e-41
VHN660 (VHN660Q) /CSM/VH/VHN6-C/VHN660Q.Seq.d/                         44   0.002
VHB858 (VHB858Q) /CSM/VH/VHB8-C/VHB858Q.Seq.d/                         44   0.002
VFO388 (VFO388Q) /CSM/VF/VFO3-D/VFO388Q.Seq.d/                         44   0.002
VFM765 (VFM765Q) /CSM/VF/VFM7-C/VFM765Q.Seq.d/                         44   0.002
VFM568 (VFM568Q) /CSM/VF/VFM5-C/VFM568Q.Seq.d/                         44   0.002
VFK641 (VFK641Q) /CSM/VF/VFK6-B/VFK641Q.Seq.d/                         44   0.002
VFK235 (VFK235Q) /CSM/VF/VFK2-B/VFK235Q.Seq.d/                         44   0.002
VFJ649 (VFJ649Q) /CSM/VF/VFJ6-C/VFJ649Q.Seq.d/                         44   0.002
own update 2004.12.25
Homology vs DNA 

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

T17996|T17996.1 0315c3 cbsPfHB3.1, Debopam Chakrabarti Plasmodium falciparum cDNA clone 0315c 5', mRNA sequence.    40  9e-05  2
AL487217|AL487217.1 T. brucei sheared genomic DNA clone 279e09, forward sequence.    38  7e-04  2
AC116305|AC116305.2 Dictyostelium discoideum chromosome 2 map 1005175-1418323 strain AX4, complete sequence.    36  0.003  7
BM275970|BM275970.1 PfESToaa88d12.y1 Plasmodium falciparum 3D7 gametocyte cDNA library Plasmodium falciparum 3D7 cDNA 5', mRNA sequence.    40  0.004  2
BM274372|BM274372.1 PfESToaa44h12.y1 Plasmodium falciparum 3D7 gametocyte cDNA library Plasmodium falciparum 3D7 cDNA 5', mRNA sequence.    40  0.004  2
AC094450|AC094450.6 Rattus norvegicus clone CH230-4G3, *** SEQUENCING IN PROGRESS ***, 1 ordered piece.    52  0.007  2
AC125752|AC125752.3 Rattus norvegicus clone CH230-140I15, *** SEQUENCING IN PROGRESS ***, 13 unordered pieces.    52  0.007  1
AL844507|AL844507.1 Plasmodium falciparum chromosome 8.           44  0.010  6
AC117075|AC117075.2 Dictyostelium discoideum chromosome 2 map 5201047-5455781 strain AX4, complete sequence.    40  0.011  5
BQ452118|BQ452118.1 PfESToaa92c01.y1 Plasmodium falciparum 3D7 asexual cDNA Plasmodium falciparum cDNA 5', mRNA sequence.    36  0.011  2
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: 232,036,427
protein update 2009. 7.30
PSORT 

 psg: 0.66  gvh: 0.12  alm: 0.56  top: 0.53  tms: 0.00  mit: 0.17  mip: 0.00
 nuc: 0.04  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 

	 48.0 %: nuclear
	 24.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  8.0 %: vacuolar
	  8.0 %: mitochondrial
	  4.0 %: Golgi

>> prediction for VSD860 is nuc
5' end seq. ID VSD860F
5' end seq. 
>VSD860F.Seq
GAAACAAATAGAACAACCAATTGAACAATCAATTGAAAAACAAAATGAAGAACAAATAAT
AGAACAAATAATAGAACAAACAATAGAACAAAAAGAATTAGTTTTTGATAATGAAAATAA
TAATAGTAACATTCAAGCCAATGAAGATGATGAAGAGTTAGGTTGGGATTAAAAAACAAA
AACATAACCAAAAATAAAATTAAAAATAAAAAAAACATAACCAAAAACAAAAAATTTTTG
GAAATTGGGAAATAAAAAAAAAA----------
Length of 5' end seq. 263
3' end seq. ID VSD860Z
3' end seq. 
>VSD860Z.Seq
----------GAAACAAATAGAACAACCAATTGAACAATCAATTGAAAAACAAAATGAAG
AACAAATAATAGAACAAATAATAGAACAAACAATAGAACAAAAAGAATTAGTTTTTGATA
ATGAAAATAATAATAGTAACATTCAAGCCAATGAAGATGATGAAGAGTTAGGTTGGGATT
AAAAAACAAAAACATAACCAAAAATAAAATTAAAAATAAAAAAAACATAACCAAAAACAA
AAAATTTT
Length of 3' end seq. 238
Connected seq. ID VSD860P
Connected seq. 
>VSD860P.Seq
GAAACAAATAGAACAACCAATTGAACAATCAATTGAAAAACAAAATGAAGAACAAATAAT
AGAACAAATAATAGAACAAACAATAGAACAAAAAGAATTAGTTTTTGATAATGAAAATAA
TAATAGTAACATTCAAGCCAATGAAGATGATGAAGAGTTAGGTTGGGATTAAAAAACAAA
AACATAACCAAAAATAAAATTAAAAATAAAAAAAACATAACCAAAAACAAAAAATTTTTG
GAAATTGGGAAATAAAAAAAAAA----------GAAACAAATAGAACAACCAATTGAACA
ATCAATTGAAAAACAAAATGAAGAACAAATAATAGAACAAATAATAGAACAAACAATAGA
ACAAAAAGAATTAGTTTTTGATAATGAAAATAATAATAGTAACATTCAAGCCAATGAAGA
TGATGAAGAGTTAGGTTGGGATTAAAAAACAAAAACATAACCAAAAATAAAATTAAAAAT
AAAAAAAACATAACCAAAAACAAAAAATTTT
Length of connected seq. 501
Full length Seq ID -
Full length Seq. -
Length of full length seq. -