Contig-U13009-1
Contig ID Contig-U13009-1
Contig update 2002.12.18
Contig sequence
>Contig-U13009-1 (Contig-U13009-1Q) /CSM_Contig/Contig-U13009-1Q.Seq.d
AAAAAAAAAAAAAATTTTTTTTTTTTTTTTNNAAAAACNAAAAAAAAAAA
AACATATAATTAATAATCACGCACATAAAAATTTAAATTTATTCACTCAC
TCACTCATTCACTCCTCACACTTCACCTCACTCCTCACGCTCACATTAAT
TCACTCACTCACACATCACTCCTCACGCATAATATAAATAATAATGATAT
AATTACTCTTTCTCTTTCTTCTCTTCTATCAAACATGTTTGTTTTATTAT
TAACATGTAAATTTCACCATTTCCCGTTCGACCATCTAATATATTAAATT
AATAAAAGTAATATATTTAAAAAAATAACCATCTATTATTTAATCACTTT
TATTTTTTCTTTTTTTCCTTCATTGTATTTTTAATTTATTCTTTTTTAAA
AAAGAAAAATAAATTATATAATTTTTCTAAACAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Gap no gap
Contig length 500
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 1260001
End point 1260503
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 2
Link to clone list U13009
List of clone(s)

est1=CHI254Z,-1,423
est2=SLC777F,352,500
Translated Amino Acid sequence
kkkknfffffxktkkkktyn**srt*KFKFIHSLTHSLLTLHLTPHAHINSLTHTSLLTH
NINNNDIITLSLSSLLSNMFVLLLTCKFHHFPFDHLIY*inksnifkkitiyylitfifs
ffpslyf*filf*krkinyiiflnkkkkkkkkkkkkkkkkkkkkkk


Translated Amino Acid sequence (All Frames)
Frame A:
kkkknfffffxktkkkktyn**srt*KFKFIHSLTHSLLTLHLTPHAHINSLTHTSLLTH
NINNNDIITLSLSSLLSNMFVLLLTCKFHHFPFDHLIY*inksnifkkitiyylitfifs
ffpslyf*filf*krkinyiiflnkkkkkkkkkkkkkkkkkkkkkk


Frame B:
kkkkiffffxxkxkkkkhiinnhahknlnlfthslihsshftslltltlihslthhssri
i*iimi*llflfllfyqtclfyy*hvnftisrsti*yiklikviylkk*psii*sllffl
fflhcifnlfffkkek*ii*ff*tkkkkkkkkkkkkkkkkkkkkkk


Frame C:
kkkkfffffxknxkkkni*liithiki*iyslthsftphtsphssrsh*fthshitpha*
yk***ynysfsffssikhvcfiinm*ispfpvrpsniln**k*yi*knnhllfnhfyfff
fsfivfliysflkkknklynfskqkkkkkkkkkkkkkkkkkkkkkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13009-1 (Contig-U13009-1Q)
/CSM_Contig/Contig-U13009-1Q.Seq.d
(500 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U13009-1 (Contig-U13009-1Q) /CSM_Contig/Conti... 295 2e-80
Contig-U11911-1 (Contig-U11911-1Q) /CSM_Contig/Conti... 40 0.002
Contig-U01619-1 (Contig-U01619-1Q) /CSM_Contig/Conti... 40 0.002
Contig-U14332-1 (Contig-U14332-1Q) /CSM_Contig/Conti... 38 0.009
Contig-U09342-1 (Contig-U09342-1Q) /CSM_Contig/Conti... 38 0.009
Contig-U01148-1 (Contig-U01148-1Q) /CSM_Contig/Conti... 38 0.009
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti... 36 0.035
Contig-U11240-1 (Contig-U11240-1Q) /CSM_Contig/Conti... 36 0.035
Contig-U09125-1 (Contig-U09125-1Q) /CSM_Contig/Conti... 36 0.035
Contig-U06263-1 (Contig-U06263-1Q) /CSM_Contig/Conti... 36 0.035

>Contig-U13009-1 (Contig-U13009-1Q) /CSM_Contig/Contig-U13009-1Q.Seq.d
Length = 500

Score = 295 bits (149), Expect = 2e-80
Identities = 163/170 (95%)
Strand = Plus / Plus


Query: 177 gcataatataaataataatgatataattactctttctctttcttctcttctatcaaacat 236
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 177 gcataatataaataataatgatataattactctttctctttcttctcttctatcaaacat 236


Query: 237 gtttgttttattattaacatgtaaatttcaccatttcccgttcgaccatctaatatatta 296
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237 gtttgttttattattaacatgtaaatttcaccatttcccgttcgaccatctaatatatta 296


Query: 297 aattaataaaagtaatatatttnnnnnnntaaccatctattatttaatca 346
|||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 297 aattaataaaagtaatatatttaaaaaaataaccatctattatttaatca 346


Score = 75.8 bits (38), Expect = 4e-14
Identities = 38/38 (100%)
Strand = Plus / Plus


Query: 53 catataattaataatcacgcacataaaaatttaaattt 90
||||||||||||||||||||||||||||||||||||||
Sbjct: 53 catataattaataatcacgcacataaaaatttaaattt 90


>Contig-U11911-1 (Contig-U11911-1Q) /CSM_Contig/Contig-U11911-1Q.Seq.d
Length = 850

Score = 40.1 bits (20), Expect = 0.002
Identities = 23/24 (95%)
Strand = Plus / Plus


Query: 179 ataatataaataataatgatataa 202
||||||||||||||||| ||||||
Sbjct: 444 ataatataaataataataatataa 467


Score = 28.2 bits (14), Expect = 8.5
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 187 aataataatgatat 200
||||||||||||||
Sbjct: 554 aataataatgatat 567


Score = 28.2 bits (14), Expect = 8.5
Identities = 17/18 (94%)
Strand = Plus / Plus


Query: 185 taaataataatgatataa 202
||||||||||| ||||||
Sbjct: 435 taaataataataatataa 452


>Contig-U01619-1 (Contig-U01619-1Q) /CSM_Contig/Contig-U01619-1Q.Seq.d
Length = 1066

Score = 40.1 bits (20), Expect = 0.002
Identities = 23/24 (95%)
Strand = Plus / Plus


Query: 179 ataatataaataataatgatataa 202
||||||||||||||||| ||||||
Sbjct: 204 ataatataaataataataatataa 227


Score = 38.2 bits (19), Expect = 0.009
Identities = 22/23 (95%)
Strand = Plus / Plus


Query: 179 ataatataaataataatgatata 201
||||||||||||||||| |||||
Sbjct: 177 ataatataaataataataatata 199


Score = 34.2 bits (17), Expect = 0.14
Identities = 17/17 (100%)
Strand = Plus / Plus


Query: 179 ataatataaataataat 195
|||||||||||||||||
Sbjct: 264 ataatataaataataat 280


Score = 30.2 bits (15), Expect = 2.1
Identities = 15/15 (100%)
Strand = Plus / Plus


Query: 179 ataatataaataata 193
|||||||||||||||
Sbjct: 255 ataatataaataata 269


Score = 30.2 bits (15), Expect = 2.1
Identities = 15/15 (100%)
Strand = Plus / Plus


Query: 179 ataatataaataata 193
|||||||||||||||
Sbjct: 246 ataatataaataata 260


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: 9087
Number of Sequences: 6905
Number of extensions: 9087
Number of successful extensions: 1305
Number of sequences better than 10.0: 443
length of query: 500
length of database: 5,674,871
effective HSP length: 16
effective length of query: 484
effective length of database: 5,564,391
effective search space: 2693165244
effective search space used: 2693165244
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 2008.12. 5
Homology vs DNA
Query= Contig-U13009-1 (Contig-U13009-1Q) /CSM_Contig/Contig-U13009-1Q.Seq.d
(500 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

(BJ380581) Dictyostelium discoideum cDNA clone:ddc38k14, 3' ... 281 6e-94 3
(AC116920) Dictyostelium discoideum chromosome 2 map 4415041... 281 5e-85 2
(AC114263) Dictyostelium discoideum chromosome 2 map 215673-... 40 0.003 5
(AB265369) Naxa seriaria gene for 16S rRNA, partial sequence. 34 0.056 3
(AE014852) Plasmodium falciparum 3D7 chromosome 12, section ... 50 0.076 1
(AC006279) Plasmodium falciparum chromosome 12 clone 3D7, **... 50 0.076 1
(EL506741) B08_PF-SAU3A-T3-S-P30.AB1 Blood stage Plasmodium ... 50 0.076 1
(BX701299) Xenopus tropicalis EST, clone TNeu125l02 3'. 50 0.076 1
(BQ633586) PfESToab44a04.y1 Plasmodium falciparum 3D7 asexua... 50 0.076 1
(EY312950) CAWX24683.fwd CAWX Helobdella robusta Primary Ear... 50 0.076 1
(AC104485) Sus scrofa clone RP44-73K12, WORKING DRAFT SEQUEN... 40 0.095 4
(CR848707) Zebrafish DNA sequence from clone CH211-276P5 in ... 36 0.13 5
(AC192613) Trichinella spiralis BAC clone TS195-33H12 from c... 36 0.18 2
(DX559803) GH_MBb0035E15r GH_MBb Gossypium hirsutum genomic ... 30 0.20 4
(AC219512) Bos taurus clone CH240-332A4, WORKING DRAFT SEQUE... 40 0.28 2
(CR759953) Zebrafish DNA sequence from clone DKEY-68D15 in l... 48 0.30 1
(CU655990) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 48 0.30 1
(CU469341) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 48 0.30 1
(CR790371) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 48 0.30 1
(BM166009) EST568532 PyBS Plasmodium yoelii yoelii cDNA clon... 48 0.30 1
(BM159754) EST562277 PyBS Plasmodium yoelii yoelii cDNA clon... 48 0.30 1
(EY392794) CAXA9998.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY392790) CAXA9996.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY392604) CAXA9897.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY392393) CAXA9788.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY392392) CAXA9788.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY390217) CAXA8614.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY390213) CAXA8612.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY390197) CAXA8605.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY390196) CAXA8605.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY389059) CAXA7643.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY388317) CAXA7238.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY388149) CAXA7143.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY388148) CAXA7143.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY384804) CAXA5349.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY383501) CAXA4641.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY383500) CAXA4641.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY383426) CAXA4599.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY383418) CAXA4594.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY382736) CAXA4205.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY380718) CAXA3035.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY380717) CAXA3035.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY380587) CAXA2960.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY380586) CAXA2960.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY380387) CAXA2848.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY379112) CAXA17620.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY378748) CAXA17426.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY378442) CAXA17263.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY378441) CAXA17263.rev CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY377900) CAXA16969.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY377899) CAXA16969.rev CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY377574) CAXA16795.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY374644) CAXA1519.fwd CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY374643) CAXA1519.rev CAXA Helobdella robusta Subtracted L... 48 0.30 1
(EY374003) CAXA14849.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY374002) CAXA14849.rev CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY370102) CAXA12731.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY368520) CAXA11854.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY368519) CAXA11854.rev CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY368044) CAXA11584.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY367919) CAXA11514.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY367672) CAXA11380.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY366653) CAXA10841.fwd CAXA Helobdella robusta Subtracted ... 48 0.30 1
(EY361312) CAWZ7657.fwd CAWZ Helobdella robusta Primary Late... 48 0.30 1
(EY358526) CAWZ5843.fwd CAWZ Helobdella robusta Primary Late... 48 0.30 1
(EY354620) CAWZ3257.fwd CAWZ Helobdella robusta Primary Late... 48 0.30 1
(EY351161) CAWZ17976.fwd CAWZ Helobdella robusta Primary Lat... 48 0.30 1
(EY347520) CAWZ15660.fwd CAWZ Helobdella robusta Primary Lat... 48 0.30 1
(AC104480) Sus scrofa clone RP44-327E13, WORKING DRAFT SEQUE... 40 0.33 2
(AC104486) Sus scrofa clone RP44-82G22, WORKING DRAFT SEQUEN... 40 0.35 2
(AL844509) Plasmodium falciparum chromosome 13. 36 0.40 7
(AL884329) Xenopus tropicalis EST, clone TEgg007j09 3'. 44 0.43 2
(CX452861) JGI_XZG24222.fwd NIH_XGC_tropGas7 Xenopus (Silura... 44 0.44 2
(AX392735) Sequence 25 from Patent WO0212526. 38 0.45 4
(AR707082) Sequence 25 from patent US 6933145. 38 0.45 4
(BX749833) Xenopus tropicalis EST, clone TGas070j21 3'. 44 0.46 2
(EL724878) CBSS5998.rev NICHD_XGC_tropSp1 Xenopus (Silurana)... 44 0.46 2
(EL822072) CBWN6216.g1 NICHD_XGC_tropTe1 Xenopus (Silurana) ... 44 0.46 2
(DN018075) JGI_CAAR871.rev NIH_XGC_tropLiv1 Xenopus (Siluran... 44 0.47 2
(EY337775) CAWY8555.rev CAWY Helobdella robusta Subtracted E... 42 0.47 2
(CX960908) JGI_CAAO11121.rev NIH_XGC_tropTe5 Xenopus (Silura... 44 0.47 2
(EL672825) CBST5066.rev NICHD_XGC_tropThy1 Xenopus (Silurana... 44 0.47 2
(AC130800) Medicago truncatula clone mth2-36b7, complete seq... 36 0.47 4
(AC210455) Oryza glaberrima clone OG_BBa0020J03, *** SEQUENC... 40 0.47 4
(EL851216) CBXT9053.g1 NICHD_XGC_trop_25 Xenopus (Silurana) ... 44 0.47 2
(BX696716) Xenopus tropicalis EST, clone TNeu081m08 3'. 44 0.48 2
(EL699364) CBSU10225.rev NICHD_XGC_tropLimb_m Xenopus (Silur... 44 0.48 2
(CX961012) JGI_CAAO11175.rev NIH_XGC_tropTe5 Xenopus (Silura... 44 0.49 2
(DC154463) Xenopus tropicalis NBRP cDNA clone:rst72k21, 3' end. 44 0.50 2
(EL852572) CBXT10235.g1 NICHD_XGC_trop_25 Xenopus (Silurana)... 44 0.51 2
(DU103424) JBnY029N10F Brassica napus BAC library JBnY Brass... 42 0.51 2
(CR414387) Xenopus tropicalis EST, clone TTbA009c24 3'. 44 0.52 2
(DT412114) JGI_CABI11130.rev NIH_XGC_tropOvi1 Xenopus (Silur... 44 0.52 2
(CX449142) JGI_XZG26643.rev NIH_XGC_tropGas7 Xenopus (Silura... 44 0.52 2
(CR567954) Xenopus tropicalis EST, clone THdA028p20 5'. 44 0.53 2
(DN024035) JGI_CAAR4442.fwd NIH_XGC_tropLiv1 Xenopus (Silura... 44 0.54 2
(CX973642) JGI_CAAP8138.rev NIH_XGC_tropInt1 Xenopus (Silura... 44 0.54 2
(CR567955) Xenopus tropicalis EST, clone THdA028p20 3'. 44 0.54 2
(DR848300) JGI_CABE11885.rev NIH_XGC_tropOva1 Xenopus (Silur... 44 0.54 2
(DT398395) JGI_CABI2210.rev NIH_XGC_tropOvi1 Xenopus (Silura... 44 0.55 2

>(BJ380581) Dictyostelium discoideum cDNA clone:ddc38k14, 3' end,
single read.
Length = 425

Score = 281 bits (142), Expect(3) = 6e-94
Identities = 142/142 (100%)
Strand = Plus / Minus


Query: 177 gcataatataaataataatgatataattactctttctctttcttctcttctatcaaacat 236
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247 gcataatataaataataatgatataattactctttctctttcttctcttctatcaaacat 188


Query: 237 gtttgttttattattaacatgtaaatttcaccatttcccgttcgaccatctaatatatta 296
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 187 gtttgttttattattaacatgtaaatttcaccatttcccgttcgaccatctaatatatta 128


Query: 297 aattaataaaagtaatatattt 318
||||||||||||||||||||||
Sbjct: 127 aattaataaaagtaatatattt 106

Score = 77.8 bits (39), Expect(3) = 6e-94
Identities = 39/39 (100%)
Strand = Plus / Minus


Query: 53 catataattaataatcacgcacataaaaatttaaattta 91
|||||||||||||||||||||||||||||||||||||||
Sbjct: 371 catataattaataatcacgcacataaaaatttaaattta 333

Score = 44.1 bits (22), Expect(3) = 6e-94
Identities = 22/22 (100%)
Strand = Plus / Minus


Query: 326 taaccatctattatttaatcac 347
||||||||||||||||||||||
Sbjct: 98 taaccatctattatttaatcac 77

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 350,578,824
Number of extensions: 28365946
Number of successful extensions: 3238488
Number of sequences better than 10.0: 571
Length of query: 500
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 477
Effective length of database: 93,106,754,628
Effective search space: 44411921957556
Effective search space used: 44411921957556
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7. 5
Homology vs Protein
Query= Contig-U13009-1 (Contig-U13009-1Q) /CSM_Contig/Contig-U13009-1Q.Seq.d
(500 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: 278,483,541
Number of extensions: 3067084
Number of successful extensions: 4857
Number of sequences better than 10.0: 0
Number of HSP's gapped: 4853
Number of HSP's successfully gapped: 0
Length of query: 166
Length of database: 1,051,180,864
Length adjustment: 119
Effective length of query: 47
Effective length of database: 666,030,343
Effective search space: 31303426121
Effective search space used: 31303426121
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: 30 (16.2 bits)

PSORT

psg: 0.87 gvh: 0.58 alm: 0.30 top: 0.63 tms: 0.07 mit: 0.38 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: 1.00 tyr: 0.16 leu: 0.31 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 1.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 0.00

48.0 %: nuclear
28.0 %: cytoplasmic
8.0 %: Golgi
8.0 %: mitochondrial
4.0 %: plasma membrane
4.0 %: vesicles of secretory system

>> prediction for Contig-U13009-1 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) 1
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