Contig-U12772-1
Contig ID Contig-U12772-1
Contig update 2002.12.18
Contig sequence
>Contig-U12772-1 (Contig-U12772-1Q) /CSM_Contig/Contig-U12772-1Q.Seq.d
CTGTTGGCCTACTGGNAATAATAATAATAGTAGTAATAATAGTAATAATA
ATAGTAATAGTAATAGTATTAATAGTAGTAATAGTCATAAATTAAAATCA
TTAAAATTTAATAAATTCACTGAAAAGGATAACGAAGATGATGAAACTGA
TTTAGTATTTGATCAAAAAGTTAGCGATACAAGTAGATTTAAAGTTAGAA
ATCAAAAGAAAGATTGGGATGATGAATTTGATAATTTCGGTTCAAGTGGT
GATGAATCTGAATCTTCAACAGCAACAACAAATGCAGCAATAAATTCAAA
TATTGCAAAGAAAATACTACCATCAAATAGAATCATTAGATATAGTAGTA
GTGGTCAACTTAAACAACAACAACAACAATTACTTCTACAACAACAACAA
CAACAACAACAACAACATTTACAACAACCATTATCGCCATCAGAAATGAA
ATTAAAAGTTAAAGAAACTTCAGAAGAATGGGATACAGAATTTGAAGAAT
CGTTTGATACAATATCATGGTCAGANNNNNNNNN

Gap no gap
Contig length 534
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1355954
End point 1355445
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U12772
List of clone(s)

est1=AHM408F,1,525
Translated Amino Acid sequence
CWPTGNNNNSSNNSNNNSNSNSINSSNSHKLKSLKFNKFTEKDNEDDETDLVFDQKVSDT
SRFKVRNQKKDWDDEFDNFGSSGDESESSTATTNAAINSNIAKKILPSNRIIRYSSSGQL
KQQQQQLLLQQQQQQQQQHLQQPLSPSEMKLKVKETSEEWDTEFEESFDTISWSXXX


Translated Amino Acid sequence (All Frames)
Frame A:
llaywx****************y*****s*ikiiki**ih*kg*rr**n*fsi*sks*ry
k*i*s*kskerlg**i**frfkw**i*ifnsnnkcsnkfkyckenttik*nh*i***wst
*tttttitsttttttttttftttiiairneiks*rnfrrmgyri*riv*ynimvrxxx


Frame B:
CWPTGNNNNSSNNSNNNSNSNSINSSNSHKLKSLKFNKFTEKDNEDDETDLVFDQKVSDT
SRFKVRNQKKDWDDEFDNFGSSGDESESSTATTNAAINSNIAKKILPSNRIIRYSSSGQL
KQQQQQLLLQQQQQQQQQHLQQPLSPSEMKLKVKETSEEWDTEFEESFDTISWSXXX


Frame C:
vgllxiiiivviiviiivivivlivvivin*nh*nlinslkritkmmkli*ylikklaiq
vdlkleikrkigmmnliisvqvvmnlnlqqqqqmqq*iqilqrkyyhqiesldivvvvnl
nnnnnnyfynnnnnnnnniynnhyrhqk*n*klkklqkngiqnlknrliqyhgqxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U12772-1 (Contig-U12772-1Q)
/CSM_Contig/Contig-U12772-1Q.Seq.d
(534 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U12772-1 (Contig-U12772-1Q) /CSM_Contig/Conti... 529 e-150
Contig-U03010-1 (Contig-U03010-1Q) /CSM_Contig/Conti... 44 2e-04
Contig-U14284-1 (Contig-U14284-1Q) /CSM_Contig/Conti... 36 0.037
Contig-U13199-1 (Contig-U13199-1Q) /CSM_Contig/Conti... 36 0.037
Contig-U12538-1 (Contig-U12538-1Q) /CSM_Contig/Conti... 36 0.037
Contig-U11328-1 (Contig-U11328-1Q) /CSM_Contig/Conti... 36 0.037
Contig-U11145-1 (Contig-U11145-1Q) /CSM_Contig/Conti... 36 0.037
Contig-U14651-1 (Contig-U14651-1Q) /CSM_Contig/Conti... 34 0.15
Contig-U13909-1 (Contig-U13909-1Q) /CSM_Contig/Conti... 34 0.15
Contig-U12355-1 (Contig-U12355-1Q) /CSM_Contig/Conti... 28 9.1

>Contig-U12772-1 (Contig-U12772-1Q) /CSM_Contig/Contig-U12772-1Q.Seq.d
Length = 534

Score = 529 bits (267), Expect = e-150
Identities = 267/267 (100%)
Strand = Plus / Plus


Query: 96 aatcattaaaatttaataaattcactgaaaaggataacgaagatgatgaaactgatttag 155
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 96 aatcattaaaatttaataaattcactgaaaaggataacgaagatgatgaaactgatttag 155


Query: 156 tatttgatcaaaaagttagcgatacaagtagatttaaagttagaaatcaaaagaaagatt 215
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 156 tatttgatcaaaaagttagcgatacaagtagatttaaagttagaaatcaaaagaaagatt 215


Query: 216 gggatgatgaatttgataatttcggttcaagtggtgatgaatctgaatcttcaacagcaa 275
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 216 gggatgatgaatttgataatttcggttcaagtggtgatgaatctgaatcttcaacagcaa 275


Query: 276 caacaaatgcagcaataaattcaaatattgcaaagaaaatactaccatcaaatagaatca 335
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 276 caacaaatgcagcaataaattcaaatattgcaaagaaaatactaccatcaaatagaatca 335


Query: 336 ttagatatagtagtagtggtcaactta 362
|||||||||||||||||||||||||||
Sbjct: 336 ttagatatagtagtagtggtcaactta 362


Score = 192 bits (97), Expect = 3e-49
Identities = 97/97 (100%)
Strand = Plus / Plus


Query: 429 cattatcgccatcagaaatgaaattaaaagttaaagaaacttcagaagaatgggatacag 488
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 429 cattatcgccatcagaaatgaaattaaaagttaaagaaacttcagaagaatgggatacag 488


Query: 489 aatttgaagaatcgtttgatacaatatcatggtcaga 525
|||||||||||||||||||||||||||||||||||||
Sbjct: 489 aatttgaagaatcgtttgatacaatatcatggtcaga 525


Score = 30.2 bits (15), Expect = 2.3
Identities = 15/15 (100%)
Strand = Plus / Plus


Query: 1 ctgttggcctactgg 15
|||||||||||||||
Sbjct: 1 ctgttggcctactgg 15


>Contig-U03010-1 (Contig-U03010-1Q) /CSM_Contig/Contig-U03010-1Q.Seq.d
Length = 775

Score = 44.1 bits (22), Expect = 2e-04
Identities = 25/26 (96%)
Strand = Plus / Plus


Query: 330 gaatcattagatatagtagtagtggt 355
||||||||||| ||||||||||||||
Sbjct: 279 gaatcattagaaatagtagtagtggt 304


Score = 32.2 bits (16), Expect = 0.58
Identities = 16/16 (100%)
Strand = Plus / Minus


Query: 135 aagatgatgaaactga 150
||||||||||||||||
Sbjct: 500 aagatgatgaaactga 485


>Contig-U14284-1 (Contig-U14284-1Q) /CSM_Contig/Contig-U14284-1Q.Seq.d
Length = 760

Score = 36.2 bits (18), Expect = 0.037
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 267 caacagcaacaacaaatg 284
||||||||||||||||||
Sbjct: 445 caacagcaacaacaaatg 462


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: 8868
Number of Sequences: 6905
Number of extensions: 8868
Number of successful extensions: 1815
Number of sequences better than 10.0: 885
length of query: 534
length of database: 5,674,871
effective HSP length: 16
effective length of query: 518
effective length of database: 5,564,391
effective search space: 2882354538
effective search space used: 2882354538
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 2008.12. 3
Homology vs DNA
Query= Contig-U12772-1 (Contig-U12772-1Q) /CSM_Contig/Contig-U12772-1Q.Seq.d
(534 letters)

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

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

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

(BJ336808) Dictyostelium discoideum cDNA clone:dda55p02, 5' ... 486 0.0 3
(AC115584) Dictyostelium discoideum chromosome 2 map complem... 44 0.21 4
(AC193814) Trichinella spiralis BAC clone TS195-31H12 from c... 48 0.32 1
(EJ412751) 1093012160974 Global-Ocean-Sampling_GS-28-01-01-1... 38 0.54 2
(AC142555) Pan troglodytes clone CH251-526K6, WORKING DRAFT ... 36 0.83 4
(AF310892) Dictyostelium discoideum citrate synthase (gltA) ... 44 0.96 2
(BJ336901) Dictyostelium discoideum cDNA clone:dda55f14, 5' ... 30 1.0 3
(BJ364114) Dictyostelium discoideum cDNA clone:ddc30c04, 5' ... 30 1.2 3
(CU915378) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 1.3 1
(AC223189) Bos taurus clone CH240-426L19, WORKING DRAFT SEQU... 46 1.3 1
(AC223092) Bos taurus clone CH240-429J8, WORKING DRAFT SEQUE... 46 1.3 1
(BB938390) Trifolium pratense cDNA clone:RCC11638. 46 1.3 1
(BB932975) Trifolium pratense cDNA clone:RCC05036. 46 1.3 1
(FE384176) CBNT2899.fwd CBNT_Daphnia_pulex_Chosen_One_Librar... 46 1.3 1
(FE384175) CBNT2899.rev CBNT_Daphnia_pulex_Chosen_One_Librar... 46 1.3 1
(FE291143) CANI491.fwd CANI_Daphnia_pulex_Log50_Library_18 D... 46 1.3 1
(FE291142) CANI491.rev CANI_Daphnia_pulex_Log50_Library_18 D... 46 1.3 1
(CP000422) Pediococcus pentosaceus ATCC 25745, complete genome. 46 1.3 1
(BJ393053) Dictyostelium discoideum cDNA clone:dds29m23, 5' ... 30 1.3 3
(BJ392061) Dictyostelium discoideum cDNA clone:dds26a11, 5' ... 30 1.5 3
(AY484462) Dictyostelium discoideum kinesin family member 8 ... 34 2.0 3
(AM200038) Paracentrotus lividus EST, clone MPMGp1172C0649Q,... 40 2.0 2
(AM557944) Paracentrotus lividus EST, clone MPMGp1172K1264Q,... 40 2.4 2
(EB542884) AGENCOURT_52936399 D. erecta EST Drosophila erect... 34 3.3 2
(EB542518) AGENCOURT_52937142 D. erecta EST Drosophila erect... 34 3.3 2
(EB552348) AGENCOURT_52953869 D. erecta EST Drosophila erect... 34 3.3 2
(EB534627) AGENCOURT_52963658 D. erecta EST Drosophila erect... 34 3.3 2
(BJ370131) Dictyostelium discoideum cDNA clone:ddc53d02, 5' ... 30 3.8 3
(AP003431) Oryza sativa Japonica Group genomic DNA, chromoso... 42 4.2 3
(AC115305) Mus musculus BAC clone RP24-372L1 from 18, comple... 42 5.0 2
(L00766) Human chromosome 4 sequence-tagged site STS4-252, s... 44 5.0 1
(G33314) human STS SHGC-24203, sequence tagged site. 44 5.0 1
(AL928926) Mouse DNA sequence from clone RP23-443G7 on chrom... 44 5.0 1
(AC097510) Homo sapiens BAC clone RP11-390C19 from 4, comple... 44 5.0 1
(AC128578) Rattus norvegicus clone CH230-154H20, WORKING DRA... 44 5.0 1
(AC126631) Rattus norvegicus clone CH230-205O19, *** SEQUENC... 44 5.0 1
(CT737204) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 5.0 1
(BH031051) RPCI-24-341I12.TJ RPCI-24 Mus musculus genomic cl... 44 5.0 1
(AQ602461) HS_2128_A1_E10_T7C CIT Approved Human Genomic Spe... 44 5.0 1
(DX372141) 3B_036_H03_FM1 Triticum aestivum chromosome 3B-sp... 44 5.0 1
(DE103053) Oryzias latipes DNA, clone: ola1-136N11.F, genomi... 44 5.0 1
(DE102522) Oryzias latipes DNA, clone: ola1-136B08.R, genomi... 44 5.0 1
(ES846463) UFL_133_63 Cotton fiber 0-10 day post anthesis Go... 44 5.0 1
(DW515054) GH_TMIRS_187_G10_F Cotton Normalized Library dT p... 44 5.0 1
(DV141323) CV03128A1B08.f1 CV03-normalized library Euphorbia... 44 5.0 1
(DT467297) GH_CHX20D03.r GH_CHX Gossypium hirsutum cDNA clon... 44 5.0 1
(DT467296) GH_CHX20D03.f GH_CHX Gossypium hirsutum cDNA clon... 44 5.0 1
(DT462097) GH_CHX08F07.x GH_CHX Gossypium hirsutum cDNA clon... 44 5.0 1
(AU074278) Dictyostelium discoideum slug cDNA, clone SSK211. 44 5.0 1
(CV559928) UI-M-HZ0-ctl-a-21-0-UI.r1 NIH_BMAP_HZ0 Mus muscul... 44 5.0 1
(BQ594867) E012262-024-024-K05-SP6 MPIZ-ADIS-024-developing ... 44 5.0 1
(BQ594782) E012441-024-024-K05-SP6 MPIZ-ADIS-024-developing ... 44 5.0 1
(BQ411988) GA__Ed0044G04r Gossypium arboreum 7-10 dpa fiber ... 44 5.0 1
(BP527626) Nicotiana tabacum cDNA, clone: BY12429, primer: M... 44 5.0 1
(BJ328719) Dictyostelium discoideum cDNA clone:dda29o03, 5' ... 44 5.0 1
(FG478188) 020918KALA009448HT (KALA) Dormant kiwifruit buds ... 44 5.0 1
(EY729487) CS00-C3-704-017-F01-CT.F Sweet orange fruit, deve... 44 5.0 1
(AV916299) Hordeum vulgare subsp. vulgare cv.Haruna Nijo cDN... 44 5.0 1
(AE017263) Mesoplasma florum L1 complete genome. 44 5.0 1
(AC074335) Mus Musculus Strain C57BL6/J Chromosome 18 BAC, R... 42 6.3 2
(AC101998) Mus musculus chromosome 10 clone RP24-449N22 map ... 38 6.5 2
(AF525505) Fusobacterium nucleatum outer membrane protein ge... 42 6.7 2
(DV738894) ID0AFF12AA02CM1 ID0AFF Acyrthosiphon pisum cDNA c... 36 6.8 2
(AC136273) Rattus norvegicus clone CH230-446C17, *** SEQUENC... 36 7.5 4
(AL110292) Human chromosome 14 DNA sequence BAC R-384J4 of l... 40 7.5 5
(AC116982) Dictyostelium discoideum chromosome 2 map 3622643... 38 7.7 5
(CC632482) OGLAV23TV ZM_0.7_1.5_KB Zea mays genomic clone ZM... 34 8.0 2
(CJ467103) Macaca fascicularis mRNA, clone: QnpA-16545, 5' e... 36 8.2 2
(CJ435270) Macaca fascicularis mRNA, clone: QccE-12305, 5' e... 38 8.5 2
(DT739843) EST1173692 Aquilegia cDNA library Aquilegia formo... 34 8.8 2
(ET034388) MUGQ_CH252P337C09Sp6_CP625_045 CHORI-252 Vervet M... 36 8.8 2
(AC206539) Pongo abelii BAC clone CH276-55H24 from chromosom... 32 8.9 2
(CC632472) OGLAV23TH ZM_0.7_1.5_KB Zea mays genomic clone ZM... 34 9.0 2
(AC212172) Pongo abelii chromosome UNKNOWN clone CH276-207B5... 32 9.0 2
(DR914492) EST1106031 Aquilegia cDNA library Aquilegia formo... 34 9.2 2
(DR936380) EST1127919 Aquilegia cDNA library Aquilegia formo... 34 9.2 2
(CC624734) OGUKR53TH ZM_0.7_1.5_KB Zea mays genomic clone ZM... 34 9.3 2
(CC624739) OGUKR53TV ZM_0.7_1.5_KB Zea mays genomic clone ZM... 34 9.6 2
(AL408673) T7 end of clone AV0AA010A09 of library AV0AA from... 40 9.8 2

>(BJ336808) Dictyostelium discoideum cDNA clone:dda55p02, 5' end,
single read.
Length = 525

Score = 486 bits (245), Expect(3) = 0.0
Identities = 245/245 (100%)
Strand = Plus / Plus


Query: 118 cactgaaaaggataacgaagatgatgaaactgatttagtatttgatcaaaaagttagcga 177
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 118 cactgaaaaggataacgaagatgatgaaactgatttagtatttgatcaaaaagttagcga 177


Query: 178 tacaagtagatttaaagttagaaatcaaaagaaagattgggatgatgaatttgataattt 237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 178 tacaagtagatttaaagttagaaatcaaaagaaagattgggatgatgaatttgataattt 237


Query: 238 cggttcaagtggtgatgaatctgaatcttcaacagcaacaacaaatgcagcaataaattc 297
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238 cggttcaagtggtgatgaatctgaatcttcaacagcaacaacaaatgcagcaataaattc 297


Query: 298 aaatattgcaaagaaaatactaccatcaaatagaatcattagatatagtagtagtggtca 357
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 298 aaatattgcaaagaaaatactaccatcaaatagaatcattagatatagtagtagtggtca 357


Query: 358 actta 362
|||||
Sbjct: 358 actta 362

Score = 192 bits (97), Expect(3) = 0.0
Identities = 97/97 (100%)
Strand = Plus / Plus


Query: 429 cattatcgccatcagaaatgaaattaaaagttaaagaaacttcagaagaatgggatacag 488
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 429 cattatcgccatcagaaatgaaattaaaagttaaagaaacttcagaagaatgggatacag 488


Query: 489 aatttgaagaatcgtttgatacaatatcatggtcaga 525
|||||||||||||||||||||||||||||||||||||
Sbjct: 489 aatttgaagaatcgtttgatacaatatcatggtcaga 525

Score = 30.2 bits (15), Expect(3) = 0.0
Identities = 15/15 (100%)
Strand = Plus / Plus


Query: 1 ctgttggcctactgg 15
|||||||||||||||
Sbjct: 1 ctgttggcctactgg 15

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 456,202,155
Number of extensions: 28787099
Number of successful extensions: 3061589
Number of sequences better than 10.0: 81
Length of query: 534
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 511
Effective length of database: 93,106,754,628
Effective search space: 47577551614908
Effective search space used: 47577551614908
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7. 4
Homology vs Protein
Query= Contig-U12772-1 (Contig-U12772-1Q) /CSM_Contig/Contig-U12772-1Q.Seq.d
(534 letters)

Database: nrp_B
3,236,559 sequences; 1,051,180,864 total letters

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

Score E
Sequences producing significant alignments: (bits) Value

CP001034_2460(CP001034|pid:none) Natranaerobius thermophilus JW/... 33 5.9
AM270079_53(AM270079|pid:none) Aspergillus niger contig An04c018... 32 7.7

>CP001034_2460(CP001034|pid:none) Natranaerobius thermophilus
JW/NM-WN-LF, complete genome.
Length = 1176

Score = 32.7 bits (73), Expect = 5.9
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Frame = +2

Query: 119 TEKDNEDDETDLVFDQKVSDTSRFKVRNQKKDWD-DEFDNFGSSGDESE 262
T + +ED E +L D +++D+ R+K R +DWD DE D+ DE++
Sbjct: 602 TVETDEDGEAEL--DYEMNDSGRYKFRAIAEDWDSDEMDDEDVEWDETK 648

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: 314,643,531
Number of extensions: 3221347
Number of successful extensions: 8317
Number of sequences better than 10.0: 2
Number of HSP's gapped: 8231
Number of HSP's successfully gapped: 2
Length of query: 178
Length of database: 1,051,180,864
Length adjustment: 120
Effective length of query: 58
Effective length of database: 662,793,784
Effective search space: 38442039472
Effective search space used: 38442039472
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: 30 (16.2 bits)

PSORT

psg: 0.68 gvh: 0.19 alm: 0.57 top: 0.53 tms: 0.00 mit: 0.39 mip: 0.00
nuc: 0.00 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

52.0 %: nuclear
24.0 %: mitochondrial
16.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: peroxisomal

>> prediction for Contig-U12772-1 is nuc

VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
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