Contig-U12399-1
Contig ID Contig-U12399-1
Contig update 2002.12.18
Contig sequence
>Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Contig-U12399-1Q.Seq.d
CTGTTGGCCTACTGGNATTCGAAAATCACCAAACGTAGATTCATAATTCG
TATAATGATTGATTTATTTTGTGTTGATATCATTCATTCCTATCAACCAA
TTTATAAATTGGTTAGTAAACTTTCAACCTCTTCAACCATTGAACAAGAT
AAAGAGAGTGGATATGGTAATTTATTAACATTTTTAGTATTTTTAAAACA
ATTTCAACAAGTTTCAAATTATAAAGATAAAATACCAGATTTAATAAATC
TATTTCATAGTTTATTAACTACTGAAGAAATTACAAATACTAAAAACTTA
ATTTCAAATTATTATCAAACTTTATGTAATTTTTTAACAAAAGAGAAATC
TCTATTAAGAGATAGAGAAAAAGAAATTAAATTATTTATGAGAACAAAAG
GTGAAGTACCAGAAGAATCATCAAAAGATTATGATTCAATGAGAAAACAN
TATGAAAAGTTAATTACAAATATATCACAGNTTTGCANAATTAATTGGTG
AACCAATTCCNAATAATGATNNNNNNNNN----------NNNNNNNNNNC
GTCACGTAATTTGGAAGCTTTATGAAGAGATCACCATTGGCTTGAAAAGA
ACGATTTCAATTACANCCAAAAGAGAATCATGCAAGTCACACTATTTGGC
GAATTGTATAATGCATGTTTATTGGAGACTAATCATATCTTTGATTTACT
CATTGGTGCACTCGAATTTGGGTATACCACTAGTCATCTCTTCCCTTCCA
ATATCTTTAGAGAGAGAGATCTCCTAAAGAGTAGACCAAAACCAAATTTG
GATGATTTCGACCCAATCAATGATTGCTTCAGAGTTAGGTTCATTTCCAC
TTTACTTTTAGTTTGTAAAGATTGTTTCCCTTTAGAAGATATTGAACAAC
ATTTAAAACCATATTTAGTATTCTTTCAACGTTATACTCTAACAAAATTA
TTACCTCTAGAAATTGAATTTATGATTACCGATTGTTTACAAATTGTACC
AGATATTAAAGTTTTTAAAACTTGGGAAGAAGCAAATGATGAATGTATGA
TTTTATCAGGTATTACACCACAATCAAAACAAGAATTACAAAAACAAAAA
CAAGAATTACAACAACAACAACAACAACAACCAAAAATTAAAATCCAATC
AAATAAATCAAAATCACCTTCATCTATGTCTTCTACTTCTCCACAACTTT
CTTCTTCTTCACCATTACCATTACAGCAACAACCACAACCTCAACAACCA
CAACCTCAACCAATTATTATTGAAAGTGAACAAGATGTTTTAAATATTAT
TCAAGATAATGATGAAGATGATATTAGTCTGAGGAAGATATTCTTAAAGA
ATTTAACAAATGTTAACA

Gap gap included
Contig length 1358
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 4712677
End point 4711450
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U12399
List of clone(s)

est1=VHB404F,1,520
est2=VHB404Z,521,1340
Translated Amino Acid sequence
cwptgirkspnvds*fv**liyfvlisfipinqfinwlvnfqplqplnkikrvdmviy*h
f*yf*nnfnkfqiikikyqi**iyfivy*llkklqilkt*fqiiiklyvif*qkrnly*e
iekkklnyl*eqkvkyqknhqkimiq*enxmks*LQIYHXFAXLIGEPIPNNDXXX---

---XXXRHVIWKLYEEITIGLKRTISITXKRESCKSHYLANCIMHVYWRLIISLIYSLVH
SNLGIPLVISSLPISLEREIS*rvdqnqiwmistqsmiaselgsfplyf*fvkivsl*ki
lnni*nhi*ysfnvil*qnyyl*klnl*lpivyklyqilkflklgkkqmmnv*fyqvlhh
nqnknyknknknynnnnnnnqklksnqinqnhlhlcllllhnflllhhyhysnnhnlnnh
nlnqlllkvnkmf*ilfkimmkmilv*grys*ri*qmlt


Translated Amino Acid sequence (All Frames)
Frame A:
llaywxskitkrrfiirimidlfcvdiihsyqpiyklvsklstsstieqdkesgygnllt
flvflkqfqqvsnykdkipdlinlfhslltteeitntknlisnyyqtlcnfltkeksllr
drekeiklfmrtkgevpeesskdydsmrkxyeklitnisqxcxinw*tnsx**xxx---

---xxxxsrnleal*rdhhwlekndfnyxqkrimqvtlfgelynaclletnhifdlliga
lefgyttshlfpsnifrerdllksrpkpnlddfdpindcfrvrfistlllvckdcfpled
ieqhlkpylvffqrytltkllpleiefmitdclqivpdikvfktweeandecmilsgitp
qskqelqkqkqelqqqqqqqpkikiqsnkskspssmsstspqlssssplplqqqpqpqqp
qpqpiiieseqdvlniiqdndeddislrkiflknltnvn

Frame B:
cwptgirkspnvds*fv**liyfvlisfipinqfinwlvnfqplqplnkikrvdmviy*h
f*yf*nnfnkfqiikikyqi**iyfivy*llkklqilkt*fqiiiklyvif*qkrnly*e
iekkklnyl*eqkvkyqknhqkimiq*enxmks*LQIYHXFAXLIGEPIPNNDXXX---

---XXXRHVIWKLYEEITIGLKRTISITXKRESCKSHYLANCIMHVYWRLIISLIYSLVH
SNLGIPLVISSLPISLEREIS*rvdqnqiwmistqsmiaselgsfplyf*fvkivsl*ki
lnni*nhi*ysfnvil*qnyyl*klnl*lpivyklyqilkflklgkkqmmnv*fyqvlhh
nqnknyknknknynnnnnnnqklksnqinqnhlhlcllllhnflllhhyhysnnhnlnnh
nlnqlllkvnkmf*ilfkimmkmilv*grys*ri*qmlt

Frame C:
vgllxfenhqt*ihnsynd*filc*yhsflstnl*ig**tfnlfnh*tr*rewiw*fini
fsifktistsfkl*r*ntrfnksis*finy*rnyky*klnfkllsnfm*ffnkreisikr
*rkrn*iiyenkr*strriikrl*fnektx*kvnykyitxlxn*lvnqfximxxx---

---xxxvt*fgsfmkrspla*kerfqlxpkenhashtiwriv*cmfigd*syl*fthwct
riwvyh*sslpfqyl*rerspke*tktkfg*frpnq*llqs*vhfhftfsl*rlfpfrry
*ttfktifsilstlysnkiitsrn*iydyrlftnctry*sf*nlgrsk**mydfiryytt
iktritktktrittttttttkn*npik*ikitfiyvfyfsttfffftititattttsttt
tstnyy*k*trcfkyysr***r*y*seedilkefnkc*

own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U12399-1 (Contig-U12399-1Q)
/CSM_Contig/Contig-U12399-1Q.Seq.d
(1368 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Conti... 1009 0.0
Contig-U14399-1 (Contig-U14399-1Q) /CSM_Contig/Conti... 38 0.025
Contig-U12065-1 (Contig-U12065-1Q) /CSM_Contig/Conti... 38 0.025
Contig-U10018-1 (Contig-U10018-1Q) /CSM_Contig/Conti... 38 0.025
Contig-U14190-1 (Contig-U14190-1Q) /CSM_Contig/Conti... 36 0.097
Contig-U14131-1 (Contig-U14131-1Q) /CSM_Contig/Conti... 36 0.097
Contig-U13916-1 (Contig-U13916-1Q) /CSM_Contig/Conti... 36 0.097
Contig-U12059-1 (Contig-U12059-1Q) /CSM_Contig/Conti... 36 0.097
Contig-U12039-1 (Contig-U12039-1Q) /CSM_Contig/Conti... 36 0.097
Contig-U12006-1 (Contig-U12006-1Q) /CSM_Contig/Conti... 36 0.097

>Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Contig-U12399-1Q.Seq.d
Length = 1368

Score = 1009 bits (509), Expect = 0.0
Identities = 512/512 (100%)
Strand = Plus / Plus


Query: 550 cgtcacgtaatttggaagctttatgaagagatcaccattggcttgaaaagaacgatttca 609
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 550 cgtcacgtaatttggaagctttatgaagagatcaccattggcttgaaaagaacgatttca 609


Query: 610 attacanccaaaagagaatcatgcaagtcacactatttggcgaattgtataatgcatgtt 669
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 610 attacanccaaaagagaatcatgcaagtcacactatttggcgaattgtataatgcatgtt 669


Query: 670 tattggagactaatcatatctttgatttactcattggtgcactcgaatttgggtatacca 729
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 670 tattggagactaatcatatctttgatttactcattggtgcactcgaatttgggtatacca 729


Query: 730 ctagtcatctcttcccttccaatatctttagagagagagatctcctaaagagtagaccaa 789
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 730 ctagtcatctcttcccttccaatatctttagagagagagatctcctaaagagtagaccaa 789


Query: 790 aaccaaatttggatgatttcgacccaatcaatgattgcttcagagttaggttcatttcca 849
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 790 aaccaaatttggatgatttcgacccaatcaatgattgcttcagagttaggttcatttcca 849


Query: 850 ctttacttttagtttgtaaagattgtttccctttagaagatattgaacaacatttaaaac 909
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 850 ctttacttttagtttgtaaagattgtttccctttagaagatattgaacaacatttaaaac 909


Query: 910 catatttagtattctttcaacgttatactctaacaaaattattacctctagaaattgaat 969
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 910 catatttagtattctttcaacgttatactctaacaaaattattacctctagaaattgaat 969


Query: 970 ttatgattaccgattgtttacaaattgtaccagatattaaagtttttaaaacttgggaag 1029
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 970 ttatgattaccgattgtttacaaattgtaccagatattaaagtttttaaaacttgggaag 1029


Query: 1030 aagcaaatgatgaatgtatgattttatcaggt 1061
||||||||||||||||||||||||||||||||
Sbjct: 1030 aagcaaatgatgaatgtatgattttatcaggt 1061


Score = 1001 bits (505), Expect = 0.0
Identities = 520/520 (100%)
Strand = Plus / Plus


Query: 1 ctgttggcctactggnattcgaaaatcaccaaacgtagattcataattcgtataatgatt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ctgttggcctactggnattcgaaaatcaccaaacgtagattcataattcgtataatgatt 60


Query: 61 gatttattttgtgttgatatcattcattcctatcaaccaatttataaattggttagtaaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 gatttattttgtgttgatatcattcattcctatcaaccaatttataaattggttagtaaa 120


Query: 121 ctttcaacctcttcaaccattgaacaagataaagagagtggatatggtaatttattaaca 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ctttcaacctcttcaaccattgaacaagataaagagagtggatatggtaatttattaaca 180


Query: 181 tttttagtatttttaaaacaatttcaacaagtttcaaattataaagataaaataccagat 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tttttagtatttttaaaacaatttcaacaagtttcaaattataaagataaaataccagat 240


Query: 241 ttaataaatctatttcatagtttattaactactgaagaaattacaaatactaaaaactta 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 ttaataaatctatttcatagtttattaactactgaagaaattacaaatactaaaaactta 300


Query: 301 atttcaaattattatcaaactttatgtaattttttaacaaaagagaaatctctattaaga 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 atttcaaattattatcaaactttatgtaattttttaacaaaagagaaatctctattaaga 360


Query: 361 gatagagaaaaagaaattaaattatttatgagaacaaaaggtgaagtaccagaagaatca 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 gatagagaaaaagaaattaaattatttatgagaacaaaaggtgaagtaccagaagaatca 420


Query: 421 tcaaaagattatgattcaatgagaaaacantatgaaaagttaattacaaatatatcacag 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 tcaaaagattatgattcaatgagaaaacantatgaaaagttaattacaaatatatcacag 480


Query: 481 ntttgcanaattaattggtgaaccaattccnaataatgat 520
||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 ntttgcanaattaattggtgaaccaattccnaataatgat 520


Score = 208 bits (105), Expect = 1e-53
Identities = 105/105 (100%)
Strand = Plus / Plus


Query: 1264 ttattattgaaagtgaacaagatgttttaaatattattcaagataatgatgaagatgata 1323
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1264 ttattattgaaagtgaacaagatgttttaaatattattcaagataatgatgaagatgata 1323


Query: 1324 ttagtctgaggaagatattcttaaagaatttaacaaatgttaaca 1368
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1324 ttagtctgaggaagatattcttaaagaatttaacaaatgttaaca 1368


Score = 176 bits (89), Expect = 4e-44
Identities = 89/89 (100%)
Strand = Plus / Plus


Query: 1138 ttaaaatccaatcaaataaatcaaaatcaccttcatctatgtcttctacttctccacaac 1197
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1138 ttaaaatccaatcaaataaatcaaaatcaccttcatctatgtcttctacttctccacaac 1197


Query: 1198 tttcttcttcttcaccattaccattacag 1226
|||||||||||||||||||||||||||||
Sbjct: 1198 tttcttcttcttcaccattaccattacag 1226


Score = 40.1 bits (20), Expect = 0.006
Identities = 20/20 (100%)
Strand = Plus / Minus


Query: 95 aaccaatttataaattggtt 114
||||||||||||||||||||
Sbjct: 114 aaccaatttataaattggtt 95


>Contig-U14399-1 (Contig-U14399-1Q) /CSM_Contig/Contig-U14399-1Q.Seq.d
Length = 1289

Score = 38.2 bits (19), Expect = 0.025
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 1147 aatcaaataaatcaaaatc 1165
|||||||||||||||||||
Sbjct: 376 aatcaaataaatcaaaatc 394


Score = 30.2 bits (15), Expect = 6.0
Identities = 18/19 (94%)
Strand = Plus / Plus


Query: 358 agagatagagaaaaagaaa 376
||||||||||||| |||||
Sbjct: 663 agagatagagaaagagaaa 681


Score = 30.2 bits (15), Expect = 6.0
Identities = 15/15 (100%)
Strand = Plus / Minus


Query: 789 aaaccaaatttggat 803
|||||||||||||||
Sbjct: 1230 aaaccaaatttggat 1216


>Contig-U12065-1 (Contig-U12065-1Q) /CSM_Contig/Contig-U12065-1Q.Seq.d
Length = 1415

Score = 38.2 bits (19), Expect = 0.025
Identities = 19/19 (100%)
Strand = Plus / Minus


Query: 118 aaactttcaacctcttcaa 136
|||||||||||||||||||
Sbjct: 212 aaactttcaacctcttcaa 194


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: 24,527
Number of Sequences: 6905
Number of extensions: 24527
Number of successful extensions: 3460
Number of sequences better than 10.0: 712
length of query: 1368
length of database: 5,674,871
effective HSP length: 16
effective length of query: 1352
effective length of database: 5,564,391
effective search space: 7523056632
effective search space used: 7523056632
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.11.30
Homology vs DNA
Query= Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Contig-U12399-1Q.Seq.d
(1368 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

(BJ437066) Dictyostelium discoideum cDNA clone:ddv33h02, 3' ... 1025 0.0 1
(BJ418536) Dictyostelium discoideum cDNA clone:ddv33h02, 5' ... 1001 0.0 1
(CP000049) Borrelia turicatae 91E135, complete genome. 36 0.005 20
(BH378861) AG-ND-169A24.TR ND-TAM Anopheles gambiae genomic ... 40 0.006 2
(BH162972) ENTSX27TR Entamoeba histolytica Sheared DNA Entam... 36 0.045 2
(AC168330) Strongylocentrotus purpuratus clone R3-58P5, WORK... 40 0.13 8
(EK583692) 1095522018812 Global-Ocean-Sampling_GS-32-01-01-1... 40 0.20 2
(AF022186) Cyanidium caldarium strain RK1 chloroplast, compl... 50 0.22 1
(AM486653) Vitis vinifera contig VV78X000436.15, whole genom... 36 0.31 4
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720... 34 0.71 13
(AL139337) Human DNA sequence *** SEQUENCING CANCELLED *** f... 42 0.74 7
(AC147497) Medicago truncatula chromosome 6 clone mth2-138p6... 40 0.79 7
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470... 36 0.83 13
(BX004784) Zebrafish DNA sequence from clone DKEY-82I7 in li... 48 0.89 1
(AL929172) Zebrafish DNA sequence from clone DKEYP-46C10 in ... 48 0.89 1
(AX356445) Sequence 79 from Patent WO0181622. 48 0.89 1
(AR552170) Sequence 7301 from patent US 6747137. 48 0.89 1
(AC005035) Homo sapiens BAC clone RP11-353P23 from 2, comple... 48 0.89 1
(AC157156) Bos taurus clone CH240-71B1, WORKING DRAFT SEQUEN... 48 0.89 1
(BZ037719) oeh82h05.b1 B.oleracea002 Brassica oleracea genom... 48 0.89 1
(AC116305) Dictyostelium discoideum chromosome 2 map 1005175... 32 0.92 19
(EJ505668) 1095403701944 Global-Ocean-Sampling_GS-28-01-01-1... 40 1.00 3
(ER306815) 1092343758903 Global-Ocean-Sampling_GS-34-01-01-1... 46 1.1 2
(CU179697) M.truncatula DNA sequence from clone MTH2-63I19 o... 32 1.2 8
(AC192443) Pan troglodytes BAC clone CH251-440J19 from chrom... 42 1.2 5
(ER315527) 1092344138862 Global-Ocean-Sampling_GS-34-01-01-1... 46 1.2 2
(CP000770) Candidatus Sulcia muelleri GWSS, complete genome. 34 1.2 11
(AE017263) Mesoplasma florum L1 complete genome. 32 1.3 21
(ES406146) MUT12-I14.x1d-t SHGC-MUT Mytilus californianus cD... 40 1.3 2
(AE014849) Plasmodium falciparum 3D7 chromosome 12, section ... 32 1.4 12
(AC209034) Populus trichocarpa clone POP003-C07, complete se... 42 1.4 4
(AE014821) Plasmodium falciparum 3D7 chromosome 14 section 6... 32 1.4 12
(BX649388) Zebrafish DNA sequence from clone CH211-225P5 in ... 40 1.5 6
(AC202480) Medicago truncatula clone mth2-166i6, WORKING DRA... 34 1.6 9
(CU329672) Schizosaccharomyces pombe chromosome III. 44 1.8 23
(CP000013) Borrelia garinii PBi, complete genome. 34 1.8 18
(CQ585716) Sequence 13474 from Patent WO0171042. 42 1.8 2
(CT573399) Zebrafish DNA sequence from clone DKEYP-51B9 in l... 32 1.9 2
(BX276114) Zebrafish DNA sequence from clone CH211-176L11 in... 42 1.9 5
(AC087886) Homo sapiens 12 BAC RP11-578A9 (Roswell Park Canc... 40 2.0 6
(AM468507) Vitis vinifera, whole genome shotgun sequence, co... 34 2.0 2
(AM489268) Vitis vinifera contig VV78X113159.9, whole genome... 38 2.1 4
(AL359081) Human DNA sequence from clone RP11-541F9 on chrom... 36 2.1 6
(EU306659) Medicago truncatula zinc finger protein, GH1 prot... 34 2.1 8
(AF250284) Amsacta moorei entomopoxvirus, complete genome. 36 2.1 12
(AC129406) Rattus norvegicus clone CH230-507M10, *** SEQUENC... 34 2.3 8
(EJ525241) 1092955181009 Global-Ocean-Sampling_GS-29-01-01-1... 36 2.4 2
(EJ555680) 1092959496562 Global-Ocean-Sampling_GS-29-01-01-1... 36 2.4 2
(AM051970) Dasytricha ruminantium EST, clone Day_D09. 36 2.4 2
(AC165540) Bos taurus clone CH240-168P15, WORKING DRAFT SEQU... 42 2.4 5
(AC178175) Strongylocentrotus purpuratus clone R3-3082B11, W... 36 2.5 8
(AC115599) Dictyostelium discoideum chromosome 2 map 4229098... 32 2.6 9
(EJ167578) 1092344071373 Global-Ocean-Sampling_GS-27-01-01-1... 38 2.7 3
(CU302328) Medicago truncatula chromosome 5 clone mth4-35c1,... 36 2.8 8
(AC117176) Dictyostelium discoideum chromosome 2 map 5018074... 32 3.0 11
(AC186379) Zea mays chromosome 2 clone CH201-323I15; ZMMBBc0... 40 3.1 2
(AC181264) Strongylocentrotus purpuratus clone R3-4012D7, WO... 36 3.4 6
(AC166745) Medicago truncatula clone mth2-193e13, complete s... 36 3.4 5
(CT572991) Mouse DNA sequence from clone RP24-434I23 on chro... 46 3.5 1
(AL731647) Mouse DNA sequence from clone RP23-226L1 on chrom... 46 3.5 1
(AC165233) Mus musculus chromosome 8, clone RP23-307O2, comp... 46 3.5 1
(AC159629) Mus musculus BAC clone RP24-178C15 from chromosom... 46 3.5 1
(AC123843) Mus musculus BAC clone RP23-407D18 from chromosom... 46 3.5 1
(AP008209) Oryza sativa (japonica cultivar-group) genomic DN... 46 3.5 1
(AC174339) Medicago truncatula clone mth2-161b15, complete s... 46 3.5 1
(AC091532) Oryza sativa chromosome 3 BAC OSJNBa0078A17 genom... 46 3.5 1
(AC115578) Dictyostelium discoideum chromosome 2 map complem... 46 3.5 1
(AL356018) Human chromosome 14 DNA sequence BAC C-2277K2 of ... 46 3.5 1
(AL137918) Human chromosome 14 DNA sequence BAC R-442G21 of ... 46 3.5 1
(AC105917) Homo sapiens BAC clone RP11-395C17 from 4, comple... 46 3.5 1
(AC119023) Rattus norvegicus clone CH230-429P17, *** SEQUENC... 46 3.5 1
(AC202479) Medicago truncatula clone mth2-164l8, WORKING DRA... 46 3.5 1
(AC194575) Macaca mulatta clone CH250-319M11, WORKING DRAFT ... 46 3.5 1
(AC025602) Homo sapiens chromosome 16 clone RP11-560G2 map 1... 46 3.5 1
(AC021330) Homo sapiens clone RP11-24D20, WORKING DRAFT SEQU... 46 3.5 1
(AC013710) Homo sapiens clone RP11-22M9, WORKING DRAFT SEQUE... 46 3.5 1
(AZ526518) 256PbD05 Pb MBN #21 Plasmodium berghei genomic 3'... 46 3.5 1
(ET822491) CHO_OF761xd22f1.ab1 CHO_OF Nicotiana tabacum geno... 46 3.5 1
(EJ342540) 1092963526280 Global-Ocean-Sampling_GS-28-01-01-1... 46 3.5 1
(DE582395) Bombyx mori genomic DNA, Fosmid clone:GBMFno232_k... 46 3.5 1
(DE343777) Bombyx mori genomic DNA, BAC clone:BET_044_B21. 46 3.5 1
(DE342801) Bombyx mori genomic DNA, BAC clone:BET_041_E20. 46 3.5 1
(DE342782) Bombyx mori genomic DNA, BAC clone:BET_041_D23. 46 3.5 1
(DY296817) IC0AAA91AB08RM1 CitNFL Citrus clementina cDNA 5',... 46 3.5 1
(DY292135) IC0AAA7AE03RM1 CitNFL Citrus clementina cDNA 5', ... 46 3.5 1
(AU282716) Molgula tectiformis mRNA, clone:MT06B1A05T, 3' end. 46 3.5 1
(CJ420475) Molgula tectiformis cDNA, larva clone:mtlv004i09,... 46 3.5 1
(CJ420365) Molgula tectiformis cDNA, larva clone:mtlv004d07,... 46 3.5 1
(BY269705) Mus musculus visual cortex cDNA, RIKEN full-lengt... 46 3.5 1
(BM086335) sah38g01.y1 Gm-c1036 Glycine max cDNA clone SOYBE... 46 3.5 1
(W49680) zc43b11.r1 Soares_senescent_fibroblasts_NbHSF Homo ... 46 3.5 1
(EY810914) PT11-C1-900-012-G04-CT.F Poncirus trifoliata leaf... 46 3.5 1
(EY667342) CS00-C1-102-030-C04-CT.F Sweet orange leaf, infec... 46 3.5 1
(EY197898) BC_009_21 Cotton ovule and fiber 3-5 days post an... 46 3.5 1
(EX168431) F05_R-18_044 Cotton 1-14 day post anthesis Lambda... 46 3.5 1
(CR543861) Acinetobacter sp. ADP1 complete genome. 46 3.5 1
(BA000028) Oceanobacillus iheyensis HTE831 DNA, complete gen... 46 3.5 1
(Y14674) Plasmodium falciparum mRNA for gamma-glutamylcystei... 36 3.5 3
(AC215647) Populus trichocarpa clone POP035-N09, complete se... 44 3.6 6
(AK162330) Mus musculus adult male cecum cDNA, RIKEN full-le... 38 3.6 2

>(BJ437066) Dictyostelium discoideum cDNA clone:ddv33h02, 3' end,
single read.
Length = 820

Score = 1025 bits (517), Expect = 0.0
Identities = 520/520 (100%)
Strand = Plus / Minus


Query: 550 cgtcacgtaatttggaagctttatgaagagatcaccattggcttgaaaagaacgatttca 609
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 820 cgtcacgtaatttggaagctttatgaagagatcaccattggcttgaaaagaacgatttca 761


Query: 610 attacanccaaaagagaatcatgcaagtcacactatttggcgaattgtataatgcatgtt 669
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 760 attacanccaaaagagaatcatgcaagtcacactatttggcgaattgtataatgcatgtt 701


Query: 670 tattggagactaatcatatctttgatttactcattggtgcactcgaatttgggtatacca 729
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 700 tattggagactaatcatatctttgatttactcattggtgcactcgaatttgggtatacca 641


Query: 730 ctagtcatctcttcccttccaatatctttagagagagagatctcctaaagagtagaccaa 789
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 640 ctagtcatctcttcccttccaatatctttagagagagagatctcctaaagagtagaccaa 581


Query: 790 aaccaaatttggatgatttcgacccaatcaatgattgcttcagagttaggttcatttcca 849
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 580 aaccaaatttggatgatttcgacccaatcaatgattgcttcagagttaggttcatttcca 521


Query: 850 ctttacttttagtttgtaaagattgtttccctttagaagatattgaacaacatttaaaac 909
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 520 ctttacttttagtttgtaaagattgtttccctttagaagatattgaacaacatttaaaac 461


Query: 910 catatttagtattctttcaacgttatactctaacaaaattattacctctagaaattgaat 969
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 460 catatttagtattctttcaacgttatactctaacaaaattattacctctagaaattgaat 401


Query: 970 ttatgattaccgattgtttacaaattgtaccagatattaaagtttttaaaacttgggaag 1029
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 400 ttatgattaccgattgtttacaaattgtaccagatattaaagtttttaaaacttgggaag 341


Query: 1030 aagcaaatgatgaatgtatgattttatcaggtattacacc 1069
||||||||||||||||||||||||||||||||||||||||
Sbjct: 340 aagcaaatgatgaatgtatgattttatcaggtattacacc 301

Score = 208 bits (105), Expect(2) = 2e-79
Identities = 105/105 (100%)
Strand = Plus / Minus


Query: 1264 ttattattgaaagtgaacaagatgttttaaatattattcaagataatgatgaagatgata 1323
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106 ttattattgaaagtgaacaagatgttttaaatattattcaagataatgatgaagatgata 47


Query: 1324 ttagtctgaggaagatattcttaaagaatttaacaaatgttaaca 1368
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 46 ttagtctgaggaagatattcttaaagaatttaacaaatgttaaca 2

Score = 121 bits (61), Expect(2) = 2e-79
Identities = 61/61 (100%)
Strand = Plus / Minus


Query: 1166 accttcatctatgtcttctacttctccacaactttcttcttcttcaccattaccattaca 1225
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204 accttcatctatgtcttctacttctccacaactttcttcttcttcaccattaccattaca 145


Query: 1226 g 1226
|
Sbjct: 144 g 144

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 1,632,380,212
Number of extensions: 126183787
Number of successful extensions: 9768112
Number of sequences better than 10.0: 169
Length of query: 1368
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 1344
Effective length of database: 97,308,875,965
Effective search space: 130783129296960
Effective search space used: 130783129296960
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)

protein update 2009. 7. 3
Homology vs Protein
Query= Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Contig-U12399-1Q.Seq.d
(1368 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

AM270125_16(AM270125|pid:none) Aspergillus niger contig An07c007... 78 7e-13
AM920427_625(AM920427|pid:none) Penicillium chrysogenum Wisconsi... 76 2e-12
AC004697_9(AC004697|pid:none) Arabidopsis thaliana chromosome 2 ... 70 2e-10
AC151520_3(AC151520|pid:none) Medicago truncatula chromosome 2 c... 70 2e-10
FM986818_1(FM986818|pid:none) Danio rerio partial mRNA for UPF2 ... 66 3e-09
AL928735_1(AL928735|pid:none) Mouse DNA sequence from clone RP23... 63 2e-08
AL080198_1(AL080198|pid:none) Homo sapiens mRNA; cDNA DKFZp434D2... 63 2e-08
AB049839_1(AB049839|pid:none) Macaca fascicularis brain cDNA, cl... 63 2e-08
AY013249_1(AY013249|pid:none) Homo sapiens hUPF2 mRNA, complete ... 63 2e-08
BC168584_1(BC168584|pid:none) Xenopus tropicalis hypothetical pr... 61 8e-08
AB037829_1(AB037829|pid:none) Homo sapiens mRNA for KIAA1408 pro... 60 2e-07
BC100230_1(BC100230|pid:none) Xenopus laevis hypothetical protei... 60 2e-07
CP001325_627(CP001325|pid:none) Micromonas sp. RCC299 chromosome... 59 5e-07
EF187726_1(EF187726|pid:none) Nicotiana attenuata UPF2 mRNA, par... 55 5e-06
CR382124_552(CR382124|pid:none) Kluyveromyces lactis strain NRRL... 53 2e-05
AE014298_1159(AE014298|pid:none) Drosophila melanogaster chromos... 51 9e-05
CP000584_164(CP000584|pid:none) Ostreococcus lucimarinus CCE9901... 50 2e-04
FN357484_17(FN357484|pid:none) Schistosoma mansoni genome sequen... 49 3e-04
AE016820_733(AE016820|pid:none) Ashbya gossypii (= Eremothecium ... 49 6e-04
CR382137_872(CR382137|pid:none) Debaryomyces hansenii strain CBS... 48 7e-04
CR954204_176(CR954204|pid:none) Ostreococcus tauri strain OTTH05... 47 0.002
CR382131_1015(CR382131|pid:none) Yarrowia lipolytica strain CLIB... 47 0.002
AK096191_1(AK096191|pid:none) Homo sapiens cDNA FLJ38872 fis, cl... 45 0.006
(O13824) RecName: Full=Nonsense-mediated mRNA decay protein 2; A... 44 0.010
(P38798) RecName: Full=Nonsense-mediated mRNA decay protein 2; A... 41 0.089
AE017308_342(AE017308|pid:none) Mycoplasma mobile 163K complete ... 40 0.15
AM910995_124(AM910995|pid:none) Plasmodium knowlesi strain H chr... 37 2.2
CR767821_823(CR767821|pid:none) Ehrlichia ruminantium strain Wel... 37 2.2
BX571863_75(BX571863|pid:none) Photorhabdus luminescens subsp. l... 35 4.9
CP001230_475(CP001230|pid:none) Persephonella marina EX-H1, comp... 35 6.4
AM746676_1232(AM746676|pid:none) Sorangium cellulosum 'So ce 56'... 35 6.4
AB049751_12(AB049751|pid:none) Escherichia coli gene cluster (co... 35 8.3

>AM270125_16(AM270125|pid:none) Aspergillus niger contig An07c0070,
complete genome.
Length = 1126

Score = 78.2 bits (191), Expect = 7e-13
Identities = 47/132 (35%), Positives = 68/132 (51%), Gaps = 1/132 (0%)
Frame = +3

Query: 591 LEKNDFNYXQKRIMQVTLFGELYNACLLETNHIFDLLIGALEFGYTTSHLFPSNIFRERD 770
LE+NDF + QKRI +V GELYN ++++ IFD L + FG+ P I
Sbjct: 775 LEQNDFKFNQKRIAEVKYLGELYNYKMIDSPVIFDTLYRIITFGHEGGTPMPGRI----- 829

Query: 771 LLKSRPKPNLDDFDPINDCFRVRFISTLLLVCKDCFPLEDIEQHLKPYLVFFQRYTLTK- 947
+ D +D FRVR + TLL C CF ++ L +L FFQ Y TK
Sbjct: 830 ----------NPLDLPDDFFRVRLVCTLLDTCGHCFDRGSAKKKLDFFLTFFQYYMHTKD 879

Query: 948 LLPLEIEFMITD 983
LP++++F++ D
Sbjct: 880 PLPMDVDFLVQD 891

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: 1,604,339,528
Number of extensions: 31369288
Number of successful extensions: 69411
Number of sequences better than 10.0: 32
Number of HSP's gapped: 69355
Number of HSP's successfully gapped: 41
Length of query: 456
Length of database: 1,051,180,864
Length adjustment: 132
Effective length of query: 324
Effective length of database: 623,955,076
Effective search space: 202161444624
Effective search space used: 202161444624
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: 32 (16.9 bits)

PSORT

psg: 0.85 gvh: 0.34 alm: 0.36 top: 0.40 tms: 0.00 mit: 0.15 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

48.0 %: cytoplasmic
44.0 %: nuclear
4.0 %: vesicles of secretory system
4.0 %: endoplasmic reticulum

>> prediction for Contig-U12399-1 is cyt

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