Contig-U02244-1
Contig ID Contig-U02244-1
Contig update 2001. 8.29
Contig sequence
>Contig-U02244-1 (Contig-U02244-1Q) /CSM_Contig/Contig-U02244-1Q.Seq.d
CTCAAAAAAAGTAATAAAGCAAATAATTAATTTAGAAGAAAAAGCATACT
CTAAAGTTTTTTTAAGTTAAAAATAAAAACTCTAAAAAAAGCTTTTGGAA
ATATTAGCTCTTTTTTCTTTTTTTTTTTTAAAATAATAAAAAAAAAAAAA
CCCTTGGNTTTTTTTTTGGTTGGAAAAAAAAAAAAAAAAAAAATTTTTTT
NTTTNCNTTTTTCCCNGNCCNAAAAA----------TTTTTTTTTTTTAA
AAAAAAAAAAAAAAAAAACCCGGNTTTTTTTTTTTGGTTTTAAAAAAAAA
AAAAAAAAAAATATTTTAATTTACTATTTTACCGGN

Gap gap included
Contig length 326
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 8
Number of EST 9
Link to clone list U02244
List of clone(s)

est1=VSB156E,1,210
est2=VSH525F,1,183
est3=VSH220F,16,227
est4=VSE442E,39,203
est5=VSD568F,40,140
est6=VSG668F,71,205
est7=VSJ833F,84,183
est8=VSJ118F,114,227
est9=VSH220Z,228,328
Translated Amino Acid sequence
lkksnkann*frrksil*SFFKLKIKTLKKAFGNISSFFFFFFKIIKKKKPLXFFLVGKK
KKKKIFXFXFFPXXK---

---FFFLKKKKKKTRXFFFGFKKKKKKNILIYYFTG


Translated Amino Acid sequence (All Frames)
Frame A:
lkksnkann*frrksil*SFFKLKIKTLKKAFGNISSFFFFFFKIIKKKKPLXFFLVGKK
KKKKIFXFXFFPXXK---

---ffffkkkkkknpxfffwf*kkkkkkyfnllfyr

Frame B:
skkvikqiinleekayskvfls*k*kl*kklleilalfsffflk**kkknpwxffwlekk
kkkkffxxxfsxxxk---

---FFFLKKKKKKTRXFFFGFKKKKKKNILIYYFTG

Frame C:
qkk**sk*li*kkkhtlkff*vknknskksfwky*lfflfff*nnkkkktlgfffgwkkk
kkknffxxxfpxpk---

---fff*kkkkkkpgffflvlkkkkkkif*ftilp

own update 2004. 6. 9
Homology vs CSM-cDNA
Query= Contig-U02244-1 (Contig-U02244-1Q)
/CSM_Contig/Contig-U02244-1Q.Seq.d
(336 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U02244-1 (Contig-U02244-1Q) /CSM_Contig/Conti... 92 5e-19
Contig-U14721-1 (Contig-U14721-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U13896-1 (Contig-U13896-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U13321-1 (Contig-U13321-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U11853-1 (Contig-U11853-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U11805-1 (Contig-U11805-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U11702-1 (Contig-U11702-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U11596-1 (Contig-U11596-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U09176-1 (Contig-U09176-1Q) /CSM_Contig/Conti... 42 4e-04
Contig-U13524-1 (Contig-U13524-1Q) /CSM_Contig/Conti... 30 1.4

>Contig-U02244-1 (Contig-U02244-1Q) /CSM_Contig/Contig-U02244-1Q.Seq.d
Length = 336

Score = 91.7 bits (46), Expect = 5e-19
Identities = 46/46 (100%)
Strand = Plus / Plus


Query: 11 gtaataaagcaaataattaatttagaagaaaaagcatactctaaag 56
||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11 gtaataaagcaaataattaatttagaagaaaaagcatactctaaag 56


Score = 81.8 bits (41), Expect = 4e-16
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 130 aaaataataaaaaaaaaaaaacccttggntttttttttggttgg 173
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 130 aaaataataaaaaaaaaaaaacccttggntttttttttggttgg 173


Score = 48.1 bits (24), Expect = 6e-06
Identities = 24/24 (100%)
Strand = Plus / Plus


Query: 312 tattttaatttactattttaccgg 335
||||||||||||||||||||||||
Sbjct: 312 tattttaatttactattttaccgg 335


Score = 40.1 bits (20), Expect = 0.001
Identities = 23/23 (100%)
Strand = Plus / Plus


Query: 269 cccggntttttttttttggtttt 291
|||||||||||||||||||||||
Sbjct: 269 cccggntttttttttttggtttt 291


Score = 40.1 bits (20), Expect = 0.001
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 91 gcttttggaaatattagctc 110
||||||||||||||||||||
Sbjct: 91 gcttttggaaatattagctc 110


Score = 32.2 bits (16), Expect = 0.36
Identities = 29/34 (85%)
Strand = Plus / Plus


Query: 138 aaaaaaaaaaaaacccttggntttttttttggtt 171
|||||||||||||||| |||||||||||||
Sbjct: 256 aaaaaaaaaaaaacccggntttttttttttggtt 289


Score = 28.2 bits (14), Expect = 5.6
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 137 taaaaaaaaaaaaa 150
||||||||||||||
Sbjct: 248 taaaaaaaaaaaaa 261


Score = 28.2 bits (14), Expect = 5.6
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 137 taaaaaaaaaaaaa 150
||||||||||||||
Sbjct: 291 taaaaaaaaaaaaa 304


>Contig-U14721-1 (Contig-U14721-1Q) /CSM_Contig/Contig-U14721-1Q.Seq.d
Length = 493

Score = 42.1 bits (21), Expect = 4e-04
Identities = 21/21 (100%)
Strand = Plus / Plus


Query: 130 aaaataataaaaaaaaaaaaa 150
|||||||||||||||||||||
Sbjct: 430 aaaataataaaaaaaaaaaaa 450


Score = 30.2 bits (15), Expect = 1.4
Identities = 18/19 (94%)
Strand = Plus / Plus


Query: 132 aataataaaaaaaaaaaaa 150
||||| |||||||||||||
Sbjct: 435 aataaaaaaaaaaaaaaaa 453


>Contig-U13896-1 (Contig-U13896-1Q) /CSM_Contig/Contig-U13896-1Q.Seq.d
Length = 1529

Score = 42.1 bits (21), Expect = 4e-04
Identities = 21/21 (100%)
Strand = Plus / Plus


Query: 131 aaataataaaaaaaaaaaaac 151
|||||||||||||||||||||
Sbjct: 133 aaataataaaaaaaaaaaaac 153


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: 152,152
Number of Sequences: 6905
Number of extensions: 152152
Number of successful extensions: 55585
Number of sequences better than 10.0: 2729
length of query: 336
length of database: 5,674,871
effective HSP length: 15
effective length of query: 321
effective length of database: 5,571,296
effective search space: 1788386016
effective search space used: 1788386016
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 2009. 5.16
Homology vs DNA
Query= Contig-U02244-1 (Contig-U02244-1Q) /CSM_Contig/Contig-U02244-1Q.Seq.d
(336 letters)

Database: ddbj_A
102,105,510 sequences; 101,790,757,118 total letters

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

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

(AU267575) Dictyostelium discoideum vegetative cDNA clone:VS... 92 9e-21 2
(AU267090) Dictyostelium discoideum vegetative cDNA clone:VS... 82 8e-18 2
(CZ056638) OM__Ba0050G16.f OM__Ba Oryza minuta genomic clone... 50 0.053 1
(DX246391) OR_ABa0132G01.r OR_ABa Oryza ridleyi genomic clon... 48 0.21 1
(AU267091) Dictyostelium discoideum vegetative cDNA clone:VS... 48 0.21 1
(AG278059) Mus musculus molossinus DNA, clone:MSMg01-048D21.... 46 0.83 1
(DC231059) Plasmodium berghei strain ANKA cDNA clone:SG02067... 46 0.83 1
(DC230979) Plasmodium berghei strain ANKA cDNA clone:SG02043... 46 0.83 1
(DC228496) Plasmodium berghei strain ANKA cDNA clone:SG01246... 46 0.83 1
(CT485992) S.lycopersicum DNA sequence from clone LE_HBa-31H... 44 3.3 1
(AC119668) Rattus norvegicus clone CH230-56J3, *** SEQUENCIN... 44 3.3 1
(AC108322) Rattus norvegicus clone CH230-261G16, *** SEQUENC... 44 3.3 1
(AC226361) Oryza minuta clone OM__Ba0134C08, *** SEQUENCING ... 44 3.3 1
(AC196208) Zea mays chromosome 5 clone CH201-502L10; ZMMBBc0... 44 3.3 1
(AC190856) Zea mays chromosome 5 clone CH201-197H24; ZMMBBc0... 44 3.3 1
(DH081770) Oryzias latipes Fosmid clone:GOLWFno171_a22, reve... 44 3.3 1

>(AU267575) Dictyostelium discoideum vegetative cDNA clone:VSH525,
5' end single read.
Length = 184

Score = 91.7 bits (46), Expect(2) = 9e-21
Identities = 46/46 (100%)
Strand = Plus / Plus


Query: 11 gtaataaagcaaataattaatttagaagaaaaagcatactctaaag 56
||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11 gtaataaagcaaataattaatttagaagaaaaagcatactctaaag 56

Score = 40.1 bits (20), Expect(2) = 9e-21
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 91 gcttttggaaatattagctc 110
||||||||||||||||||||
Sbjct: 91 gcttttggaaatattagctc 110

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 139,833,418
Number of extensions: 9863164
Number of successful extensions: 767680
Number of sequences better than 10.0: 17
Length of query: 336
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 313
Effective length of database: 99,442,330,388
Effective search space: 31125449411444
Effective search space used: 31125449411444
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.19
Homology vs Protein
Query= Contig-U02244-1 (Contig-U02244-1Q) /CSM_Contig/Contig-U02244-1Q.Seq.d
(336 letters)

Database: nrp_B
3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 105,691,199
Number of extensions: 2041544
Number of successful extensions: 734
Number of sequences better than 10.0: 0
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 0
Length of query: 112
Length of database: 1,051,180,864
Length adjustment: 79
Effective length of query: 33
Effective length of database: 795,492,703
Effective search space: 26251259199
Effective search space used: 26251259199
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: 28 (15.4 bits)

PSORT

psg: 0.72 gvh: 0.31 alm: 0.40 top: 0.53 tms: 0.00 mit: 0.40 mip: 0.00
nuc: 1.42 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 %: mitochondrial
4.0 %: cytoskeletal
4.0 %: plasma membrane
4.0 %: cytoplasmic

>> prediction for Contig-U02244-1 is nuc

VS (DIR, S) 8
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