Contig-U14672-1
Contig ID Contig-U14672-1
Contig update 2002.12.18
Contig sequence
>Contig-U14672-1 (Contig-U14672-1Q) /CSM_Contig/Contig-U14672-1Q.Seq.d
GGGAATCAACTATCTATGACATACAATAATATACAACACCAATAATATTA
CTATTATAAAAAATTTATTATTTATATAGTATTTGTTTTATTATTTGTTT
TTTAATATCACTTTCACTTACCATTTTTAGACTTTTTTTTTGTGTGTTTG
TTTTCAACTTAAAAAAAAAACCACCAAAGTTTCANACCTTGCTATTTATT
TTTAAATATATTATTCTAANCNCAAAAAAAATAAAATAAAAATAAAAATT
AAAATTAAAATAAAAATAAAAATAAAATAATATATTAGCNCTCTTTTTTT
TTTTTTTTTTNAAAAAAAAANNNNNNNNN

Gap no gap
Contig length 329
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 267176
End point 267495
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U14672
List of clone(s)

est1=SHL835F,1,320
Translated Amino Acid sequence
estiydiq*yttpiilll*KIYYLYSICFIICFLISLSLTIFRLFFCVFVFNLKKKPPKF
XTLLFIFKYIILXXKKIK*k*klklk*k*k*nnilalfffffxkkkxxx


Translated Amino Acid sequence (All Frames)
Frame A:
gnqlsmtynniqhq*yyyykkfiiyivfvllfvf*yhfhlpfldfffvclfst*kknhqs
fxpcylflnilf*xqkk*nknkn*n*nknknkiiy*xsfffffxkkxxx


Frame B:
ginyl*htiiyntnnitiiknllfi*ylfyylffnitftyhf*tfflcvcfqlkkkttkv
sxlaiyf*iyysxxkknkikikikikikikik*yisxlfffffxkkxxx


Frame C:
estiydiq*yttpiilll*KIYYLYSICFIICFLISLSLTIFRLFFCVFVFNLKKKPPKF
XTLLFIFKYIILXXKKIK*k*klklk*k*k*nnilalfffffxkkkxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U14672-1 (Contig-U14672-1Q)
/CSM_Contig/Contig-U14672-1Q.Seq.d
(329 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U14672-1 (Contig-U14672-1Q) /CSM_Contig/Conti... 92 4e-19
Contig-U10643-1 (Contig-U10643-1Q) /CSM_Contig/Conti... 36 0.023
Contig-U05231-1 (Contig-U05231-1Q) /CSM_Contig/Conti... 36 0.023
Contig-U04878-1 (Contig-U04878-1Q) /CSM_Contig/Conti... 36 0.023
Contig-U03819-1 (Contig-U03819-1Q) /CSM_Contig/Conti... 34 0.089
Contig-U01739-1 (Contig-U01739-1Q) /CSM_Contig/Conti... 34 0.089
Contig-U14719-1 (Contig-U14719-1Q) /CSM_Contig/Conti... 32 0.35
Contig-U14094-1 (Contig-U14094-1Q) /CSM_Contig/Conti... 32 0.35
Contig-U13860-1 (Contig-U13860-1Q) /CSM_Contig/Conti... 32 0.35
Contig-U11754-1 (Contig-U11754-1Q) /CSM_Contig/Conti... 32 0.35

>Contig-U14672-1 (Contig-U14672-1Q) /CSM_Contig/Contig-U14672-1Q.Seq.d
Length = 329

Score = 91.7 bits (46), Expect = 4e-19
Identities = 49/49 (100%)
Strand = Plus / Plus


Query: 171 ccaccaaagtttcanaccttgctatttatttttaaatatattattctaa 219
|||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 171 ccaccaaagtttcanaccttgctatttatttttaaatatattattctaa 219


Score = 79.8 bits (40), Expect = 2e-15
Identities = 40/40 (100%)
Strand = Plus / Plus


Query: 1 gggaatcaactatctatgacatacaataatatacaacacc 40
||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 gggaatcaactatctatgacatacaataatatacaacacc 40


>Contig-U10643-1 (Contig-U10643-1Q) /CSM_Contig/Contig-U10643-1Q.Seq.d
Length = 592

Score = 36.2 bits (18), Expect = 0.023
Identities = 21/22 (95%)
Strand = Plus / Plus


Query: 192 ctatttatttttaaatatatta 213
||||||||||||| ||||||||
Sbjct: 5 ctatttatttttagatatatta 26


>Contig-U05231-1 (Contig-U05231-1Q) /CSM_Contig/Contig-U05231-1Q.Seq.d
Length = 716

Score = 36.2 bits (18), Expect = 0.023
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 195 tttatttttaaatatatt 212
||||||||||||||||||
Sbjct: 63 tttatttttaaatatatt 46


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: 3035
Number of Sequences: 6905
Number of extensions: 3035
Number of successful extensions: 421
Number of sequences better than 10.0: 151
length of query: 329
length of database: 5,674,871
effective HSP length: 15
effective length of query: 314
effective length of database: 5,571,296
effective search space: 1749386944
effective search space used: 1749386944
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 2008.12.28
Homology vs DNA
Query= Contig-U14672-1 (Contig-U14672-1Q) /CSM_Contig/Contig-U14672-1Q.Seq.d
(329 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

(BJ397714) Dictyostelium discoideum cDNA clone:dds47f10, 5' ... 92 3e-25 3
(EH012363) USDA-FP_185271 Lysiphlebus testaceipes adult whol... 48 0.19 1
(BX167406) Danio rerio genomic clone DKEY-153P4, genomic sur... 40 0.73 2
(BX159384) Danio rerio genomic clone DKEY-153M6, genomic sur... 40 0.75 2
(CU571395) Zebrafish DNA sequence from clone CH73-346M18 in ... 46 0.76 1
(CU278559) Zebrafish DNA sequence from clone DKEY-77P23 in l... 46 0.76 1
(CU041320) Zebrafish DNA sequence from clone CH211-167E17 in... 46 0.76 1
(CU019562) Zebrafish DNA sequence from clone DKEY-6D5 in lin... 46 0.76 1
(CT025748) Zebrafish DNA sequence from clone CH73-166N24 in ... 46 0.76 1
(CR854907) Zebrafish DNA sequence from clone DKEYP-51H1 in l... 46 0.76 1
(CR749163) Zebrafish DNA sequence from clone CH211-216B21 in... 46 0.76 1
(CR385026) Zebrafish DNA sequence from clone DKEY-186K21 in ... 46 0.76 1
(CR352251) Zebrafish DNA sequence from clone CH211-138M21 in... 46 0.76 1
(CR318585) Zebrafish DNA sequence from clone CH211-153H7 in ... 46 0.76 1
(BX908726) Zebrafish DNA sequence from clone DKEY-74I2 in li... 46 0.76 1
(BX890602) Zebrafish DNA sequence from clone DKEYP-109H9 in ... 46 0.76 1
(BX682548) Zebrafish DNA sequence from clone DKEY-94A14 in l... 46 0.76 1
(BX571803) Zebrafish DNA sequence from clone DKEY-273G3 in l... 46 0.76 1
(BX571694) Zebrafish DNA sequence from clone CH211-159E21 in... 46 0.76 1
(BX511189) Zebrafish DNA sequence from clone DKEY-28G23 in l... 46 0.76 1
(BX324212) Zebrafish DNA sequence from clone CH211-209N20 in... 46 0.76 1
(BX323073) Zebrafish DNA sequence from clone DKEY-117J3 in l... 46 0.76 1
(BX088549) Zebrafish DNA sequence from clone CH211-208G1 in ... 46 0.76 1
(BX000984) Zebrafish DNA sequence from clone CH211-157C7 in ... 46 0.76 1
(AL929596) Zebrafish DNA sequence from clone DKEY-53H9. 46 0.76 1
(AL929295) Zebrafish DNA sequence from clone BUSM1-71B9 in l... 46 0.76 1
(AL928637) Zebrafish DNA sequence from clone CH211-227I6. 46 0.76 1
(AL807749) Zebrafish DNA sequence from clone CH211-197F20. 46 0.76 1
(Z98551) Plasmodium falciparum MAL3P6. 46 0.76 1
(CU062651) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 0.76 1
(BX784039) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 0.76 1
(AL845540) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 0.76 1
(FH717477) CHO_OF5056xg17f1.ab1 CHO_OF5 Nicotiana tabacum ge... 46 0.76 1
(EJ899307) 1093018482404 Global-Ocean-Sampling_GS-30-02-01-1... 46 0.76 1
(EJ884171) 1093018409348 Global-Ocean-Sampling_GS-30-02-01-1... 46 0.76 1
(BX152428) Danio rerio genomic clone DKEY-114L17, genomic su... 46 0.76 1
(DX528805) GH_MBb0021H06r GH_MBb Gossypium hirsutum genomic ... 42 1.2 2
(AC170420) Macaca mulatta clone CH250-258E2, WORKING DRAFT S... 34 1.4 2
(AC170766) Macaca mulatta clone CH250-253A7, WORKING DRAFT S... 34 1.4 2
(AC170201) Macaca mulatta clone CH250-192I12, WORKING DRAFT ... 34 1.4 2
(AC170203) Macaca mulatta clone CH250-155N20, WORKING DRAFT ... 34 1.5 2
(CT573110) Zebrafish DNA sequence from clone CH211-122E16 in... 44 3.0 1
(CT027705) Zebrafish DNA sequence from clone DKEY-13P1 in li... 44 3.0 1
(CR854822) Zebrafish DNA sequence from clone DKEY-34K3 in li... 44 3.0 1
(BX539349) Zebrafish DNA sequence from clone DKEY-74L17 in l... 44 3.0 1
(BX248391) Zebrafish DNA sequence from clone CH211-212M14 in... 44 3.0 1
(AC121148) Mus musculus chromosome 3, clone RP24-369K4, comp... 44 3.0 1
(AC102417) Mus musculus chromosome 3, clone RP24-499J8, comp... 44 3.0 1
(EU590119) Dunaliella salina ATPase alpha subunit (atpA) gen... 44 3.0 1
(AP006715) Porphyra yezoensis chloroplast DNA, complete genome. 44 3.0 1
(AM448343) Vitis vinifera contig VV78X136481.3, whole genome... 44 3.0 1
(AM448269) Vitis vinifera contig VV78X236520.7, whole genome... 44 3.0 1
(AM446880) Vitis vinifera contig VV78X212750.5, whole genome... 44 3.0 1
(AC183810) Glycine max clone gmp1-95h18, complete sequence. 44 3.0 1
(AC159805) Glycine max clone gmw2-173d12, complete sequence. 44 3.0 1
(AC121334) Homo sapiens 12 BAC RP11-242C24 (Roswell Park Can... 44 3.0 1
(AC162560) Bos taurus clone CH240-120D5, WORKING DRAFT SEQUE... 44 3.0 1
(AC155736) Bos taurus clone CH240-45N16, WORKING DRAFT SEQUE... 44 3.0 1
(CU606889) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 3.0 1
(CU104740) Zebrafish DNA sequence *** SEQUENCING CANCELLED *... 44 3.0 1
(AC218053) Solanum lycopersicum chromosome 1 clone C01HBa000... 44 3.0 1
(AC188651) Canis familiaris chromosome 18 clone XX-418A13 ma... 44 3.0 1
(AC167785) Glycine max clone gmw2-2o24, WORKING DRAFT SEQUEN... 44 3.0 1
(BH051425) RPCI-24-319K18.TV RPCI-24 Mus musculus genomic cl... 44 3.0 1
(FH215940) CHO_OF3265xd15r1.ab1 CHO_OF3 Nicotiana tabacum ge... 44 3.0 1
(FH069752) CHO_OF3026xi09f1.ab1 CHO_OF3 Nicotiana tabacum ge... 44 3.0 1
(CE719007) tigr-gss-dog-17000329647446 Dog Library Canis lup... 44 3.0 1
(CE614360) tigr-gss-dog-17000313551972 Dog Library Canis lup... 44 3.0 1
(CE455519) tigr-gss-dog-17000319520529 Dog Library Canis lup... 44 3.0 1
(EH570397) FDR202-P00036-DEPE-R_P17 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH567417) FDR202-P00028-DEPE-R_N03 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH563347) FDR202-P00017-DEPE-R_M10 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH562983) FDR202-P00016-DEPE-R_M16 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH549276) FDR202-P00036-DEPE-F_P17 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH546271) FDR202-P00028-DEPE-F_N03 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH542205) FDR202-P00017-DEPE-F_M10 FDR202 Danio rerio cDNA ... 44 3.0 1
(EH541835) FDR202-P00016-DEPE-F_M16 FDR202 Danio rerio cDNA ... 44 3.0 1
(DT537753) DR010007B20B09 Canine normalized retinal cDNA lib... 44 3.0 1
(DN865479) nac16a12.y1 Dog eye lens. Unnormalized (nac) Cani... 44 3.0 1
(DN747447) GL-Cf-4239 GLGC-LIB0001-cf Canis familiaris Norma... 44 3.0 1
(DN402104) LIB4004-021-Q1-K1-H9 LIB4004 Canis lupus familiar... 44 3.0 1
(CO594432) DG2-95k21 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO594285) DG2-93f6 DG2-brain Canis lupus familiaris cDNA 3'... 44 3.0 1
(CO594282) DG2-93f17 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO592765) DG2-65k1 DG2-brain Canis lupus familiaris cDNA 3'... 44 3.0 1
(CO591427) DG2-49i6 DG2-brain Canis lupus familiaris cDNA 3'... 44 3.0 1
(CO591322) DG2-48b10 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO589741) DG2-30a9 DG2-brain Canis lupus familiaris cDNA 3'... 44 3.0 1
(CO589451) DG2-28l15 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO587968) DG2-18i20 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO587716) DG2-16h10 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO587345) DG2-143k16 DG2-brain Canis lupus familiaris cDNA ... 44 3.0 1
(CO586978) DG2-139m18 DG2-brain Canis lupus familiaris cDNA ... 44 3.0 1
(CO586955) DG2-139e16 DG2-brain Canis lupus familiaris cDNA ... 44 3.0 1
(CO586332) DG2-12e13 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO585905) DG2-122g5 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO584889) DG2-10a14 DG2-brain Canis lupus familiaris cDNA 3... 44 3.0 1
(CO584412) DG2-103b16 DG2-brain Canis lupus familiaris cDNA ... 44 3.0 1
(CO584033) DG3-2e13 DG3-brain Canis lupus familiaris cDNA 3'... 44 3.0 1
(AL721669) Danio rerio embryonic inner ear subtracted cDNA l... 44 3.0 1

>(BJ397714) Dictyostelium discoideum cDNA clone:dds47f10, 5' end,
single read.
Length = 320

Score = 91.7 bits (46), Expect(3) = 3e-25
Identities = 49/49 (100%)
Strand = Plus / Plus


Query: 171 ccaccaaagtttcanaccttgctatttatttttaaatatattattctaa 219
|||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 171 ccaccaaagtttcanaccttgctatttatttttaaatatattattctaa 219

Score = 40.1 bits (20), Expect(3) = 3e-25
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 1 gggaatcaactatctatgac 20
||||||||||||||||||||
Sbjct: 1 gggaatcaactatctatgac 20

Score = 38.2 bits (19), Expect(3) = 3e-25
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 142 gtgtgtttgttttcaactt 160
|||||||||||||||||||
Sbjct: 142 gtgtgtttgttttcaactt 160

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 136,786,717
Number of extensions: 11466060
Number of successful extensions: 1176959
Number of sequences better than 10.0: 107
Length of query: 329
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 306
Effective length of database: 93,106,754,628
Effective search space: 28490666916168
Effective search space used: 28490666916168
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.12
Homology vs Protein
Query= Contig-U14672-1 (Contig-U14672-1Q) /CSM_Contig/Contig-U14672-1Q.Seq.d
(329 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: 180,801,565
Number of extensions: 1370829
Number of successful extensions: 1781
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1780
Number of HSP's successfully gapped: 0
Length of query: 109
Length of database: 1,051,180,864
Length adjustment: 77
Effective length of query: 32
Effective length of database: 801,965,821
Effective search space: 25662906272
Effective search space used: 25662906272
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: 1.00 gvh: 0.61 alm: 0.20 top: 0.67 tms: 0.07 mit: 0.44 mip: 0.00
nuc: 0.03 erl: 0.00 erm: 0.80 pox: 0.00 px2: 0.00 vac: 0.00 rnp: 0.00
act: 0.00 caa: 0.00 yqr: 1.00 tyr: 0.00 leu: 0.09 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 1.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 0.00

32.0 %: cytoplasmic
24.0 %: mitochondrial
20.0 %: nuclear
8.0 %: plasma membrane
8.0 %: endoplasmic reticulum
4.0 %: vesicles of secretory system
4.0 %: peroxisomal

>> prediction for Contig-U14672-1 is cyt

VS (DIR, S) 0
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) 1
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0