Contig-U06646-1
Contig ID Contig-U06646-1
Contig update 2001. 8.30
Contig sequence
>Contig-U06646-1 (Contig-U06646-1Q) /CSM_Contig/Contig-U06646-1Q.Seq.d
AAAAAAAATTCAAAATAATTTTTTATTTTCACCACCATAACCAAACCATT
AATTATTTATTACCTTTCTATTATTACCATATTTTATATATAATTTTATT
ATTATCATTATTTTCACTTTTTTTTTTTTTTCTTTAAAATAATAATTTTT
TAAATATAAAATACTTTGTATAAATTATAATTTGTAAATAAAATAAAATA
AAAATAAAAAAACCACCACATA

Gap no gap
Contig length 222
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 2103217
End point 2102994
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06646
List of clone(s)

est1=VSE516E,1,223
Translated Amino Acid sequence
KKFKIIFYFHHHNQTINYLLPFYYYHILYIILLLSLFSLFFFFL*nnnflnikyfv*iii
ck*nkikikkpph


Translated Amino Acid sequence (All Frames)
Frame A:
kknsk*ffifttitkpliiyylsiitifyi*fyyyhyfhffffffkiiif*i*ntlykl*
fvnkik*k*knhhi


Frame B:
kkiqnnflfspp*pnh*lfitflllpyfiynfiiiiiftffffslk**ffkykilcinyn
l*ik*nknkkttt


Frame C:
KKFKIIFYFHHHNQTINYLLPFYYYHILYIILLLSLFSLFFFFL*nnnflnikyfv*iii
ck*nkikikkpph


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U06646-1 (Contig-U06646-1Q)
/CSM_Contig/Contig-U06646-1Q.Seq.d
(222 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U06646-1 (Contig-U06646-1Q) /CSM_Contig/Conti... 76 2e-14
Contig-U11879-1 (Contig-U11879-1Q) /CSM_Contig/Conti... 34 0.059
Contig-U09782-1 (Contig-U09782-1Q) /CSM_Contig/Conti... 34 0.059
Contig-U06416-1 (Contig-U06416-1Q) /CSM_Contig/Conti... 34 0.059
Contig-U05090-1 (Contig-U05090-1Q) /CSM_Contig/Conti... 34 0.059
Contig-U14257-1 (Contig-U14257-1Q) /CSM_Contig/Conti... 32 0.23
Contig-U12706-1 (Contig-U12706-1Q) /CSM_Contig/Conti... 32 0.23
Contig-U11921-1 (Contig-U11921-1Q) /CSM_Contig/Conti... 32 0.23
Contig-U11720-1 (Contig-U11720-1Q) /CSM_Contig/Conti... 32 0.23
Contig-U11413-1 (Contig-U11413-1Q) /CSM_Contig/Conti... 32 0.23

>Contig-U06646-1 (Contig-U06646-1Q) /CSM_Contig/Contig-U06646-1Q.Seq.d
Length = 222

Score = 75.8 bits (38), Expect = 2e-14
Identities = 38/38 (100%)
Strand = Plus / Plus


Query: 9 ttcaaaataattttttattttcaccaccataaccaaac 46
||||||||||||||||||||||||||||||||||||||
Sbjct: 9 ttcaaaataattttttattttcaccaccataaccaaac 46


Score = 28.2 bits (14), Expect = 3.6
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 104 atcattattttcac 117
||||||||||||||
Sbjct: 104 atcattattttcac 117


>Contig-U11879-1 (Contig-U11879-1Q) /CSM_Contig/Contig-U11879-1Q.Seq.d
Length = 1549

Score = 34.2 bits (17), Expect = 0.059
Identities = 23/25 (92%)
Strand = Plus / Minus


Query: 19 ttttttattttcaccaccataacca 43
|||||||| | ||||||||||||||
Sbjct: 97 ttttttatatccaccaccataacca 73


>Contig-U09782-1 (Contig-U09782-1Q) /CSM_Contig/Contig-U09782-1Q.Seq.d
Length = 1322

Score = 34.2 bits (17), Expect = 0.059
Identities = 17/17 (100%)
Strand = Plus / Minus


Query: 13 aaataattttttatttt 29
|||||||||||||||||
Sbjct: 627 aaataattttttatttt 611


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: 5460
Number of Sequences: 6905
Number of extensions: 5460
Number of successful extensions: 1703
Number of sequences better than 10.0: 175
length of query: 222
length of database: 5,674,871
effective HSP length: 15
effective length of query: 207
effective length of database: 5,571,296
effective search space: 1153258272
effective search space used: 1153258272
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. 9
Homology vs DNA
Query= Contig-U06646-1 (Contig-U06646-1Q) /CSM_Contig/Contig-U06646-1Q.Seq.d
(222 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

(AU263161) Dictyostelium discoideum vegetative cDNA clone:VS... 78 1e-10 1
(CR762407) Zebrafish DNA sequence from clone DKEY-262N17 in ... 46 0.50 1
(AC106452) Rattus norvegicus clone CH230-200L23, *** SEQUENC... 46 0.50 1
(BX927120) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 0.50 1
(AM442280) Vitis vinifera contig VV78X263112.4, whole genome... 44 2.0 1
(AC209042) Populus trichocarpa clone POP052-O09, complete se... 44 2.0 1
(AL494179) T. brucei sheared genomic DNA clone 364e10, forwa... 44 2.0 1
(EJ458120) 1093017975688 Global-Ocean-Sampling_GS-28-01-01-1... 44 2.0 1
(EY134094) CBTH4338.b1_D05.ab1:P Triphysaria pusilla root ti... 44 2.0 1
(CP000743) Methanococcus aeolicus Nankai-3, complete genome. 44 2.0 1
(CU302309) Zebrafish DNA sequence from clone DKEY-80C17 in l... 42 7.7 1
(CU062487) Zebrafish DNA sequence from clone DKEY-254E3 in l... 42 7.7 1
(BV677728) SMURF2 _6867 Rhesus macaque genomic DNA Macaca mu... 42 7.7 1
(AP010519) Lotus japonicus genomic DNA, chromosome 5, clone:... 42 7.7 1
(AM489156) Vitis vinifera contig VV78X074996.14, whole genom... 42 7.7 1
(AM462251) Vitis vinifera contig VV78X147749.46, whole genom... 42 7.7 1
(AM454845) Vitis vinifera contig VV78X198954.16, whole genom... 42 7.7 1
(AM448849) Vitis vinifera, whole genome shotgun sequence, co... 42 7.7 1
(AM443549) Vitis vinifera contig VV78X049638.9, whole genome... 42 7.7 1
(AM436279) Vitis vinifera contig VV78X222214.5, whole genome... 42 7.7 1
(AM427433) Vitis vinifera contig VV78X173193.2, whole genome... 42 7.7 1
(AC209268) Populus trichocarpa clone ACSB209-O03, complete s... 42 7.7 1
(AC069552) Genomic Sequence For Arabidopsis thaliana Clone F... 42 7.7 1
(DJ357763) METHODS AND NUCLEIC ACIDS FOR THE ANALYSIS OF GEN... 42 7.7 1
(CS113482) Sequence 240 from Patent WO2005054517. 42 7.7 1
(CU855702) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 7.7 1
(AC194681) Macaca mulatta clone CH250-212N1, WORKING DRAFT S... 42 7.7 1
(AC176797) Strongylocentrotus purpuratus clone R3-3107A15, W... 42 7.7 1
(AC168734) Strongylocentrotus purpuratus clone R3-3010H5, WO... 42 7.7 1
(FH678082) CHO_OF5047xj03r1.ab1 CHO_OF5 Nicotiana tabacum ge... 42 7.7 1
(FH607211) CHO_OF4931xk19r1.ab1 CHO_OF4 Nicotiana tabacum ge... 42 7.7 1
(FH607131) CHO_OF4931xk19f1.ab1 CHO_OF4 Nicotiana tabacum ge... 42 7.7 1
(FH146434) CHO_OF3874xo23f1.ab1 CHO_OF3 Nicotiana tabacum ge... 42 7.7 1
(ER844802) PPTFF95TR Solanum tuberosum RHPOTKEY BAC ends Sol... 42 7.7 1
(ER597221) 1093016226852 Global-Ocean-Sampling_GS-36-01-01-2... 42 7.7 1
(EK232398) 1095460184300 Global-Ocean-Sampling_GS-31-01-01-1... 42 7.7 1
(EK086645) 1092961158082 Global-Ocean-Sampling_GS-31-01-01-1... 42 7.7 1
(EK029166) 1092955394678 Global-Ocean-Sampling_GS-31-01-01-1... 42 7.7 1
(EJ958957) 1093018989982 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(EJ856820) 1093017947617 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(AL494692) T. brucei sheared genomic DNA clone 364e11, rever... 42 7.7 1
(AL460632) T. brucei sheared genomic DNA clone 107h07, rever... 42 7.7 1
(EJ734168) 1092961064999 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(EJ726238) 1092959506327 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(EJ683636) 1092955154553 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(EJ679449) 1092955117689 Global-Ocean-Sampling_GS-30-02-01-1... 42 7.7 1
(EJ464345) 1095388024768 Global-Ocean-Sampling_GS-28-01-01-1... 42 7.7 1
(EJ393498) 1093011982966 Global-Ocean-Sampling_GS-28-01-01-1... 42 7.7 1
(EJ059890) 1095456058348 Global-Ocean-Sampling_GS-26-01-01-1... 42 7.7 1
(EJ059531) 1095456055671 Global-Ocean-Sampling_GS-26-01-01-1... 42 7.7 1
(EI806783) MUGQ_CH252P253L21T7_CN516_085 CHORI-252 Vervet Mo... 42 7.7 1
(EI343273) GM_WBc0087P19.f GM_WBc Glycine max genomic clone ... 42 7.7 1
(ED768696) GM_WBb0142L15.f GM_WBb Glycine max genomic clone ... 42 7.7 1
(DX435543) BE1093_N11_R IASMA L1 HindIII BAC library Vitis v... 42 7.7 1
(DU051823) 149738 Tomato HindIII BAC Library Solanum lycoper... 42 7.7 1
(CU843032) A BAC library has been constructed from PN40024 g... 42 7.7 1
(CU113796) Equus caballus GSS, BAC clone CH241-224H5, SP6 en... 42 7.7 1
(CL877219) abf16b08.y1 Soybean random, unfiltered genomic li... 42 7.7 1
(B29090) T26C16TF TAMU Arabidopsis thaliana genomic clone T2... 42 7.7 1

>(AU263161) Dictyostelium discoideum vegetative cDNA clone:VSE516,
3' end single read.
Length = 223

Score = 77.8 bits (39), Expect = 1e-10
Identities = 39/39 (100%)
Strand = Plus / Plus


Query: 9 ttcaaaataattttttattttcaccaccataaccaaacc 47
|||||||||||||||||||||||||||||||||||||||
Sbjct: 9 ttcaaaataattttttattttcaccaccataaccaaacc 47

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 95,270,559
Number of extensions: 10133006
Number of successful extensions: 3195206
Number of sequences better than 10.0: 59
Length of query: 222
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 199
Effective length of database: 93,106,754,628
Effective search space: 18528244170972
Effective search space used: 18528244170972
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.22
Homology vs Protein
Query= Contig-U06646-1 (Contig-U06646-1Q) /CSM_Contig/Contig-U06646-1Q.Seq.d
(222 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: 158,212,481
Number of extensions: 1632461
Number of successful extensions: 3285
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3264
Number of HSP's successfully gapped: 0
Length of query: 74
Length of database: 1,040,966,779
Length adjustment: 45
Effective length of query: 29
Effective length of database: 896,773,954
Effective search space: 26006444666
Effective search space used: 26006444666
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: 0.84 gvh: 0.54 alm: 0.17 top: 0.47 tms: 0.07 mit: 0.39 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: 0.93 leu: 0.19 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 0.00 m2 : 1.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 0.00

24.0 %: endoplasmic reticulum
20.0 %: nuclear
16.0 %: Golgi
16.0 %: mitochondrial
16.0 %: cytoplasmic
4.0 %: plasma membrane
4.0 %: vesicles of secretory system

>> prediction for Contig-U06646-1 is end

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