Contig-U11937-1
Contig ID Contig-U11937-1
Contig update 2002.12.18
Contig sequence
>Contig-U11937-1 (Contig-U11937-1Q) /CSM_Contig/Contig-U11937-1Q.Seq.d
ATTACTATTTAAAACTATAAAATCAAATTATACAAGTAGTATAAATTGCT
TTAATTAGCTATTAGCAATATATTTTTATCATTTAATTGATTGTATTCTA
GTTTTAACCGTTTTTATTCGTTATTTAAATTAAAAAAAATATATATATTT
ATATATAATTTATTTTTTTTATTAATCTATTTATTAATCTTAACCTATAT
AACATTTTTGTTTTTTTTATTATTATTATTATTATTATTATTTTCTTTTT
TTATTTTTTTATTTATATATTTAAAAATTTCATTTATTCAATTTATTTAT
TTGTCGTTTGTGTGATTTTCGCCAATTGACAATGGTTGAAATTAATAAAA
TTAAATTTTTAATAAAAAAAAAANNNNNNNNN----------NNNNNNNN
NNAAAGAAAGNAAAGAAAGNAAAGAAAGNAAAGAAAAAAGATAAAAATTC
CAGTAGTGACGATGATGATGATGATGATGATGATAATAATGATAGTCGAA
ATGATAAAGAAAAANCTGAAAAGAAAAAAGATAAATATAAAGATAAAGAT
AAAAATAATGAGATAATTCCAAACTCAAATGGTCACNCAGAAAAACCCAA
AAATTATAATGATAATGGTGGTCGTGTTGATGATGNANGAAGAGATGATA
GATATAGGGATAGNGATCATTCCGATAGAAGGGATGCCAGTCTATAGAGA
TAGTG

Gap gap included
Contig length 695
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 1260591
End point 1259915
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U11937
List of clone(s)

est1=CHR308F,1,373
est2=CHR308Z,374,677
Translated Amino Acid sequence
llfktiksnytssincfn*llaiyfyhlidcilvltvfiryln*kkyiylyiiyffy*si
y*s*pi*hfcffyyyyyyyyflflffylyi*KFHLFNLFICRLCDFRQLTMVEINKIKFL
IKKKXXX---

---XXXKKXKKXKKXKKKDKNSSSDDDDDDDDDNNDSRNDKEKXEKKKDKYKDKDKNNEI
IPNSNGHXEKPKNYNDNGGRVDDXXRDDRYRDXDHSDRRDASL*r*


Translated Amino Acid sequence (All Frames)
Frame A:
iti*nykiklyk*ykll*laisniflsfn*lyssfnrfyslfklkkiyifiynlfflliy
lliltyitflffllllllllfsffiflfiylkisfiqfiylsfv*fspidng*n**n*if
nkkkxxx---

---xxxxrkxrkxrkxrkkikipvvtmmmmmmmiimivemikkxlkrkkinikikikimr
*fqtqmvtqknpkiimimvvvlmmxeemidigixiipiegmpvyrds

Frame B:
llfktiksnytssincfn*llaiyfyhlidcilvltvfiryln*kkyiylyiiyffy*si
y*s*pi*hfcffyyyyyyyyflflffylyi*KFHLFNLFICRLCDFRQLTMVEINKIKFL
IKKKXXX---

---xxxkexkexkexkekr*kfq**r***********sk**rkx*kekr*i*r*r*k**d
nsklkwsxrktqkl***wwsc**xxkr**i*g*xsfr*kgcqsieiv

Frame C:
yylkl*nqiiqvv*ialisy*qyifii*livf*f*pflfvi*ikkniyiyi*fiffinlf
inlnlynifvffiiiiiiiifffyffiyifknfiysiylfvvcvifan*qwlkliklnf*
*kkxxx---

---XXXKKXKKXKKXKKKDKNSSSDDDDDDDDDNNDSRNDKEKXEKKKDKYKDKDKNNEI
IPNSNGHXEKPKNYNDNGGRVDDXXRDDRYRDXDHSDRRDASL*r*

own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U11937-1 (Contig-U11937-1Q)
/CSM_Contig/Contig-U11937-1Q.Seq.d
(705 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U11937-1 (Contig-U11937-1Q) /CSM_Contig/Conti... 268 7e-72
Contig-U05015-1 (Contig-U05015-1Q) /CSM_Contig/Conti... 42 8e-04
Contig-U11745-1 (Contig-U11745-1Q) /CSM_Contig/Conti... 40 0.003
Contig-U10908-1 (Contig-U10908-1Q) /CSM_Contig/Conti... 40 0.003
Contig-U05408-1 (Contig-U05408-1Q) /CSM_Contig/Conti... 40 0.003
Contig-U08409-1 (Contig-U08409-1Q) /CSM_Contig/Conti... 38 0.013
Contig-U13006-1 (Contig-U13006-1Q) /CSM_Contig/Conti... 36 0.049
Contig-U11762-1 (Contig-U11762-1Q) /CSM_Contig/Conti... 36 0.049
Contig-U11746-1 (Contig-U11746-1Q) /CSM_Contig/Conti... 36 0.049
Contig-U11737-1 (Contig-U11737-1Q) /CSM_Contig/Conti... 36 0.049

>Contig-U11937-1 (Contig-U11937-1Q) /CSM_Contig/Contig-U11937-1Q.Seq.d
Length = 705

Score = 268 bits (135), Expect = 7e-72
Identities = 147/147 (100%)
Strand = Plus / Plus


Query: 559 tgagataattccaaactcaaatggtcacncagaaaaacccaaaaattataatgataatgg 618
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 559 tgagataattccaaactcaaatggtcacncagaaaaacccaaaaattataatgataatgg 618


Query: 619 tggtcgtgttgatgatgnangaagagatgatagatatagggatagngatcattccgatag 678
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 619 tggtcgtgttgatgatgnangaagagatgatagatatagggatagngatcattccgatag 678


Query: 679 aagggatgccagtctatagagatagtg 705
|||||||||||||||||||||||||||
Sbjct: 679 aagggatgccagtctatagagatagtg 705


Score = 260 bits (131), Expect = 2e-69
Identities = 131/131 (100%)
Strand = Plus / Plus


Query: 1 attactatttaaaactataaaatcaaattatacaagtagtataaattgctttaattagct 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 attactatttaaaactataaaatcaaattatacaagtagtataaattgctttaattagct 60


Query: 61 attagcaatatatttttatcatttaattgattgtattctagttttaaccgtttttattcg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 attagcaatatatttttatcatttaattgattgtattctagttttaaccgtttttattcg 120


Query: 121 ttatttaaatt 131
|||||||||||
Sbjct: 121 ttatttaaatt 131


Score = 87.7 bits (44), Expect = 2e-17
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 320 cgccaattgacaatggttgaaattaataaaattaaatttttaat 363
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 320 cgccaattgacaatggttgaaattaataaaattaaatttttaat 363


Score = 34.2 bits (17), Expect = 0.20
Identities = 17/17 (100%)
Strand = Plus / Plus


Query: 485 aataatgatagtcgaaa 501
|||||||||||||||||
Sbjct: 485 aataatgatagtcgaaa 501


>Contig-U05015-1 (Contig-U05015-1Q) /CSM_Contig/Contig-U05015-1Q.Seq.d
Length = 805

Score = 42.1 bits (21), Expect = 8e-04
Identities = 21/21 (100%)
Strand = Plus / Plus


Query: 339 aaattaataaaattaaatttt 359
|||||||||||||||||||||
Sbjct: 730 aaattaataaaattaaatttt 750


>Contig-U11745-1 (Contig-U11745-1Q) /CSM_Contig/Contig-U11745-1Q.Seq.d
Length = 1763

Score = 40.1 bits (20), Expect = 0.003
Identities = 20/20 (100%)
Strand = Plus / Minus


Query: 6 tatttaaaactataaaatca 25
||||||||||||||||||||
Sbjct: 184 tatttaaaactataaaatca 165


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: 8233
Number of Sequences: 6905
Number of extensions: 8233
Number of successful extensions: 1096
Number of sequences better than 10.0: 161
length of query: 705
length of database: 5,674,871
effective HSP length: 16
effective length of query: 689
effective length of database: 5,564,391
effective search space: 3833865399
effective search space used: 3833865399
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 2008.11.27
Homology vs DNA
Query= Contig-U11937-1 (Contig-U11937-1Q) /CSM_Contig/Contig-U11937-1Q.Seq.d
(705 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

(BJ370985) Dictyostelium discoideum cDNA clone:ddc56p01, 5' ... 218 4e-71 2
(BJ385806) Dictyostelium discoideum cDNA clone:ddc56p01, 3' ... 250 2e-62 2
(EJ006101) 1091138307032 Global-Ocean-Sampling_GS-26-01-01-1... 44 0.30 2
(EJ017597) 1095439020349 Global-Ocean-Sampling_GS-26-01-01-1... 44 0.34 2
(AC155650) Mus musculus 6 BAC RP24-151E20 (Roswell Park Canc... 48 0.45 1
(BD061520) Genome DNA of symbiotic bacteria of aphid. 48 0.45 1
(AR409405) Sequence 1 from patent US 6632935. 48 0.45 1
(BA000003) Buchnera aphidicola str. APS (Acyrthosiphon pisum... 48 0.45 1
(AC159281) Mus musculus BAC clone RP23-321H9 from chromosome... 46 1.8 1
(AC122462) Mus musculus BAC clone RP24-294G11 from 3, comple... 46 1.8 1
(AC217914) Solanum lycopersicum chromosome 1 clone C01HBa003... 46 1.8 1
(CT826384) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 1.8 1
(AC230324) Bos taurus clone CH240-512J24, WORKING DRAFT SEQU... 46 1.8 1
(AC175849) Strongylocentrotus purpuratus clone R3-15L14, WOR... 46 1.8 1
(BH430841) BOHFK08TR BOHF Brassica oleracea genomic clone BO... 46 1.8 1
(EJ717452) 1092959430043 Global-Ocean-Sampling_GS-30-02-01-1... 46 1.8 1
(EE146927) SiJWH08BBD2 Lausanne fire ant library Solenopsis ... 46 1.8 1
(CP000123) Mycoplasma capricolum subsp. capricolum ATCC 2734... 46 1.8 1
(BA000021) Wigglesworthia glossinidia endosymbiont of Glossi... 46 1.8 1
(DQ292702) Nascus paulliniae voucher 99-SRNP-15218 cytochrom... 40 2.8 2
(AC116920) Dictyostelium discoideum chromosome 2 map 4415041... 44 3.0 4
(AC188385) Callithrix jacchus BAC clone CH259-87H12 from chr... 42 3.1 2
(DQ292701) Nascus paulliniae voucher 95-SRNP-9964 cytochrome... 40 3.1 2
(DQ292712) Nascus paulliniae voucher 04-SRNP-14706 cytochrom... 40 3.3 2
(DQ292711) Nascus paulliniae voucher 04-SRNP-34021 cytochrom... 40 3.3 2
(DQ292710) Nascus paulliniae voucher 04-SRNP-34682 cytochrom... 40 3.3 2
(DQ292709) Nascus paulliniae voucher 04-SRNP-14655 cytochrom... 40 3.3 2
(DQ292708) Nascus paulliniae voucher 04-SRNP-55249 cytochrom... 40 3.3 2
(DQ292707) Nascus paulliniae voucher 04-SRNP-55654 cytochrom... 40 3.3 2
(DQ292706) Nascus paulliniae voucher 04-SRNP-55794 cytochrom... 40 3.3 2
(DQ292705) Nascus paulliniae voucher 04-SRNP-55367 cytochrom... 40 3.3 2
(DQ292704) Nascus paulliniae voucher 04-SRNP-55964 cytochrom... 40 3.3 2
(DQ292703) Nascus paulliniae voucher 02-SRNP-6701 cytochrome... 40 3.3 2
(AC023825) Homo sapiens chromosome 16 clone RP11-322D14, com... 32 3.4 2
(AC020769) Homo sapiens clone RP11-11M3, WORKING DRAFT SEQUE... 32 3.4 2
(AC178935) Strongylocentrotus purpuratus clone R3-3115P14, W... 34 3.5 2
(AC203539) Glycine tomentella clone gtd1-128d9, WORKING DRAF... 36 4.3 4
(EK516147) 1095515499728 Global-Ocean-Sampling_GS-32-01-01-1... 40 4.4 2
(EK501284) 1095505214798 Global-Ocean-Sampling_GS-32-01-01-1... 40 4.5 2
(BH700402) BOHZW19TF BO_2_3_KB Brassica oleracea genomic clo... 34 4.6 2
(BH944445) obu89f02.g1 B.oleracea002 Brassica oleracea genom... 34 4.6 2
(DQ338584) Magneuptychia n. sp. 4 CP-2006 cytochrome c oxida... 40 6.8 2
(CT573050) Zebrafish DNA sequence from clone CH211-81A6 in l... 44 7.0 1
(AC162900) Mus musculus BAC clone RP23-416N10 from chromosom... 44 7.0 1
(AC101778) Mus musculus chromosome 1, clone RP24-125B8, comp... 44 7.0 1
(AC198188) MACACA MULATTA BAC clone CH250-392N11 from chromo... 44 7.0 1
(AC149044) Pan troglodytes chromosome X clone PTB-089E19 map... 44 7.0 1
(AP009393) Solanum lycopersicum genomic DNA, chromosome 8, c... 44 7.0 1
(AP009297) Solanum lycopersicum genomic DNA, chromosome 8, c... 44 7.0 1
(AP007151) Aspergillus oryzae RIB40 genomic DNA, SC005. 44 7.0 1
(AP006374) Lotus japonicus genomic DNA, chromosome 5, clone:... 44 7.0 1
(AM488737) Vitis vinifera contig VV78X107684.13, whole genom... 44 7.0 1
(EA062083) Sequence 36 from patent US 7169970. 44 7.0 1
(EA062079) Sequence 32 from patent US 7169970. 44 7.0 1
(DD058661) HERBICIDE RESISTANT PLANTS. 44 7.0 1
(DD058657) HERBICIDE RESISTANT PLANTS. 44 7.0 1
(AX405122) Sequence 36 from Patent WO0226995. 44 7.0 1
(AX405118) Sequence 32 from Patent WO0226995. 44 7.0 1
(AL139353) Human chromosome 14 DNA sequence BAC R-176H8 of l... 44 7.0 1
(AL137016) Human DNA sequence from clone RP4-595A18 on chrom... 44 7.0 1
(AL136418) Human chromosome 14 DNA sequence BAC R-596D21 of ... 44 7.0 1
(AC131420) Rattus norvegicus clone CH230-97B20, WORKING DRAF... 44 7.0 1
(AC126871) Rattus norvegicus clone CH230-40L18, WORKING DRAF... 44 7.0 1
(AC122964) Rattus norvegicus clone CH230-33K9, *** SEQUENCIN... 44 7.0 1
(AC118142) Rattus norvegicus clone CH230-344H15, *** SEQUENC... 44 7.0 1
(AC115245) Rattus norvegicus clone CH230-257P8, *** SEQUENCI... 44 7.0 1
(AC106986) Rattus norvegicus clone CH230-221F4, *** SEQUENCI... 44 7.0 1
(AC098751) Rattus norvegicus clone CH230-27K19, *** SEQUENCI... 44 7.0 1
(AC093945) Rattus norvegicus clone CH230-143O3, WORKING DRAF... 44 7.0 1
(AC092847) Homo sapiens chromosome UNK clone RP11-657C9, WOR... 44 7.0 1
(AP008116) Lotus japonicus genomic DNA, chromosome 1, clone:... 44 7.0 1
(AL139054) Human chromosome 14 DNA sequence *** IN PROGRESS ... 44 7.0 1
(AC203479) Microcebus murinus clone CH257-13H6, WORKING DRAF... 44 7.0 1
(AC203111) Microcebus murinus clone CH257-396B7, WORKING DRA... 44 7.0 1
(AC201461) Strongylocentrotus purpuratus clone R3-3040D21, W... 44 7.0 1
(AC184637) Strongylocentrotus purpuratus clone R3-1005M13, W... 44 7.0 1
(ET994648) CHO_OF260xn03f2.ab1 CHO_OF Nicotiana tabacum geno... 44 7.0 1
(ET966107) CHO_OF424xd20f1.ab1 CHO_OF Nicotiana tabacum geno... 44 7.0 1
(EK356822) 1095468598868 Global-Ocean-Sampling_GS-31-01-01-1... 44 7.0 1
(EK125454) 1092976900333 Global-Ocean-Sampling_GS-31-01-01-1... 44 7.0 1
(EJ990105) 1093023042263 Global-Ocean-Sampling_GS-30-02-01-1... 44 7.0 1
(EJ835585) 1093017626353 Global-Ocean-Sampling_GS-30-02-01-1... 44 7.0 1
(EJ449440) 1093015402051 Global-Ocean-Sampling_GS-28-01-01-1... 44 7.0 1
(EJ272134) 1095353021984 Global-Ocean-Sampling_GS-27-01-01-1... 44 7.0 1
(EJ086432) 1095460109858 Global-Ocean-Sampling_GS-26-01-01-1... 44 7.0 1
(ED778934) GM_WBb0157C09.r GM_WBb Glycine max genomic clone ... 44 7.0 1
(ED477693) AUAC-aaf36f09.g1 Ascaris suum whole genome shotgu... 44 7.0 1
(ED263672) AUAC-aae12d06.g1 Ascaris suum whole genome shotgu... 44 7.0 1
(AG970837) Drosophila simulans DNA, clone: DSM1-009J15.R.fa,... 44 7.0 1
(AG970768) Drosophila simulans DNA, clone: DSM1-009H16.R.fa,... 44 7.0 1
(DE864251) Macropus eugenii DNA, BAC clone: MEB1-031O15_R, 3... 44 7.0 1
(CZ540183) SRAA-aad30c01.b1 Strongyloides ratti whole genome... 44 7.0 1
(AG626326) Macaca fuscata fuscata DNA, clone: MSB2-022N09_R,... 44 7.0 1
(CL141799) ISB1-119G10_T7.1 ISB1 Xenopus (Silurana) tropical... 44 7.0 1
(EB379170) nbc45e10.y1 Rabbit trigeminal nerve. Unnormalized... 44 7.0 1
(DW347762) PP_LEc0023O02f Peach shoot Prunus persica cDNA cl... 44 7.0 1
(DW347532) PP_LEc0022B13f Peach shoot Prunus persica cDNA cl... 44 7.0 1
(BJ061762) Xenopus laevis cDNA clone:XL073p14, 5' end, singl... 44 7.0 1
(BG726324) sae08h02.y1 Gm-c1055 Glycine max cDNA clone GENOM... 44 7.0 1
(AW158713) za45d03.x1 Xenopus EST library Xenopus laevis cDN... 44 7.0 1

>(BJ370985) Dictyostelium discoideum cDNA clone:ddc56p01, 5' end,
single read.
Length = 373

Score = 218 bits (110), Expect(2) = 4e-71
Identities = 110/110 (100%)
Strand = Plus / Plus


Query: 1 attactatttaaaactataaaatcaaattatacaagtagtataaattgctttaattagct 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 attactatttaaaactataaaatcaaattatacaagtagtataaattgctttaattagct 60


Query: 61 attagcaatatatttttatcatttaattgattgtattctagttttaaccg 110
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 attagcaatatatttttatcatttaattgattgtattctagttttaaccg 110

Score = 87.7 bits (44), Expect(2) = 4e-71
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 320 cgccaattgacaatggttgaaattaataaaattaaatttttaat 363
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 320 cgccaattgacaatggttgaaattaataaaattaaatttttaat 363

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 368,475,093
Number of extensions: 26492874
Number of successful extensions: 2630878
Number of sequences better than 10.0: 105
Length of query: 705
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 681
Effective length of database: 97,308,875,965
Effective search space: 66267344532165
Effective search space used: 66267344532165
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)

protein update 2009. 7. 1
Homology vs Protein
Query= Contig-U11937-1 (Contig-U11937-1Q) /CSM_Contig/Contig-U11937-1Q.Seq.d
(705 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: 357,953,964
Number of extensions: 5510051
Number of successful extensions: 3247
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3246
Number of HSP's successfully gapped: 0
Length of query: 235
Length of database: 1,051,180,864
Length adjustment: 125
Effective length of query: 110
Effective length of database: 646,610,989
Effective search space: 71127208790
Effective search space used: 71127208790
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: 31 (16.5 bits)

PSORT

psg: 0.62 gvh: 0.39 alm: 0.45 top: 0.53 tms: 0.00 mit: 0.27 mip: 0.03
nuc: 0.27 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

68.0 %: nuclear
20.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: vesicles of secretory system

>> prediction for Contig-U11937-1 is nuc

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