Contig-U06320-1
Contig ID Contig-U06320-1
Contig update 2001. 8.30
Contig sequence
>Contig-U06320-1 (Contig-U06320-1Q) /CSM_Contig/Contig-U06320-1Q.Seq.d
ACACCAATTATAACATCTGGTGGCTCAACCCCAGTATGTAATGACTTTTT
TAAAATTATAGTGGACGAGATTGAAAATGATAAAATTCGAACTCAAGTAT
TTTTACTTAAAAGAATCAATGATTACTCTCCACCTATAGTTTGTAAGTAT
GGTAAGAAAATGGCAGTACAAATGAAACATATACCACCTCCACCTATTCA
AATTCCAACATTTAGTGAAAGTAGTTTAAAAGATCTCTAAAAAAAAATAA
AAATAAAAATAAAAATAAAATAAAA

Gap no gap
Contig length 275
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 3533703
End point 3533978
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U06320
List of clone(s)

est1=VSA841Z,1,276
Translated Amino Acid sequence
TPIITSGGSTPVCNDFFKIIVDEIENDKIRTQVFLLKRINDYSPPIVCKYGKKMAVQMKH
IPPPPIQIPTFSESSLKDL*kkikikikik*


Translated Amino Acid sequence (All Frames)
Frame A:
TPIITSGGSTPVCNDFFKIIVDEIENDKIRTQVFLLKRINDYSPPIVCKYGKKMAVQMKH
IPPPPIQIPTFSESSLKDL*kkikikikik*


Frame B:
hql*hlvaqpqyvmtflkl*wtrlkmikfelkyfylkesmitlhl*fvsmvrkwqyk*ni
yhlhlfkfqhlvkvv*kiskkk*k*k*k*nk


Frame C:
tnyniwwlnpsm**lf*nysgrd*k**nsnssift*knq*llstysl*vw*engstnety
ttstysnsni**k*fkrslkknknknknkik


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U06320-1 (Contig-U06320-1Q)
/CSM_Contig/Contig-U06320-1Q.Seq.d
(275 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U06320-1 (Contig-U06320-1Q) /CSM_Contig/Conti... 470 e-133
Contig-U00078-1 (Contig-U00078-1Q) /CSM_Contig/Conti... 36 0.019
Contig-U12128-1 (Contig-U12128-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U11471-1 (Contig-U11471-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U05178-1 (Contig-U05178-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U04421-1 (Contig-U04421-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U04166-1 (Contig-U04166-1Q) /CSM_Contig/Conti... 34 0.074
Contig-U11424-1 (Contig-U11424-1Q) /CSM_Contig/Conti... 32 0.29
Contig-U10885-1 (Contig-U10885-1Q) /CSM_Contig/Conti... 32 0.29
Contig-U10414-1 (Contig-U10414-1Q) /CSM_Contig/Conti... 32 0.29

>Contig-U06320-1 (Contig-U06320-1Q) /CSM_Contig/Contig-U06320-1Q.Seq.d
Length = 275

Score = 470 bits (237), Expect = e-133
Identities = 237/237 (100%)
Strand = Plus / Plus


Query: 1 acaccaattataacatctggtggctcaaccccagtatgtaatgacttttttaaaattata 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 acaccaattataacatctggtggctcaaccccagtatgtaatgacttttttaaaattata 60


Query: 61 gtggacgagattgaaaatgataaaattcgaactcaagtatttttacttaaaagaatcaat 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 gtggacgagattgaaaatgataaaattcgaactcaagtatttttacttaaaagaatcaat 120


Query: 121 gattactctccacctatagtttgtaagtatggtaagaaaatggcagtacaaatgaaacat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 gattactctccacctatagtttgtaagtatggtaagaaaatggcagtacaaatgaaacat 180


Query: 181 ataccacctccacctattcaaattccaacatttagtgaaagtagtttaaaagatctc 237
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ataccacctccacctattcaaattccaacatttagtgaaagtagtttaaaagatctc 237


>Contig-U00078-1 (Contig-U00078-1Q) /CSM_Contig/Contig-U00078-1Q.Seq.d
Length = 1340

Score = 36.2 bits (18), Expect = 0.019
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 67 gagattgaaaatgataaa 84
||||||||||||||||||
Sbjct: 568 gagattgaaaatgataaa 585


>Contig-U12128-1 (Contig-U12128-1Q) /CSM_Contig/Contig-U12128-1Q.Seq.d
Length = 2238

Score = 34.2 bits (17), Expect = 0.074
Identities = 17/17 (100%)
Strand = Plus / Minus


Query: 182 taccacctccacctatt 198
|||||||||||||||||
Sbjct: 1245 taccacctccacctatt 1229


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: 3952
Number of Sequences: 6905
Number of extensions: 3952
Number of successful extensions: 1454
Number of sequences better than 10.0: 166
length of query: 275
length of database: 5,674,871
effective HSP length: 15
effective length of query: 260
effective length of database: 5,571,296
effective search space: 1448536960
effective search space used: 1448536960
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 2008.11. 8
Homology vs DNA
Query= Contig-U06320-1 (Contig-U06320-1Q) /CSM_Contig/Contig-U06320-1Q.Seq.d
(275 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

(AC116984) Dictyostelium discoideum chromosome 2 map 2567470... 472 e-129 1
(AU261777) Dictyostelium discoideum vegetative cDNA clone:VS... 472 e-129 1
(AC175880) Strongylocentrotus purpuratus clone R3-3043D14, W... 48 0.16 1
(AC113411) Homo sapiens chromosome 5 clone RP11-488H7, WORKI... 34 0.59 7
(BH984474) ode76a02.b1 B.oleracea002 Brassica oleracea genom... 34 1.9 2
(BX901878) Zebrafish DNA sequence from clone DKEY-11O15 in l... 44 2.5 1
(AL928642) Mouse DNA sequence from clone RP24-191C1 on chrom... 44 2.5 1
(CU407247) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 2.5 1
(CR388375) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 44 2.5 1
(AC164148) Bos taurus clone CH240-137G24, *** SEQUENCING IN ... 44 2.5 1
(DV409097) NADZ896TR Aedes aegypti infected with Dengue viru... 44 2.5 1
(DV409095) NADZ896TF Aedes aegypti infected with Dengue viru... 44 2.5 1
(DV385899) NADC836TR Aedes aegypti infected with Dengue viru... 44 2.5 1
(DV385897) NADC836TF Aedes aegypti infected with Dengue viru... 44 2.5 1
(DV362033) NACAH51TF Aedes aegypti infected with Brugia Mala... 44 2.5 1
(EY342342) CAWZ11816.fwd CAWZ Helobdella robusta Primary Lat... 44 2.5 1
(CU498980) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 36 3.6 2
(BX005112) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 38 3.7 4
(EU500869) Cucumis sativus clone CS_SBa_056C11, *** SEQUENCI... 38 4.1 2
(AC019267) Homo sapiens clone RP11-7M4, WORKING DRAFT SEQUEN... 32 4.7 5
(AC096563) Homo sapiens BAC clone RP11-277J14 from 4, comple... 30 4.8 2
(AL139145) Human DNA sequence from clone RP4-579A20 on chrom... 40 5.9 3
(B57321) CIT-HSP-2009E13.TF CIT-HSP Homo sapiens genomic clo... 30 6.4 2
(AQ224005) HS_2009_A1_C07_T7 CIT Approved Human Genomic Sper... 30 6.5 2
(EK207235) 1095460079287 Global-Ocean-Sampling_GS-31-01-01-1... 34 8.7 2
(CU463284) Zebrafish DNA sequence from clone CH73-331H18 in ... 38 9.1 3
(CT573285) Zebrafish DNA sequence from clone CH211-107M4 in ... 42 9.8 1
(CT025588) Zebrafish DNA sequence from clone DKEY-29B11 in l... 42 9.8 1
(CR382377) Zebrafish DNA sequence from clone DKEY-238I13 in ... 42 9.8 1
(G96573) S208P6479RC6.T0 129S1/SvImJ Mus musculus STS genomi... 42 9.8 1
(AC159964) Mus musculus chromosome 1, clone RP24-321N12, com... 42 9.8 1
(AC159308) Mus musculus BAC clone RP23-187B11 from chromosom... 42 9.8 1
(AC132918) Mus musculus chromosome 15, clone RP24-328F10, co... 42 9.8 1
(AC120391) Mus musculus chromosome 1, clone RP24-310B3, comp... 42 9.8 1
(AC170989) Medicago truncatula chromosome 7 BAC clone mth2-7... 42 9.8 1
(AC089987) Homo sapiens 12q BAC RP11-722P11 (Roswell Park Ca... 42 9.8 1
(AC079951) Homo sapiens 12q BAC RP11-346L11 (Roswell Park Ca... 42 9.8 1
(AC136055) Rattus norvegicus clone CH230-123L10, WORKING DRA... 42 9.8 1
(AC111478) Rattus norvegicus clone CH230-85N15, WORKING DRAF... 42 9.8 1
(CU928712) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(CU856484) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(CU639463) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(CU633815) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(CU633481) Zebrafish DNA sequence *** SEQUENCING CANCELLED *... 42 9.8 1
(AC091418) Rattus norvegicus clone CH230-2G6, *** SEQUENCING... 42 9.8 1
(AC091385) Rattus norvegicus clone CH230-2C13, WORKING DRAFT... 42 9.8 1
(CU469177) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(CU468495) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 9.8 1
(AC170585) Mus musculus chromosome 1 clone RP23-86M15 map 1,... 42 9.8 1
(AC170170) Mus musculus chromosome 1 clone RP24-399P6 map 1,... 42 9.8 1
(AK036848) Mus musculus adult female vagina cDNA, RIKEN full... 42 9.8 1
(AZ811131) 2M0077E11F Mouse 10kb plasmid UUGC1M library Mus ... 42 9.8 1
(AL736930) Danio rerio genomic clone DKEY-19P14, genomic sur... 42 9.8 1
(EI210944) MUGQ_CH252P204I21Sp6_CN322_087 CHORI-252 Vervet M... 42 9.8 1
(ED436908) AUAC-aaq24h03.b1 Ascaris suum whole genome shotgu... 42 9.8 1
(ED162611) AUAC-aax35d11.g1 Ascaris suum whole genome shotgu... 42 9.8 1
(CC775456) CH240_129N7.TJ CHORI-240 Bos taurus genomic clone... 42 9.8 1
(AG130344) Pan troglodytes DNA, clone: PTB-142B08.R. 42 9.8 1
(BB629864) Mus musculus adult female vagina cDNA, RIKEN full... 42 9.8 1

>(AC116984) Dictyostelium discoideum chromosome 2 map 2567470-3108875
strain AX4, complete sequence.
Length = 541399

Score = 472 bits (238), Expect = e-129
Identities = 238/238 (100%)
Strand = Plus / Minus


Query: 1 acaccaattataacatctggtggctcaaccccagtatgtaatgacttttttaaaattata 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212730 acaccaattataacatctggtggctcaaccccagtatgtaatgacttttttaaaattata 212671


Query: 61 gtggacgagattgaaaatgataaaattcgaactcaagtatttttacttaaaagaatcaat 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212670 gtggacgagattgaaaatgataaaattcgaactcaagtatttttacttaaaagaatcaat 212611


Query: 121 gattactctccacctatagtttgtaagtatggtaagaaaatggcagtacaaatgaaacat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212610 gattactctccacctatagtttgtaagtatggtaagaaaatggcagtacaaatgaaacat 212551


Query: 181 ataccacctccacctattcaaattccaacatttagtgaaagtagtttaaaagatctct 238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212550 ataccacctccacctattcaaattccaacatttagtgaaagtagtttaaaagatctct 212493

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 314,404,448
Number of extensions: 19762218
Number of successful extensions: 1614398
Number of sequences better than 10.0: 59
Length of query: 275
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 252
Effective length of database: 93,106,754,628
Effective search space: 23462902166256
Effective search space used: 23462902166256
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.21
Homology vs Protein
Query= Contig-U06320-1 (Contig-U06320-1Q) /CSM_Contig/Contig-U06320-1Q.Seq.d
(275 letters)

Database: nrp_A
3,204,285 sequences; 1,040,966,779 total letters

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

Score E
Sequences producing significant alignments: (bits) Value

CP000975_1427(CP000975|pid:none) Methylacidiphilum infernorum V4... 36 0.49
AC139356_12(AC139356|pid:none) Medicago truncatula clone mth2-12... 32 5.4
EU727216_1(EU727216|pid:none) Lotus tenuis cation-chloride cotra... 32 7.0
CR522871_76(CR522871|pid:none) Desulfotalea psychrophila LSv54, ... 32 9.2

>CP000975_1427(CP000975|pid:none) Methylacidiphilum infernorum V4,
complete genome.
Length = 321

Score = 35.8 bits (81), Expect = 0.49
Identities = 11/34 (32%), Positives = 22/34 (64%)
Frame = -3

Query: 219 FTKCWNLNRWRWYMFHLYCHFLTILTNYRWRVII 118
F+ C LN W ++ +C F T+L++ RW++++
Sbjct: 27 FSYCQTLNPWMLFLSFFFCAFQTLLSSLRWKILL 60

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: 381,131,405
Number of extensions: 6689439
Number of successful extensions: 15229
Number of sequences better than 10.0: 4
Number of HSP's gapped: 15228
Number of HSP's successfully gapped: 4
Length of query: 91
Length of database: 1,040,966,779
Length adjustment: 60
Effective length of query: 31
Effective length of database: 848,709,679
Effective search space: 26310000049
Effective search space used: 26310000049
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: 0.88 gvh: 0.31 alm: 0.52 top: 0.27 tms: 0.00 mit: 0.17 mip: 0.00
nuc: 0.06 erl: 0.00 erm: 0.20 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

36.0 %: cytoplasmic
36.0 %: nuclear
12.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: vacuolar
4.0 %: vesicles of secretory system
4.0 %: endoplasmic reticulum

>> prediction for Contig-U06320-1 is cyt

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