Contig-U07096-1
Contig ID Contig-U07096-1
Contig update 2001. 8.30
Contig sequence
>Contig-U07096-1 (Contig-U07096-1Q) /CSM_Contig/Contig-U07096-1Q.Seq.d
CCACGCGTNCCGATATACAGAATGTTATCAATTAAAACTTGTAGATCAAT
TGTAAATTTATCAAGTAAACAAGCAAATCAACAACAATTTATTTGTGGAT
ATGCAGCAAAAGTTGTTAAAAGGGGCGGTAAAAAAGTAGTAGAAGAAGAG
GATACAGGTGTTGATCTTAGTGAAAAATATGATGTAAAAGTGTCAAAAGC
ATCTTACCAAAAGATTATACAACGTTTCCAAGTTTTATTTAAACGTCCAG
AATTTGCAGACAAAAATGAAAGTGATGAAGAGAAACGATTAAGATTAATT
AACTACAATTATACCGCATACAGTAACGAACTCAAACAAGAAAAAGAAAG
AGAAGAAAGAGAGAAATTAGATTATCAATGGGATGCAGTTATGGAATTAC
CAGAAGATCTCAGAAAAATCGCATTATTAATTGAAACAGATAAAGAAATG
CCATTAATTCCATTTTTATATGATACACCACCAACTAAAGGTGATCCAAA
GAAAACAATTCAATTAAAGAAAAAAGATAGAAATCTTAAACCATCTGAAA
GAACTTTCTTATCAAATTCACAAATTTAAAAATAGTAATAATAATAAAAA
TAATAAAAATAATAAAAATAAAATATTAATTATAA

Gap no gap
Contig length 635
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 1008749
End point 1008126
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U07096
List of clone(s)

est1=VSK328Z,1,636
est2=VSK328F,13,629
Translated Amino Acid sequence
PRVPIYRMLSIKTCRSIVNLSSKQANQQQFICGYAAKVVKRGGKKVVEEEDTGVDLSEKY
DVKVSKASYQKIIQRFQVLFKRPEFADKNESDEEKRLRLINYNYTAYSNELKQEKEREER
EKLDYQWDAVMELPEDLRKIALLIETDKEMPLIPFLYDTPPTKGDPKKTIQLKKKDRNLK
PSERTFLSNSQI*k*****k**k**k*niny


Translated Amino Acid sequence (All Frames)
Frame A:
PRVPIYRMLSIKTCRSIVNLSSKQANQQQFICGYAAKVVKRGGKKVVEEEDTGVDLSEKY
DVKVSKASYQKIIQRFQVLFKRPEFADKNESDEEKRLRLINYNYTAYSNELKQEKEREER
EKLDYQWDAVMELPEDLRKIALLIETDKEMPLIPFLYDTPPTKGDPKKTIQLKKKDRNLK
PSERTFLSNSQI*k*****k**k**k*niny


Frame B:
haxrytecyqlklvdql*iyqvnkqinnnlfvdmqqkllkgavkk**kkriqvlilvknm
m*kcqkhltkrlynvskfylnvqnlqtkmkvmkrnd*d*lttiiphtvtnsnkkkkekke
rn*iingmqlwnyqkisekshy*lkqikkch*fhfymihhqlkviqrkqfn*rkkieiln
hlkelsyqihkfknsnnnknnknnknkilii


Frame C:
trxdiqnvin*nl*inckfik*tsksttiylwicsksc*kgr*kssrrrgyrc*s**ki*
cksvksilpkdyttfpsfi*tsricrqk*k**retikin*lqlyriq*rtqtrkrkrrkr
eirlsmgcsygitrrsqknriin*nr*rnainsifi*yttn*r*skennsikekr*ks*t
i*knflikftnlkiviiikiikiikiky*l*


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U07096-1 (Contig-U07096-1Q)
/CSM_Contig/Contig-U07096-1Q.Seq.d
(635 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U07096-1 (Contig-U07096-1Q) /CSM_Contig/Conti... 662 0.0
Contig-U10146-1 (Contig-U10146-1Q) /CSM_Contig/Conti... 38 0.011
Contig-U02912-1 (Contig-U02912-1Q) /CSM_Contig/Conti... 38 0.011
Contig-U12615-1 (Contig-U12615-1Q) /CSM_Contig/Conti... 36 0.044
Contig-U12431-1 (Contig-U12431-1Q) /CSM_Contig/Conti... 36 0.044
Contig-U06919-1 (Contig-U06919-1Q) /CSM_Contig/Conti... 36 0.044
Contig-U04637-1 (Contig-U04637-1Q) /CSM_Contig/Conti... 36 0.044
Contig-U14349-1 (Contig-U14349-1Q) /CSM_Contig/Conti... 34 0.18
Contig-U14292-1 (Contig-U14292-1Q) /CSM_Contig/Conti... 34 0.18
Contig-U14129-1 (Contig-U14129-1Q) /CSM_Contig/Conti... 34 0.18

>Contig-U07096-1 (Contig-U07096-1Q) /CSM_Contig/Contig-U07096-1Q.Seq.d
Length = 635

Score = 662 bits (334), Expect = 0.0
Identities = 337/337 (100%)
Strand = Plus / Plus


Query: 1 ccacgcgtnccgatatacagaatgttatcaattaaaacttgtagatcaattgtaaattta 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ccacgcgtnccgatatacagaatgttatcaattaaaacttgtagatcaattgtaaattta 60


Query: 61 tcaagtaaacaagcaaatcaacaacaatttatttgtggatatgcagcaaaagttgttaaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tcaagtaaacaagcaaatcaacaacaatttatttgtggatatgcagcaaaagttgttaaa 120


Query: 121 aggggcggtaaaaaagtagtagaagaagaggatacaggtgttgatcttagtgaaaaatat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aggggcggtaaaaaagtagtagaagaagaggatacaggtgttgatcttagtgaaaaatat 180


Query: 181 gatgtaaaagtgtcaaaagcatcttaccaaaagattatacaacgtttccaagttttattt 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gatgtaaaagtgtcaaaagcatcttaccaaaagattatacaacgtttccaagttttattt 240


Query: 241 aaacgtccagaatttgcagacaaaaatgaaagtgatgaagagaaacgattaagattaatt 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aaacgtccagaatttgcagacaaaaatgaaagtgatgaagagaaacgattaagattaatt 300


Query: 301 aactacaattataccgcatacagtaacgaactcaaac 337
|||||||||||||||||||||||||||||||||||||
Sbjct: 301 aactacaattataccgcatacagtaacgaactcaaac 337


Score = 406 bits (205), Expect = e-113
Identities = 205/205 (100%)
Strand = Plus / Plus


Query: 367 ttagattatcaatgggatgcagttatggaattaccagaagatctcagaaaaatcgcatta 426
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 367 ttagattatcaatgggatgcagttatggaattaccagaagatctcagaaaaatcgcatta 426


Query: 427 ttaattgaaacagataaagaaatgccattaattccatttttatatgatacaccaccaact 486
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 427 ttaattgaaacagataaagaaatgccattaattccatttttatatgatacaccaccaact 486


Query: 487 aaaggtgatccaaagaaaacaattcaattaaagaaaaaagatagaaatcttaaaccatct 546
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 487 aaaggtgatccaaagaaaacaattcaattaaagaaaaaagatagaaatcttaaaccatct 546


Query: 547 gaaagaactttcttatcaaattcac 571
|||||||||||||||||||||||||
Sbjct: 547 gaaagaactttcttatcaaattcac 571


>Contig-U10146-1 (Contig-U10146-1Q) /CSM_Contig/Contig-U10146-1Q.Seq.d
Length = 1611

Score = 38.2 bits (19), Expect = 0.011
Identities = 19/19 (100%)
Strand = Plus / Minus


Query: 46 tcaattgtaaatttatcaa 64
|||||||||||||||||||
Sbjct: 1012 tcaattgtaaatttatcaa 994


>Contig-U02912-1 (Contig-U02912-1Q) /CSM_Contig/Contig-U02912-1Q.Seq.d
Length = 1341

Score = 38.2 bits (19), Expect = 0.011
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 204 ttaccaaaagattatacaa 222
|||||||||||||||||||
Sbjct: 1161 ttaccaaaagattatacaa 1179


Score = 30.2 bits (15), Expect = 2.7
Identities = 18/19 (94%)
Strand = Plus / Plus


Query: 456 aattccatttttatatgat 474
|||||||||||| ||||||
Sbjct: 734 aattccatttttctatgat 752


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: 9005
Number of Sequences: 6905
Number of extensions: 9005
Number of successful extensions: 1050
Number of sequences better than 10.0: 137
length of query: 635
length of database: 5,674,871
effective HSP length: 16
effective length of query: 619
effective length of database: 5,564,391
effective search space: 3444358029
effective search space used: 3444358029
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 2008.11.11
Homology vs DNA
Query= Contig-U07096-1 (Contig-U07096-1Q) /CSM_Contig/Contig-U07096-1Q.Seq.d
(635 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

(AU271010) Dictyostelium discoideum vegetative cDNA clone:VS... 662 0.0 2
(AU271009) Dictyostelium discoideum vegetative cDNA clone:VS... 644 0.0 2
(BX950856) Zebrafish DNA sequence from clone DKEY-205L20 in ... 50 0.098 1
(CU207303) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 36 0.22 2
(AC230427) Bos taurus clone CH240-509A3, WORKING DRAFT SEQUE... 48 0.39 1
(AC169259) Bos taurus clone CH240-248K24, WORKING DRAFT SEQU... 48 0.39 1
(EK279186) 1095462288961 Global-Ocean-Sampling_GS-31-01-01-1... 48 0.39 1
(AE009951) Fusobacterium nucleatum subsp. nucleatum ATCC 255... 38 0.46 19
(EX947016) lj67d05.g7 Gnetum gnemon leaf (NYBG) Gnetum gnemo... 36 1.1 2
(AC159978) Mus musculus chromosome 15, clone RP24-173F4, com... 46 1.5 1
(AC115878) Mus musculus chromosome 15, clone RP24-358G9, com... 46 1.5 1
(AM453081) Vitis vinifera, whole genome shotgun sequence, co... 46 1.5 1
(AL137118) Human DNA sequence from clone RP11-108P5 on chrom... 46 1.5 1
(ES864652) WS02790.CR.1_G18 SS-IL-A-FL-14 Picea sitchensis c... 46 1.5 1
(DR472948) WS00957.B21_K04 IS-B-N-A-10 Picea engelmannii x P... 46 1.5 1
(EX343038) GQ03013.SP6_P08 GQ030 - Xylem planings - daytime ... 46 1.5 1
(EX342679) GQ03013.B7_P08 GQ030 - Xylem planings - daytime a... 46 1.5 1
(AE013218) Buchnera aphidicola str. Sg (Schizaphis graminum)... 40 1.7 11
(AQ866277) nbeb0027J21r CUGI Rice BAC Library (EcoRI) Oryza ... 34 3.0 2
(CU467037) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 40 5.6 4
(CU571324) Zebrafish DNA sequence from clone CH73-223D24 in ... 44 6.0 1
(BX842692) Zebrafish DNA sequence from clone DKEY-71H2 in li... 44 6.0 1
(AC162379) Mus musculus BAC clone RP23-132A15 from chromosom... 44 6.0 1
(AC102105) Mus musculus chromosome 12, clone RP23-89G24, com... 44 6.0 1
(AC208953) MACACA MULATTA BAC clone CH250-133J8 from chromos... 44 6.0 1
(AM453813) Vitis vinifera, whole genome shotgun sequence, co... 44 6.0 1
(AF499727) Cucumis melo BAC clone PIT92-60K17, complete sequ... 44 6.0 1
(AC214628) Populus trichocarpa clone POP040-F15, complete se... 44 6.0 1
(AC152653) Bos taurus clone CH240-15I13, WORKING DRAFT SEQUE... 44 6.0 1
(BX032531) Single read from an extremity of a full-length cD... 44 6.0 1
(BH046248) RPCI-24-274I7.TV RPCI-24 Mus musculus genomic clo... 44 6.0 1
(FH243495) CHO_OF3119xh04r1.ab1 CHO_OF3 Nicotiana tabacum ge... 44 6.0 1
(CW844227) GT10776.Ds5.05.21.2002.jw37.735 Arabidopsis thali... 44 6.0 1
(CE756999) tigr-gss-dog-17000369677403 Dog Library Canis lup... 44 6.0 1
(CE752947) tigr-gss-dog-17000369630699 Dog Library Canis lup... 44 6.0 1
(CC555427) CH240_462G6.TARBAC13P2 CHORI-240 Bos taurus genom... 44 6.0 1
(EE097360) S9B00362 Ripening Berries (VvS9) Vitis vinifera c... 44 6.0 1
(AM865105) Crassostrea gigas EST, 5' end sequence, clone cdn... 44 6.0 1
(AM862487) Crassostrea gigas EST, 5' end sequence, clone cdn... 44 6.0 1
(CV095760) FAMU_USDA_FP_3783 Vitis shuttleworthii L., grape ... 44 6.0 1
(CF203083) RR890915N0007_IIa_Fa_C12 Vitis sp. RR890915N Viti... 44 6.0 1
(CB006875) VVC039A05_140808 An expressed sequence tag databa... 44 6.0 1
(CB006664) VVC036D09_139498 An expressed sequence tag databa... 44 6.0 1
(CB005122) VVC008D08_126274 An expressed sequence tag databa... 44 6.0 1
(CA814905) CA12EI201IbF_C01 Cabernet Sauvignon Leaf - CA12EI... 44 6.0 1
(CA808059) CA12LIO1IIIFb_G08 Cabernet Sauvignon Leaf - CA12L... 44 6.0 1
(EV234009) VV_PEb11e09.b1 Vitis vinifera cv. perlette LibB V... 44 6.0 1
(CP000961) Shewanella woodyi ATCC 51908, complete genome. 44 6.0 1
(CP000768) Campylobacter jejuni subsp. doylei 269.97, comple... 44 6.0 1
(CP001056) Clostridium botulinum B str. Eklund 17B, complete... 34 6.0 15
(AC155110) Bos taurus clone CH240-37D12, WORKING DRAFT SEQUE... 36 6.8 4
(DQ463413) Pierphulia rosea voucher M.L. Forister W22 cytoch... 40 7.4 2
(DQ463412) Pierphulia rosea voucher M.L. Forister W21 cytoch... 40 7.4 2
(DQ463409) Infraphulia ilyodes voucher M.L. Forister W15 cyt... 40 7.4 2
(AF159241) Dictyostelium discoideum ras interacting protein ... 32 8.2 3
(EF625819) Carica papaya clone MSY BAC PH54H01 complete sequ... 34 8.3 4
(EJ125837) 1092343393760 Global-Ocean-Sampling_GS-27-01-01-1... 38 8.3 2
(AC095264) Rattus norvegicus clone CH230-9O3, *** SEQUENCING... 34 8.8 6
(CZ730709) OC__Ba0059I04.r OC__Ba Oryza coarctata genomic cl... 36 9.2 2
(AL589883) Arabidopsis thaliana DNA chromosome 5, BAC clone ... 34 9.4 5

>(AU271010) Dictyostelium discoideum vegetative cDNA clone:VSK328,
3' end single read.
Length = 636

Score = 662 bits (334), Expect(2) = 0.0
Identities = 337/337 (100%)
Strand = Plus / Plus


Query: 1 ccacgcgtnccgatatacagaatgttatcaattaaaacttgtagatcaattgtaaattta 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ccacgcgtnccgatatacagaatgttatcaattaaaacttgtagatcaattgtaaattta 60


Query: 61 tcaagtaaacaagcaaatcaacaacaatttatttgtggatatgcagcaaaagttgttaaa 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tcaagtaaacaagcaaatcaacaacaatttatttgtggatatgcagcaaaagttgttaaa 120


Query: 121 aggggcggtaaaaaagtagtagaagaagaggatacaggtgttgatcttagtgaaaaatat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aggggcggtaaaaaagtagtagaagaagaggatacaggtgttgatcttagtgaaaaatat 180


Query: 181 gatgtaaaagtgtcaaaagcatcttaccaaaagattatacaacgtttccaagttttattt 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gatgtaaaagtgtcaaaagcatcttaccaaaagattatacaacgtttccaagttttattt 240


Query: 241 aaacgtccagaatttgcagacaaaaatgaaagtgatgaagagaaacgattaagattaatt 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aaacgtccagaatttgcagacaaaaatgaaagtgatgaagagaaacgattaagattaatt 300


Query: 301 aactacaattataccgcatacagtaacgaactcaaac 337
|||||||||||||||||||||||||||||||||||||
Sbjct: 301 aactacaattataccgcatacagtaacgaactcaaac 337

Score = 406 bits (205), Expect(2) = 0.0
Identities = 205/205 (100%)
Strand = Plus / Plus


Query: 367 ttagattatcaatgggatgcagttatggaattaccagaagatctcagaaaaatcgcatta 426
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 367 ttagattatcaatgggatgcagttatggaattaccagaagatctcagaaaaatcgcatta 426


Query: 427 ttaattgaaacagataaagaaatgccattaattccatttttatatgatacaccaccaact 486
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 427 ttaattgaaacagataaagaaatgccattaattccatttttatatgatacaccaccaact 486


Query: 487 aaaggtgatccaaagaaaacaattcaattaaagaaaaaagatagaaatcttaaaccatct 546
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 487 aaaggtgatccaaagaaaacaattcaattaaagaaaaaagatagaaatcttaaaccatct 546


Query: 547 gaaagaactttcttatcaaattcac 571
|||||||||||||||||||||||||
Sbjct: 547 gaaagaactttcttatcaaattcac 571

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 729,540,569
Number of extensions: 44957185
Number of successful extensions: 3838877
Number of sequences better than 10.0: 62
Length of query: 635
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 612
Effective length of database: 93,106,754,628
Effective search space: 56981333832336
Effective search space used: 56981333832336
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)

protein update 2009. 6.23
Homology vs Protein
Query= Contig-U07096-1 (Contig-U07096-1Q) /CSM_Contig/Contig-U07096-1Q.Seq.d
(635 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: 756,864,007
Number of extensions: 11892103
Number of successful extensions: 26937
Number of sequences better than 10.0: 0
Number of HSP's gapped: 26917
Number of HSP's successfully gapped: 0
Length of query: 211
Length of database: 1,040,966,779
Length adjustment: 123
Effective length of query: 88
Effective length of database: 646,839,724
Effective search space: 56921895712
Effective search space used: 56921895712
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: 0.67 gvh: 0.37 alm: 0.45 top: 0.53 tms: 0.00 mit: 0.49 mip: 0.08
nuc: 0.00 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

80.0 %: mitochondrial
8.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: plasma membrane
4.0 %: nuclear

>> prediction for Contig-U07096-1 is mit

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