Contig-U14580-1
Contig ID Contig-U14580-1
Contig update 2002.12.18
Contig sequence
>Contig-U14580-1 (Contig-U14580-1Q) /CSM_Contig/Contig-U14580-1Q.Seq.d
GTATTTGTTTGAAAGTGGGTGTAAATGCATGCTGTTTGATAGAGTTTGTA
TGCTGTGTGTTTAATGGGTTTTTTGAATCCTCAGTTCATATAAAAAATAA
TACAAAATCATTTATAGCAGTTAGAATAATAATTATTTTCAATTTTATTA
AAATAAAAATAAAAATAAATAAAAAAATAAATAAAAATAATAATAATAAT
AAAAAAAAAAAAAAAANTAANTAANTAATTAAAAAAANTAAAAAAAAAA

Gap no gap
Contig length 249
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 1838993
End point 1838745
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U14580
List of clone(s)

est1=SHE449F,1,249
est2=SHE449Z,1,182
Translated Amino Acid sequence
ICLKVGVNACCLIEFVCCVFNGFFESSVHIKNNTKSFIAVRIIIIFNFIKIKIKINKKIN
KNNNNNKKKKKXX*xikkxkkk


Translated Amino Acid sequence (All Frames)
Frame A:
vfv*kwv*mhav**slyavclmgflnpqfi*kiiqnhl*qle**lfsillk*k*k*ikk*
ikiiiiikkkkkxxx*lkkxkkk


Frame B:
ylfesgckcmlfdrvcmlcv*wvf*ilssykk*ykiiyss*nnnyfqfy*nknknk*knk
*k*****kkkkx*xxn*kx*kk


Frame C:
ICLKVGVNACCLIEFVCCVFNGFFESSVHIKNNTKSFIAVRIIIIFNFIKIKIKINKKIN
KNNNNNKKKKKXX*xikkxkkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U14580-1 (Contig-U14580-1Q)
/CSM_Contig/Contig-U14580-1Q.Seq.d
(249 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U14580-1 (Contig-U14580-1Q) /CSM_Contig/Conti... 293 4e-80
Contig-U04416-1 (Contig-U04416-1Q) /CSM_Contig/Conti... 38 0.004
Contig-U11511-1 (Contig-U11511-1Q) /CSM_Contig/Conti... 36 0.017
Contig-U02161-1 (Contig-U02161-1Q) /CSM_Contig/Conti... 36 0.017
Contig-U14118-1 (Contig-U14118-1Q) /CSM_Contig/Conti... 34 0.066
Contig-U13543-1 (Contig-U13543-1Q) /CSM_Contig/Conti... 34 0.066
Contig-U12434-1 (Contig-U12434-1Q) /CSM_Contig/Conti... 34 0.066
Contig-U10451-1 (Contig-U10451-1Q) /CSM_Contig/Conti... 34 0.066
Contig-U09720-1 (Contig-U09720-1Q) /CSM_Contig/Conti... 34 0.066
Contig-U12461-1 (Contig-U12461-1Q) /CSM_Contig/Conti... 32 0.26

>Contig-U14580-1 (Contig-U14580-1Q) /CSM_Contig/Contig-U14580-1Q.Seq.d
Length = 249

Score = 293 bits (148), Expect = 4e-80
Identities = 148/148 (100%)
Strand = Plus / Plus


Query: 1 gtatttgtttgaaagtgggtgtaaatgcatgctgtttgatagagtttgtatgctgtgtgt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 gtatttgtttgaaagtgggtgtaaatgcatgctgtttgatagagtttgtatgctgtgtgt 60


Query: 61 ttaatgggttttttgaatcctcagttcatataaaaaataatacaaaatcatttatagcag 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 ttaatgggttttttgaatcctcagttcatataaaaaataatacaaaatcatttatagcag 120


Query: 121 ttagaataataattattttcaattttat 148
||||||||||||||||||||||||||||
Sbjct: 121 ttagaataataattattttcaattttat 148


>Contig-U04416-1 (Contig-U04416-1Q) /CSM_Contig/Contig-U04416-1Q.Seq.d
Length = 837

Score = 38.2 bits (19), Expect = 0.004
Identities = 19/19 (100%)
Strand = Plus / Minus


Query: 123 agaataataattattttca 141
|||||||||||||||||||
Sbjct: 774 agaataataattattttca 756


>Contig-U11511-1 (Contig-U11511-1Q) /CSM_Contig/Contig-U11511-1Q.Seq.d
Length = 940

Score = 36.2 bits (18), Expect = 0.017
Identities = 21/22 (95%)
Strand = Plus / Minus


Query: 123 agaataataattattttcaatt 144
||||||||||||| ||||||||
Sbjct: 899 agaataataattactttcaatt 878


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: 4917
Number of Sequences: 6905
Number of extensions: 4917
Number of successful extensions: 1696
Number of sequences better than 10.0: 179
length of query: 249
length of database: 5,674,871
effective HSP length: 15
effective length of query: 234
effective length of database: 5,571,296
effective search space: 1303683264
effective search space used: 1303683264
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 2008.12.26
Homology vs DNA
Query= Contig-U14580-1 (Contig-U14580-1Q) /CSM_Contig/Contig-U14580-1Q.Seq.d
(249 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

(BJ393750) Dictyostelium discoideum cDNA clone:dds32b14, 5' ... 293 1e-75 1
(BJ405668) Dictyostelium discoideum cDNA clone:dds32b14, 3' ... 256 3e-64 1
(AC169425) Bos taurus clone CH240-202N8, WORKING DRAFT SEQUE... 42 0.037 2
(DU339827) 1098312126197 CHORI-243 Ovis aries genomic clone ... 44 0.068 2
(DU517656) 1098609816311 CHORI-243 Ovis aries genomic clone ... 44 0.13 2
(CR392045) Zebrafish DNA sequence from clone DKEY-167C9 in l... 48 0.14 1
(CU290012) Equus caballus GSS, BAC clone CH241-456F20, T7 en... 38 0.39 2
(CR936323) Medicago truncatula chromosome 5 clone mth2-155c8... 40 0.97 2
(AE014850) Plasmodium falciparum 3D7 chromosome 12, section ... 32 1.1 2
(AC005505) Plasmodium falciparum chromosome 12 clone 3D7, **... 32 1.2 2
(CC295147) CH261-125F11_RM1.1 CH261 Gallus gallus genomic cl... 32 1.5 2
(CC517817) CH240_364K23.TARBAC13P2 CHORI-240 Bos taurus geno... 32 1.5 2
(AU087396) Plasmodium falciparum 3D7 cDNA clone from Sugano ... 32 1.6 2
(DD293979) SUSCEPTIBILITY GENE FOR HUMAN STROKE; METHODS OF ... 44 2.2 1
(AX573239) Sequence 85 from Patent WO02074992. 44 2.2 1
(AX573238) Sequence 1 from Patent WO02074992. 44 2.2 1
(AC109486) Homo sapiens chromosome 5 clone RP11-546M4, compl... 44 2.2 1
(AC096560) Homo sapiens BAC clone RP11-241F6 from 2, complet... 44 2.2 1
(AC157422) Bos taurus clone CH240-71C4, WORKING DRAFT SEQUEN... 44 2.2 1
(AC157415) Bos taurus clone CH240-66M24, WORKING DRAFT SEQUE... 44 2.2 1
(AC155125) Bos taurus clone CH240-43B9, WORKING DRAFT SEQUEN... 44 2.2 1
(AC107887) Homo sapiens chromosome 8 clone RP11-45D21 map 8,... 44 2.2 1
(CU467037) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 2.2 1
(AY245863) Homo sapiens chromosome 5 clone RP11-151F7, *** S... 44 2.2 1
(AY245860) Homo sapiens chromosome 5 clone RP11-151G2, *** S... 44 2.2 1
(AC224506) Bos taurus clone CH240-483L18, WORKING DRAFT SEQU... 44 2.2 1
(AC182910) Bos taurus clone CH240-308K10, WORKING DRAFT SEQU... 44 2.2 1
(AC176941) Strongylocentrotus purpuratus clone R3-33M4, WORK... 44 2.2 1
(AC173014) Bos taurus clone CH240-170G1, WORKING DRAFT SEQUE... 44 2.2 1
(AC171852) Bos taurus clone CH240-165M6, WORKING DRAFT SEQUE... 44 2.2 1
(AC169355) Bos taurus clone CH240-199D12, WORKING DRAFT SEQU... 44 2.2 1
(EI234778) OR__Ba0031B07.f OR__Ba Oryza rufipogon genomic cl... 44 2.2 1
(EI214377) OR__Ba0004B17.f OR__Ba Oryza rufipogon genomic cl... 44 2.2 1
(ED761853) GM_WBb0132P01.r GM_WBb Glycine max genomic clone ... 44 2.2 1
(CW896123) RPCI42_128C8.TJ RPCI-42 Bos taurus genomic clone ... 44 2.2 1
(CU286871) Equus caballus GSS, BAC clone CH241-450K18, T7 en... 44 2.2 1
(CU274710) Equus caballus GSS, BAC clone CH241-430I19, T7 en... 44 2.2 1
(CT300764) Sus scrofa genomic clone CH242-211K10, genomic su... 44 2.2 1
(CL769069) OR_BBa0141H10.r OR_BBa Oryza nivara genomic clone... 44 2.2 1
(CE750751) tigr-gss-dog-17000369607151 Dog Library Canis lup... 44 2.2 1
(BM960670) cihA8F12S Ascidian hemocytes cDNA library Ciona i... 44 2.2 1
(EY371315) CAXA13376.rev CAXA Helobdella robusta Subtracted ... 44 2.2 1
(BH740098) gf24g12.b2 TO1000 Brassica oleracea genomic clone... 38 3.0 2
(AC151003) Bos taurus clone CH240-161J10, WORKING DRAFT SEQU... 38 3.9 3
(CT573423) Zebrafish DNA sequence from clone CH211-3M11 in l... 36 3.9 3
(AC104946) Homo sapiens chromosome 8, clone RP11-946L20, com... 32 4.2 2
(AC197406) Pan troglodytes chromosome 7 clone CH251-324M23, ... 30 4.2 2
(AC121590) Mus musculus BAC clone RP23-281L22 from 2, comple... 32 4.2 2
(AC009930) Homo sapiens chromosome 8, clone RP11-114O8, comp... 32 4.2 2
(AC006026) Homo sapiens BAC clone GS1-96J14 from 7, complete... 30 4.3 2
(BX539347) Zebrafish DNA sequence from clone CH211-262E15 in... 32 4.3 2
(AL928543) Mouse DNA sequence from clone RP23-345P1 on chrom... 32 4.4 2
(AC007941) Homo sapiens chromosome 18 clone RP11-356L1 map 1... 40 4.4 2
(AM480372) Vitis vinifera contig VV78X252469.11, whole genom... 32 4.7 2
(AM450922) Vitis vinifera contig VV78X147520.3, whole genome... 30 5.0 2
(AM424226) Vitis vinifera contig VV78X130822.5, whole genome... 30 5.1 2
(AZ116964) RPCI-23-10I12.TJ RPCI-23 Mus musculus genomic clo... 32 5.4 2
(EK219165) 1095460134302 Global-Ocean-Sampling_GS-31-01-01-1... 32 5.7 2
(EX653959) 256854289 Pea aphid whole body normalized full le... 32 5.7 2
(ED774070) GM_WBb0150E16.r GM_WBb Glycine max genomic clone ... 32 5.7 2
(EX647963) 256719668 Pea aphid whole body normalized full le... 32 5.7 2
(ED630960) GM_WBa0031N16.f GM_WBa Glycine max genomic clone ... 32 5.7 2
(ED618101) GM_WBa0011L16.r GM_WBa Glycine max genomic clone ... 30 5.8 2
(EY630301) CAWW21621.rev CAWW Capitella sp. I ECS-2004 Subtr... 30 5.8 2
(FH216476) CHO_OF3337xd05f1.ab1 CHO_OF3 Nicotiana tabacum ge... 38 5.9 2
(BH952491) odh02g08.b1 B.oleracea002 Brassica oleracea genom... 38 6.2 2
(BX248234) Zebrafish DNA sequence from clone DKEY-13E15 in l... 38 6.9 3
(DU750585) ASNF1554.g2 HF130_10-06-02 uncultured marine micr... 38 7.2 2
(AM441723) Vitis vinifera contig VV78X066821.6, whole genome... 42 8.2 2
(CR391998) Zebrafish DNA sequence from clone CH211-175F12 in... 34 8.4 3
(EF058657) Synthetic construct Saccharomyces cerevisiae clon... 42 8.8 1
(AC160062) Mus musculus 6 BAC RP23-427I18 (Roswell Park Canc... 42 8.8 1
(AC155649) Mus musculus 6 BAC RP24-234M19 (Roswell Park Canc... 42 8.8 1
(Z48756) S.cerevisiae chromosome XIII cosmid 9408. 42 8.8 1
(AP009847) Lotus japonicus genomic DNA, clone: LjT02E24, TM1... 42 8.8 1
(AM448143) Vitis vinifera contig VV78X030938.3, whole genome... 42 8.8 1
(AC009400) Arabidopsis thaliana chromosome III BAC F14P13 ge... 42 8.8 1
(DJ210326) Method for identification of useful proteins deri... 42 8.8 1
(DJ025881) Genome-wide DNA marker of Saccharomyces cerevisiae. 42 8.8 1
(DQ305038) Mytilus californianus protamine-like PL-II/PL-IV ... 42 8.8 1
(AJ844389) Zygaena cynarae subsp. samarensis mitochondrial p... 42 8.8 1
(AJ844351) Zygaena felix subsp. boursini mitochondrial parti... 42 8.8 1
(AC131237) Homo sapiens 3 BAC RP11-47L11 (Roswell Park Cance... 42 8.8 1
(AC008873) Homo sapiens chromosome 5 clone CTD-2199H11, comp... 42 8.8 1
(AC135774) Rattus norvegicus clone CH230-81K12, *** SEQUENCI... 42 8.8 1
(CU856578) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 8.8 1
(CU633215) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 8.8 1
(AC078979) Homo sapiens chromosome 3 clone RP11-296N12, WORK... 42 8.8 1
(AP007721) Lotus japonicus genomic DNA, chromosome 1, clone:... 42 8.8 1
(AC230361) Bos taurus clone CH240-510M15, WORKING DRAFT SEQU... 42 8.8 1
(AC223358) Bos taurus clone CH240-421H5, WORKING DRAFT SEQUE... 42 8.8 1
(AC181884) Strongylocentrotus purpuratus clone R3-1018M06, W... 42 8.8 1
(AC180464) Strongylocentrotus purpuratus clone R3-3102G21, W... 42 8.8 1
(AC180463) Strongylocentrotus purpuratus clone R3-3102F13, W... 42 8.8 1
(AC178877) Strongylocentrotus purpuratus clone R3-27F2, WORK... 42 8.8 1
(AC176412) Strongylocentrotus purpuratus clone R3-12J16, WOR... 42 8.8 1
(AC176235) Strongylocentrotus purpuratus clone R3-3060P13, W... 42 8.8 1
(AC174133) Strongylocentrotus purpuratus clone R3-1024I23, W... 42 8.8 1
(AC168654) Strongylocentrotus purpuratus clone R3-3017B22, W... 42 8.8 1
(AC016581) Homo sapiens chromosome 5 clone CTD-2542N23, WORK... 42 8.8 1

>(BJ393750) Dictyostelium discoideum cDNA clone:dds32b14, 5' end,
single read.
Length = 249

Score = 293 bits (148), Expect = 1e-75
Identities = 148/148 (100%)
Strand = Plus / Plus


Query: 1 gtatttgtttgaaagtgggtgtaaatgcatgctgtttgatagagtttgtatgctgtgtgt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 gtatttgtttgaaagtgggtgtaaatgcatgctgtttgatagagtttgtatgctgtgtgt 60


Query: 61 ttaatgggttttttgaatcctcagttcatataaaaaataatacaaaatcatttatagcag 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 ttaatgggttttttgaatcctcagttcatataaaaaataatacaaaatcatttatagcag 120


Query: 121 ttagaataataattattttcaattttat 148
||||||||||||||||||||||||||||
Sbjct: 121 ttagaataataattattttcaattttat 148

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 243,213,364
Number of extensions: 17112113
Number of successful extensions: 1658467
Number of sequences better than 10.0: 136
Length of query: 249
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 226
Effective length of database: 93,106,754,628
Effective search space: 21042126545928
Effective search space used: 21042126545928
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.12
Homology vs Protein
Query= Contig-U14580-1 (Contig-U14580-1Q) /CSM_Contig/Contig-U14580-1Q.Seq.d
(249 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: 226,530,822
Number of extensions: 2765303
Number of successful extensions: 4600
Number of sequences better than 10.0: 0
Number of HSP's gapped: 4600
Number of HSP's successfully gapped: 0
Length of query: 83
Length of database: 1,051,180,864
Length adjustment: 53
Effective length of query: 30
Effective length of database: 879,643,237
Effective search space: 26389297110
Effective search space used: 26389297110
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: 27 (15.0 bits)

PSORT

psg: 0.86 gvh: 0.47 alm: 0.28 top: 0.27 tms: 0.13 mit: 0.18 mip: 0.00
nuc: 0.27 erl: 0.00 erm: 0.60 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: 1.00 m3b: 0.00 m_ : 0.00

28.0 %: plasma membrane
28.0 %: endoplasmic reticulum
8.0 %: cytoplasmic
8.0 %: mitochondrial
8.0 %: extracellular, including cell wall
8.0 %: nuclear
4.0 %: cytoskeletal
4.0 %: vesicles of secretory system
4.0 %: peroxisomal

>> prediction for Contig-U14580-1 is pla

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