Contig-U10505-1
Contig ID Contig-U10505-1
Contig update 2002. 9.13
Contig sequence
>Contig-U10505-1 (Contig-U10505-1Q) /CSM_Contig/Contig-U10505-1Q.Seq.d
ATTTTCATTTTCAATCAATAACTTTTTTCTTCGTTTTATCATCATAACCC
CACTCCTCAAATATTCTTTTAATTTTAAAAGAAATCATATATAGAAGGAT
AAAAAAAAAANNNNNNNNN

Gap no gap
Contig length 119
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 820951
End point 820871
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U10505
List of clone(s)

est1=VFM812F,1,110
Translated Amino Acid sequence
FSFSINNFFLRFIIITPLLKYSFNFKRNHI*kdkkkxxx


Translated Amino Acid sequence (All Frames)
Frame A:
ififnq*lfssfyhhnptpqiff*f*kksyieg*kkxxx


Frame B:
FSFSINNFFLRFIIITPLLKYSFNFKRNHI*kdkkkxxx


Frame C:
fhfqsitfffvlss*phssnillilkeiiyrrikkkxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U10505-1 (Contig-U10505-1Q)
/CSM_Contig/Contig-U10505-1Q.Seq.d
(119 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U10505-1 (Contig-U10505-1Q) /CSM_Contig/Conti... 198 9e-52
Contig-U12720-1 (Contig-U12720-1Q) /CSM_Contig/Conti... 38 0.002
Contig-U12044-1 (Contig-U12044-1Q) /CSM_Contig/Conti... 36 0.008
Contig-U02377-1 (Contig-U02377-1Q) /CSM_Contig/Conti... 34 0.030
Contig-U01601-1 (Contig-U01601-1Q) /CSM_Contig/Conti... 34 0.030
Contig-U14745-1 (Contig-U14745-1Q) /CSM_Contig/Conti... 32 0.12
Contig-U13986-1 (Contig-U13986-1Q) /CSM_Contig/Conti... 32 0.12
Contig-U13876-1 (Contig-U13876-1Q) /CSM_Contig/Conti... 32 0.12
Contig-U13856-1 (Contig-U13856-1Q) /CSM_Contig/Conti... 32 0.12

>Contig-U10505-1 (Contig-U10505-1Q) /CSM_Contig/Contig-U10505-1Q.Seq.d
Length = 119

Score = 198 bits (100), Expect = 9e-52
Identities = 100/100 (100%)
Strand = Plus / Plus


Query: 1 attttcattttcaatcaataacttttttcttcgttttatcatcataaccccactcctcaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 attttcattttcaatcaataacttttttcttcgttttatcatcataaccccactcctcaa 60


Query: 61 atattcttttaattttaaaagaaatcatatatagaaggat 100
||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 atattcttttaattttaaaagaaatcatatatagaaggat 100


>Contig-U12720-1 (Contig-U12720-1Q) /CSM_Contig/Contig-U12720-1Q.Seq.d
Length = 507

Score = 38.2 bits (19), Expect = 0.002
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 62 tattcttttaattttaaaa 80
|||||||||||||||||||
Sbjct: 480 tattcttttaattttaaaa 498


>Contig-U12044-1 (Contig-U12044-1Q) /CSM_Contig/Contig-U12044-1Q.Seq.d
Length = 825

Score = 36.2 bits (18), Expect = 0.008
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 64 ttcttttaattttaaaag 81
||||||||||||||||||
Sbjct: 213 ttcttttaattttaaaag 196


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: 3729
Number of Sequences: 6905
Number of extensions: 3729
Number of successful extensions: 1454
Number of sequences better than 10.0: 461
length of query: 119
length of database: 5,674,871
effective HSP length: 14
effective length of query: 105
effective length of database: 5,578,201
effective search space: 585711105
effective search space used: 585711105
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.11.20
Homology vs DNA
Query= Contig-U10505-1 (Contig-U10505-1Q) /CSM_Contig/Contig-U10505-1Q.Seq.d
(119 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

(BJ416650) Dictyostelium discoideum cDNA clone:ddv26h04, 5' ... 198 3e-47 1
(AW639555) bl84d02.w1 Blackshear/Soares normalized Xenopus e... 50 0.015 1
(EJ144502) 1092343681470 Global-Ocean-Sampling_GS-27-01-01-1... 48 0.061 1
(CJ452196) Macaca fascicularis mRNA, clone: QflA-17842, 5' e... 42 0.088 2
(CU469200) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 34 0.092 4
(AC169964) Bos taurus clone CH240-220O15, WORKING DRAFT SEQU... 38 0.14 4
(AC172259) Bos taurus clone CH240-510G23, WORKING DRAFT SEQU... 34 0.14 2
(AM437317) Vitis vinifera contig VV78X122307.2, whole genome... 36 0.20 3
(AE014833) Plasmodium falciparum 3D7 chromosome 10 section 5... 46 0.24 1
(AC117161) Rattus norvegicus clone CH230-306P15, *** SEQUENC... 46 0.24 1
(AC111543) Rattus norvegicus clone CH230-160P18, *** SEQUENC... 46 0.24 1
(AC106439) Rattus norvegicus clone CH230-193N22, WORKING DRA... 46 0.24 1
(AC232106) Solanum tuberosum strain Diploid genotype RH89-03... 46 0.24 1
(DH816918) Rattus norvegicus DNA, BAC clone: RNB1-419E05, 3'... 46 0.24 1
(BQ452419) PfESToaa96d11.y1 Plasmodium falciparum 3D7 asexua... 46 0.24 1
(BJ344788) Dictyostelium discoideum cDNA clone:dda20b17, 3' ... 46 0.24 1
(DN785513) 92941369 Sea Urchin primary mesenchyme cell cDNA ... 38 0.43 2
(AP000967) Homo sapiens genomic DNA, chromosome 21q21.1-q21.... 38 0.47 3
(AM486925) Vitis vinifera contig VV78X030902.11, whole genom... 34 0.49 3
(DX561564) GH_MBb0073G03r GH_MBb Gossypium hirsutum genomic ... 34 0.67 2
(U80451) Caenorhabditis elegans cosmid F11G11, complete sequ... 38 0.77 2
(AC182890) Bos taurus clone CH240-526L24, WORKING DRAFT SEQU... 42 0.83 2
(AF200465) Homo sapiens coxsackievirus and adenovirus recept... 38 0.91 3
(BV373202) S231P6407RA7.T0 BedlingtonTerrier Canis familiari... 38 0.94 2
(BV518614) tbk44c12.b1 Clint Pan troglodytes verus STS genom... 44 0.96 1
(AC157322) Mus musculus chromosome 19, clone RP23-241E11, co... 44 0.96 1
(AC148006) Mus musculus BAC clone RP23-298P21 from chromosom... 44 0.96 1
(AC122848) Mus musculus BAC clone RP23-166K13 from chromosom... 44 0.96 1
(AC121935) Mus musculus BAC clone RP24-207G22 from chromosom... 44 0.96 1
(AM463961) Vitis vinifera, whole genome shotgun sequence, co... 44 0.96 1
(AF501611) Parietaria pensylvanica chloroplast trnL gene, pa... 44 0.96 1
(CQ329031) Sequence 3125 from Patent WO0157275. 44 0.96 1
(CQ291984) Sequence 3089 from Patent WO0186003. 44 0.96 1
(CQ254901) Sequence 3162 from Patent WO0157277. 44 0.96 1
(CQ216334) Sequence 3173 from Patent WO0157273. 44 0.96 1
(CQ200828) Sequence 3105 from Patent WO0157271. 44 0.96 1
(CQ171693) Sequence 3089 from Patent WO0157274. 44 0.96 1
(CQ133123) Sequence 3145 from Patent WO0157276. 44 0.96 1
(CQ094339) Sequence 3198 from Patent WO0157272. 44 0.96 1
(CQ067292) Sequence 3092 from Patent WO0157278. 44 0.96 1
(CQ052235) Sequence 3055 from Patent WO0157270. 44 0.96 1
(AC011451) Homo sapiens chromosome 19 clone CTC-325H20, comp... 44 0.96 1
(AC115167) Rattus norvegicus clone CH230-160B10, *** SEQUENC... 44 0.96 1
(AC100196) Mus musculus clone RP23-58A22, LOW-PASS SEQUENCE ... 44 0.96 1
(AC231459) Choloepus hoffmanni clone CH281-136C10, WORKING D... 44 0.96 1
(AC192209) Pan troglodytes chromosome 19 clone CH251-16L14, ... 44 0.96 1
(AC191960) Glyptapanteles indiensis clone 18I8 and 20D14, **... 44 0.96 1
(BH557967) BOGOM22TR BOGO Brassica oleracea genomic clone BO... 44 0.96 1
(BH547674) BOGRN50TR BOGR Brassica oleracea genomic clone BO... 44 0.96 1
(AQ588673) CITBI-E1-2643E16.TF CITBI-E1 Homo sapiens genomic... 44 0.96 1
(EJ763712) 1092963160368 Global-Ocean-Sampling_GS-30-02-01-1... 44 0.96 1
(EJ750643) 1092963032309 Global-Ocean-Sampling_GS-30-02-01-1... 44 0.96 1
(EJ143199) 1092343668750 Global-Ocean-Sampling_GS-27-01-01-1... 44 0.96 1
(CR148437) Reverse strand read from insert in 5'HPRT inserti... 44 0.96 1
(CR060011) Reverse strand read from insert in 5'HPRT inserti... 44 0.96 1
(AM478890) Vitis vinifera contig VV78X072460.8, whole genome... 34 1.2 3
(DQ983239) Vaccinia virus strain AGR-MVA-572pre genomic sequ... 42 1.2 4
(DQ983238) Vaccinia virus strain MVA-BN genomic sequence. 42 1.2 4
(DQ983237) Vaccinia virus strain MVA-572 genomic sequence. 42 1.2 4
(DQ983236) Vaccinia virus strain MVA-I721 genomic sequence. 42 1.2 4
(EF675191) Vaccinia virus strain MVATGN33.1 Modified Virus A... 42 1.2 4
(AY603355) Vaccinia virus strain Acambis 3000 Modified Virus... 42 1.2 4
(AC219527) Bos taurus clone CH240-331E7, WORKING DRAFT SEQUE... 38 1.2 3
(U94848) Vaccinia virus strain Ankara, complete genomic sequ... 42 1.4 4
(EU637017) Adineta vaga glycoprotein gene, partial cds; and ... 34 1.4 4
(AC104350) Homo sapiens chromosome 8, clone RP11-1112C15, co... 36 1.5 5
(AX344555) Sequence 6 from Patent WO0200932. 36 1.7 7
(CZ954667) 268320 Tomato EcoRI BAC Library Solanum lycopersi... 34 1.7 2
(AY678276) Vaccinia virus strain Lister, complete genome. 42 1.7 4
(AY678277) Vaccinia virus strain LC16mO, complete genome. 42 1.7 4
(AY678275) Vaccinia virus strain LC16m8, complete genome. 42 1.7 4
(AF095689) Vaccinia virus (strain Tian Tan) complete genome. 42 1.7 4
(DQ121394) Vaccinia virus strain Lister clone VACV107, compl... 42 1.7 4
(M35027) Vaccinia virus Copenhagen, complete genome. 42 1.7 4
(AM501482) Vaccinia virus complete viral coding region, stra... 42 1.7 4
(AC204137) Xenopus (Silurana) tropicalis clone ISB1-172G5, W... 36 1.8 2
(AY313848) Vaccinia virus strain Acambis clone 3, complete g... 42 1.9 4
(DJ328696) Microorganisms for Therapy. 42 1.9 3
(DD464435) Microorganisms for Therapy. 42 1.9 3
(CS106434) Sequence 34 from Patent WO2005047458. 42 1.9 3
(AC132553) Rattus norvegicus clone CH230-196F6, *** SEQUENCI... 34 1.9 2
(AP001533) Homo sapiens genomic DNA, chromosome 11q clone:RP... 32 1.9 2
(DQ377945) Vaccinia virus strain 3737, complete genome. 42 1.9 4
(DQ439815) Vaccinia virus strain DUKE, complete genome. 42 1.9 4
(AP001316) Homo sapiens genomic DNA, chromosome 11q22 clone:... 32 1.9 2
(AP001919) Homo sapiens genomic DNA, chromosome 11q clone:CT... 32 1.9 2
(AP000625) Homo sapiens genomic DNA, chromosome 11q22 clone:... 32 2.0 2
(AY525610) Homo sapiens progesterone receptor (PGR) gene, co... 32 2.0 2
(CS538693) Sequence 70 from Patent EP1772521. 32 2.0 2
(AY243312) Vaccinia virus WR, complete genome. 42 2.0 3
(AY484669) Rabbitpox virus, complete genome. 42 2.1 3
(AY313847) Vaccinia virus strain Acambis clone 2000, complet... 42 2.1 3
(EU275726) Polysphondylium pallidum strain PN500 mitochondri... 36 2.2 3
(DQ792504) Horsepox virus isolate MNR-76, complete genome. 42 2.2 4
(Z49816) H.sapiens partial gene for progesterone receptor an... 32 2.5 2
(DN915415) MCF7RNAL20B15TF Human MCF7 breast cancer cell lin... 32 2.6 2
(AY722926) Borrelia garinii PBi variable plasmid segment G1a... 36 2.7 2
(AC147428) Medicago truncatula clone mth2-34i10, complete se... 42 2.7 3
(AC139591) Rattus norvegicus clone CH230-19A23, WORKING DRAF... 42 2.9 2
(U80030) Caenorhabditis elegans cosmid K12D9, complete seque... 40 3.0 2

>(BJ416650) Dictyostelium discoideum cDNA clone:ddv26h04, 5' end,
single read.
Length = 110

Score = 198 bits (100), Expect = 3e-47
Identities = 100/100 (100%)
Strand = Plus / Plus


Query: 1 attttcattttcaatcaataacttttttcttcgttttatcatcataaccccactcctcaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 attttcattttcaatcaataacttttttcttcgttttatcatcataaccccactcctcaa 60


Query: 61 atattcttttaattttaaaagaaatcatatatagaaggat 100
||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 atattcttttaattttaaaagaaatcatatatagaaggat 100

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 193,202,062
Number of extensions: 14411645
Number of successful extensions: 4461124
Number of sequences better than 10.0: 248
Length of query: 119
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 97
Effective length of database: 93,199,600,587
Effective search space: 9040361256939
Effective search space used: 9040361256939
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)

protein update 2009. 6.28
Homology vs Protein
Query= Contig-U10505-1 (Contig-U10505-1Q) /CSM_Contig/Contig-U10505-1Q.Seq.d
(119 letters)

Database: nrp_A
3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 139,770,450
Number of extensions: 1888354
Number of successful extensions: 2460
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2460
Number of HSP's successfully gapped: 0
Length of query: 39
Length of database: 1,040,966,779
Length adjustment: 13
Effective length of query: 26
Effective length of database: 999,311,074
Effective search space: 25982087924
Effective search space used: 25982087924
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: 24 (13.9 bits)

PSORT

psg: 0.96 gvh: 0.30 alm: 0.36 top: 0.60 tms: 0.00 mit: 0.49 mip: 0.00
nuc: 0.00 erl: 0.00 erm: 0.20 pox: 0.30 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 %: mitochondrial
36.0 %: cytoplasmic
12.0 %: nuclear

>> prediction for Contig-U10505-1 is mit

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