Contig-U09802-1
Contig ID Contig-U09802-1
Contig update 2002. 9.13
Contig sequence
>Contig-U09802-1 (Contig-U09802-1Q) /CSM_Contig/Contig-U09802-1Q.Seq.d
CACCTGTGTGTTTTTTTCTGTGTGTGTGTTGAAACAACCCTTTTTTTAAT
TATTATTATTTTTATTTTATTTTTTATTTTTTTATTTTTAAATATAGTAA
TATTACATCAAAAATAAAAAAAATAAAAATAAAATTTAATGTTTTTTTTA
ATTTTTAACATTAAAAAAAAA----------GGGGGGNTTTTTNCGGGGG
GGGGGGGNAANNNCCCCCNTTTTAAAAAAAAAAAANTNNNANNNAANTTT
TAATTTTTTTTTTTTTAAAAAAGGGAANTTCCCCCCCAAAAAAAAAAAAA
AAAAAAAAANNTTNNGGGNTTTTTTTATTTTTTCCCCTTAAAAAAAAAAA
AAAAAAAAAAAAATTTAAAATAGNTTCTTNTNTCTTTNCCCCCCCNACNA
CNACCCACAACCNAAAANAAAATTTANTCNATTTTTT

Gap gap included
Contig length 427
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 2
Link to clone list U09802
List of clone(s)

est1=VSH283F,1,172
est2=VSH283Z,173,429
Translated Amino Acid sequence
hlcvffcvcvettlfliiiifilffiflflnivilhqk*kk*k*NLMFFLIFNIKKK---

---GGFXRGGGXXXPXLKKKXXXXXFNFFFFKKGXFPPKKKKKKKXXXXFFIFSP*kkkk
kkki*nxfxxlxppxxxpqpkxkfxxff


Translated Amino Acid sequence (All Frames)
Frame A:
hlcvffcvcvettlfliiiifilffiflflnivilhqk*kk*k*NLMFFLIFNIKKK---

---ggxfxggggxxpxfkkkkxxxxf*ffff*krexppqkkkkkkxxxgffyffplkkkk
kkknlk*xlxsxppxxxpttxxkixsif

Frame B:
tcvffsvcvlkqpff*lllflfyflffyf*i**yyiknkknknki*cff*fltlkk---

---GGFXRGGGXXXPXLKKKXXXXXFNFFFFKKGXFPPKKKKKKKXXXXFFIFSP*kkkk
kkki*nxfxxlxppxxxpqpkxkfxxff

Frame C:
pvcfflcvc*nnpffnyyyfyfifyffifkysnitskikkikikfnvffnf*h*kk---

---gxfxggggxxppf*kkkxxxxxliffflkkgxsppkkkkkkkxxgxflffplkkkkk
kkkfkixsxxfxppttthnxkxnlxxf

own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U09802-1 (Contig-U09802-1Q)
/CSM_Contig/Contig-U09802-1Q.Seq.d
(437 letters)

Database: CSM
6905 sequences; 5,674,871 total letters


Score E
Sequences producing significant alignments: (bits) Value

Contig-U09802-1 (Contig-U09802-1Q) /CSM_Contig/Conti... 46 3e-05
Contig-U12259-1 (Contig-U12259-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U01647-1 (Contig-U01647-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U14841-1 (Contig-U14841-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U14820-1 (Contig-U14820-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U14771-1 (Contig-U14771-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U14763-1 (Contig-U14763-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U14725-1 (Contig-U14725-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U14617-1 (Contig-U14617-1Q) /CSM_Contig/Conti... 32 0.47
Contig-U07707-1 (Contig-U07707-1Q) /CSM_Contig/Conti... 32 0.47

>Contig-U09802-1 (Contig-U09802-1Q) /CSM_Contig/Contig-U09802-1Q.Seq.d
Length = 437

Score = 46.1 bits (23), Expect = 3e-05
Identities = 23/23 (100%)
Strand = Plus / Plus


Query: 18 ctgtgtgtgtgttgaaacaaccc 40
|||||||||||||||||||||||
Sbjct: 18 ctgtgtgtgtgttgaaacaaccc 40


Score = 42.1 bits (21), Expect = 5e-04
Identities = 24/24 (100%)
Strand = Plus / Plus


Query: 316 gggntttttttattttttcccctt 339
||||||||||||||||||||||||
Sbjct: 316 gggntttttttattttttcccctt 339


Score = 40.1 bits (20), Expect = 0.002
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 90 aaatatagtaatattacatc 109
||||||||||||||||||||
Sbjct: 90 aaatatagtaatattacatc 109


Score = 38.2 bits (19), Expect = 0.008
Identities = 22/22 (100%)
Strand = Plus / Plus


Query: 214 cccccnttttaaaaaaaaaaaa 235
||||||||||||||||||||||
Sbjct: 214 cccccnttttaaaaaaaaaaaa 235


Score = 36.2 bits (18), Expect = 0.030
Identities = 21/21 (100%)
Strand = Plus / Plus


Query: 267 aaaaaagggaanttccccccc 287
|||||||||||||||||||||
Sbjct: 267 aaaaaagggaanttccccccc 287


Score = 32.2 bits (16), Expect = 0.47
Identities = 16/16 (100%)
Strand = Plus / Minus


Query: 220 ttttaaaaaaaaaaaa 235
||||||||||||||||
Sbjct: 270 ttttaaaaaaaaaaaa 255


Score = 28.2 bits (14), Expect = 7.4
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 222 ttaaaaaaaaaaaa 235
||||||||||||||
Sbjct: 338 ttaaaaaaaaaaaa 351


>Contig-U12259-1 (Contig-U12259-1Q) /CSM_Contig/Contig-U12259-1Q.Seq.d
Length = 1255

Score = 34.2 bits (17), Expect = 0.12
Identities = 19/20 (95%)
Strand = Plus / Plus


Query: 216 cccnttttaaaaaaaaaaaa 235
||| ||||||||||||||||
Sbjct: 1180 cccattttaaaaaaaaaaaa 1199


Score = 32.2 bits (16), Expect = 0.47
Identities = 16/16 (100%)
Strand = Plus / Minus


Query: 322 tttttattttttcccc 337
||||||||||||||||
Sbjct: 242 tttttattttttcccc 227


Score = 28.2 bits (14), Expect = 7.4
Identities = 14/14 (100%)
Strand = Plus / Minus


Query: 320 tttttttatttttt 333
||||||||||||||
Sbjct: 103 tttttttatttttt 90


>Contig-U01647-1 (Contig-U01647-1Q) /CSM_Contig/Contig-U01647-1Q.Seq.d
Length = 383

Score = 34.2 bits (17), Expect = 0.12
Identities = 19/20 (95%)
Strand = Plus / Plus


Query: 216 cccnttttaaaaaaaaaaaa 235
||| ||||||||||||||||
Sbjct: 206 ccccttttaaaaaaaaaaaa 225


Score = 28.2 bits (14), Expect = 7.4
Identities = 19/21 (90%)
Strand = Plus / Plus


Query: 215 ccccnttttaaaaaaaaaaaa 235
|||| ||| ||||||||||||
Sbjct: 206 ccccttttaaaaaaaaaaaaa 226


Score = 28.2 bits (14), Expect = 7.4
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 222 ttaaaaaaaaaaaa 235
||||||||||||||
Sbjct: 295 ttaaaaaaaaaaaa 308


Database: CSM
Posted date: Jun 9, 2004 7:35 PM
Number of letters in database: 5,674,871
Number of sequences in database: 6905

Lambda K H
1.37 0.711 1.31

Gapped
Lambda K H
1.37 0.711 1.31


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 81,464
Number of Sequences: 6905
Number of extensions: 81464
Number of successful extensions: 6572
Number of sequences better than 10.0: 2130
length of query: 437
length of database: 5,674,871
effective HSP length: 16
effective length of query: 421
effective length of database: 5,564,391
effective search space: 2342608611
effective search space used: 2342608611
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
dna update 2008.11.18
Homology vs DNA
Query= Contig-U09802-1 (Contig-U09802-1Q) /CSM_Contig/Contig-U09802-1Q.Seq.d
(437 letters)

Database: ddbj_A
92,845,959 sequences; 95,242,211,685 total letters

Searching..................................................done

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

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 41,701,087
Number of extensions: 2511427
Number of successful extensions: 55096
Number of sequences better than 10.0: 0
Length of query: 437
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 414
Effective length of database: 93,106,754,628
Effective search space: 38546196415992
Effective search space used: 38546196415992
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.26
Homology vs Protein
Query= Contig-U09802-1 (Contig-U09802-1Q) /CSM_Contig/Contig-U09802-1Q.Seq.d
(437 letters)

Database: nrp_A
3,204,285 sequences; 1,040,966,779 total letters

Searching..................................................done

***** 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: 3204285
Number of Hits to DB: 339,311,154
Number of extensions: 4377957
Number of successful extensions: 2704
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2537
Number of HSP's successfully gapped: 0
Length of query: 145
Length of database: 1,040,966,779
Length adjustment: 108
Effective length of query: 37
Effective length of database: 694,903,999
Effective search space: 25711447963
Effective search space used: 25711447963
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 29 (15.8 bits)

PSORT

psg: 0.51 gvh: 0.31 alm: 0.51 top: 0.53 tms: 0.00 mit: 0.27 mip: 0.00
nuc: 0.47 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

80.0 %: nuclear
8.0 %: cytoskeletal
8.0 %: cytoplasmic
4.0 %: plasma membrane

>> prediction for Contig-U09802-1 is nuc

VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0