Contig-U15233-1
Contig ID Contig-U15233-1
Contig update 2004. 6.11
Contig sequence
>Contig-U15233-1 (Contig-U15233-1Q) /CSM_Contig/Contig-U15233-1Q.Seq.d
CGTATTAATATTCAAAACTTTGTAAATCCAATTGAAGCAAGTTCCAGAGC
TGCTGCCCAAAATGATAATTAAATTTTTTTAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAACAAATTAAAGATAAATATATATATTAATAGTAAACAATT
TAAAAAAATTTGACAATGAATCATATATACATTAAATAATAATTATTGTC
AAAAAAAAAAAAAAAA

Gap no gap
Contig length 216
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 4201405
End point 4201620
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 1
Link to clone list U15233
List of clone(s)

est1=FCL-AD04Z,1,216
Translated Amino Acid sequence
vlifktl*iqlkqvpellpkmiikff*KKKKKKKKKNKLKINIYINSKQFKKI*q*iiyt
lnnnycqkkkk


Translated Amino Acid sequence (All Frames)
Frame A:
riniqnfvnpieassraaaqndn*iflkkkkkkkkkkqikdkyiy***ti*knltmnhiy
ik**llskkkkk


Frame B:
vlifktl*iqlkqvpellpkmiikff*KKKKKKKKKNKLKINIYINSKQFKKI*q*iiyt
lnnnycqkkkk


Frame C:
y*ysklcksn*skfqsccpk**lnffkkkkkkkkkktn*r*iyilivnnlkkfdnesyih
*iiiivkkkkk


own update 2004. 6.23
Homology vs CSM-cDNA
Query= Contig-U15233-1 (Contig-U15233-1Q)
/CSM_Contig/Contig-U15233-1Q.Seq.d
(216 letters)

Database: CSM
8402 sequences; 8,075,542 total letters


Score E
Sequences producing significant alignments: (bits) Value

Contig-U15233-1 (Contig-U15233-1Q) /CSM_Contig/Conti... 159 2e-39
Contig-U15431-1 (Contig-U15431-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U14438-1 (Contig-U14438-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U14418-1 (Contig-U14418-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U13080-1 (Contig-U13080-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U10114-1 (Contig-U10114-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U06873-1 (Contig-U06873-1Q) /CSM_Contig/Conti... 36 0.021
Contig-U11740-1 (Contig-U11740-1Q) /CSM_Contig/Conti... 34 0.081
Contig-U09163-1 (Contig-U09163-1Q) /CSM_Contig/Conti... 34 0.081
Contig-U16566-1 (Contig-U16566-1Q) /CSM_Contig/Conti... 32 0.32

>Contig-U15233-1 (Contig-U15233-1Q) /CSM_Contig/Contig-U15233-1Q.Seq.d
Length = 216

Score = 159 bits (80), Expect = 2e-39
Identities = 80/80 (100%)
Strand = Plus / Plus


Query: 1 cgtattaatattcaaaactttgtaaatccaattgaagcaagttccagagctgctgcccaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 cgtattaatattcaaaactttgtaaatccaattgaagcaagttccagagctgctgcccaa 60


Query: 61 aatgataattaaattttttt 80
||||||||||||||||||||
Sbjct: 61 aatgataattaaattttttt 80


Score = 135 bits (68), Expect = 3e-32
Identities = 82/89 (92%)
Strand = Plus / Plus


Query: 112 caaattaaagataaatatatatattaatagtaaacaatttnnnnnnntttgacaatgaat 171
|||||||||||||||||||||||||||||||||||||||| |||||||||||||
Sbjct: 112 caaattaaagataaatatatatattaatagtaaacaatttaaaaaaatttgacaatgaat 171


Query: 172 catatatacattaaataataattattgtc 200
|||||||||||||||||||||||||||||
Sbjct: 172 catatatacattaaataataattattgtc 200


>Contig-U15431-1 (Contig-U15431-1Q) /CSM_Contig/Contig-U15431-1Q.Seq.d
Length = 423

Score = 36.2 bits (18), Expect = 0.021
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 118 aaagataaatatatatat 135
||||||||||||||||||
Sbjct: 384 aaagataaatatatatat 401


>Contig-U14438-1 (Contig-U14438-1Q) /CSM_Contig/Contig-U14438-1Q.Seq.d
Length = 644

Score = 36.2 bits (18), Expect = 0.021
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 123 taaatatatatattaata 140
||||||||||||||||||
Sbjct: 18 taaatatatatattaata 35


Database: CSM
Posted date: Jun 21, 2004 1:35 PM
Number of letters in database: 8,075,542
Number of sequences in database: 8402

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: 8133
Number of Sequences: 8402
Number of extensions: 8133
Number of successful extensions: 3158
Number of sequences better than 10.0: 388
length of query: 216
length of database: 8,075,542
effective HSP length: 15
effective length of query: 201
effective length of database: 7,949,512
effective search space: 1597851912
effective search space used: 1597851912
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 2009. 1.17
Homology vs DNA
Query= Contig-U15233-1 (Contig-U15233-1Q) /CSM_Contig/Contig-U15233-1Q.Seq.d
(216 letters)

Database: ddbj_B
98,226,423 sequences; 98,766,808,389 total letters

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

Score E
Sequences producing significant alignments: (bits) Value N

(CU928627) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 38 0.025 3
(AC207500) Aotus nancymaae clone CH258-412I6, WORKING DRAFT ... 46 0.52 1
(AC203116) Aotus nancymaae clone CH258-5K3, WORKING DRAFT SE... 46 0.52 1
(CK606485) gmrhRww6-13_A01_T7 Soybean root hair subtracted c... 46 0.52 1
(EY369005) CAXA12125.fwd CAXA Helobdella robusta Subtracted ... 46 0.52 1
(EY369004) CAXA12125.rev CAXA Helobdella robusta Subtracted ... 46 0.52 1
(AC137961) Mus musculus chromosome 14, clone RP24-550E9, com... 44 2.1 1
(AC098742) Mus musculus BAC clone RP23-122N2 from 14, comple... 44 2.1 1
(AM482964) Vitis vinifera, whole genome shotgun sequence, co... 44 2.1 1
(AC159681) Bos taurus clone CH240-77E1, WORKING DRAFT SEQUEN... 44 2.1 1
(AC113842) Rattus norvegicus clone CH230-129E6, *** SEQUENCI... 44 2.1 1
(AC107448) Rattus norvegicus clone CH230-218A23, *** SEQUENC... 44 2.1 1
(AC106075) Rattus norvegicus clone CH230-126N13, *** SEQUENC... 44 2.1 1
(AC095924) Rattus norvegicus clone CH230-10J12, WORKING DRAF... 44 2.1 1
(CU928576) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 2.1 1
(AC178037) Strongylocentrotus purpuratus clone R3-3055M23, W... 44 2.1 1
(AC175851) Strongylocentrotus purpuratus clone R3-15K11, WOR... 44 2.1 1
(EK014627) 1092955224141 Global-Ocean-Sampling_GS-31-01-01-1... 44 2.1 1
(AC079318) Homo sapiens chromosome 12 clone RP11-62D5, WORKI... 38 2.8 2
(AL935295) Zebrafish DNA sequence from clone CH211-260C23 in... 34 3.4 4
(AC175307) Bos taurus clone CH240-90J2, WORKING DRAFT SEQUEN... 34 3.9 2
(AC152647) Bos taurus clone CH240-16J20, WORKING DRAFT SEQUE... 34 4.0 2
(CR925725) Zebrafish DNA sequence from clone DKEYP-1D6 in li... 42 4.6 4
(EE704525) AGENCOURT_88876951 NIH_ZGC_27 Danio rerio cDNA cl... 30 5.3 2
(FH356687) CHO_OF4677xk16f1.ab1 CHO_OF4 Nicotiana tabacum ge... 32 5.7 3
(FH356766) CHO_OF4677xk16r1.ab1 CHO_OF4 Nicotiana tabacum ge... 32 6.8 3
(ET170490) MUGQ_CH252P372E22Sp6_CP700_091 CHORI-252 Vervet M... 30 7.5 3
(CU855817) Zebrafish DNA sequence from clone CH73-348M5 in l... 42 8.1 1
(CR388216) Zebrafish DNA sequence from clone CH211-165L2 in ... 42 8.1 1
(AL731805) Mouse DNA sequence from clone RP23-358E19 on chro... 42 8.1 1
(AC136147) Mus musculus BAC clone RP23-18B3 from 8, complete... 42 8.1 1
(AC127350) Mus musculus BAC clone RP23-64P14 from chromosome... 42 8.1 1
(AC202783) Pongo abelii BAC clone CH276-460J20 from chromoso... 42 8.1 1
(AC200570) Pongo abelii BAC clone CH276-450H9 from chromosom... 42 8.1 1
(AC188682) Pan troglodytes BAC clone CH251-579B12 from chrom... 42 8.1 1
(AC186879) Pan troglodytes BAC clone CH251-464L18 from chrom... 42 8.1 1
(AP008213) Oryza sativa (japonica cultivar-group) genomic DN... 42 8.1 1
(AP005451) Oryza sativa Japonica Group genomic DNA, chromoso... 42 8.1 1
(AP005101) Oryza sativa Japonica Group genomic DNA, chromoso... 42 8.1 1
(AM475015) Vitis vinifera contig VV78X040164.7, whole genome... 42 8.1 1
(AC013483) Arabidopsis thaliana chromosome III BAC F17A17 ge... 42 8.1 1
(AC009176) Arabidopsis thaliana chromosome III P1 MLP3 genom... 42 8.1 1
(EA687968) Sequence 66847 from patent US 7365185. 42 8.1 1
(EA652935) Sequence 31814 from patent US 7365185. 42 8.1 1
(AX347195) Sequence 2266 from Patent WO0200928. 42 8.1 1
(AC117080) Dictyostelium discoideum chromosome 2 map complem... 42 8.1 1
(X86437) Homo sapiens PTPA gene for phosphotyrosyl phosphata... 42 8.1 1
(AL158151) Human DNA sequence from clone RP11-247A12 on chro... 42 8.1 1
(AC100770) Homo sapiens chromosome 11, clone RP11-46P12, com... 42 8.1 1
(AC090592) Homo sapiens chromosome 11, clone RP11-405K6, com... 42 8.1 1
(AC153758) Sphenodon punctatus clone VMRC12-460J19, WORKING ... 42 8.1 1
(AC150200) Papio anubis clone RP41-266M11, WORKING DRAFT SEQ... 42 8.1 1
(AC149562) Papio anubis clone RP41-291O3, WORKING DRAFT SEQU... 42 8.1 1
(AC132562) Rattus norvegicus clone CH230-5B7, WORKING DRAFT ... 42 8.1 1
(AC127121) Rattus norvegicus clone CH230-99O3, *** SEQUENCIN... 42 8.1 1
(AC125692) Rattus norvegicus clone CH230-129C2, *** SEQUENCI... 42 8.1 1
(AC117283) Rattus norvegicus clone CH230-375L23, WORKING DRA... 42 8.1 1
(AC106916) Rattus norvegicus clone CH230-59I17, *** SEQUENCI... 42 8.1 1
(AC094815) Rattus norvegicus clone CH230-5J3, WORKING DRAFT ... 42 8.1 1
(AC094611) Rattus norvegicus clone CH230-5A8, WORKING DRAFT ... 42 8.1 1
(CU550672) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 8.1 1
(CU481471) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 8.1 1
(AC211106) Chlorocebus aethiops clone CH252-202K13, WORKING ... 42 8.1 1
(AC208764) Saimiri boliviensis boliviensis clone CH254-324G1... 42 8.1 1
(AC208266) Saimiri boliviensis boliviensis clone CH254-305N1... 42 8.1 1
(AC207149) Nomascus leucogenys leucogenys clone CH271-169F23... 42 8.1 1
(AC202757) Callithrix jacchus clone CH259-330H21, WORKING DR... 42 8.1 1
(AC193840) Colobus guereza clone CH272-5N17, WORKING DRAFT S... 42 8.1 1
(AC193277) Aotus nancymaae clone CH258-479C20, WORKING DRAFT... 42 8.1 1
(AC188895) Aotus nancymaae clone CH258-111K18, WORKING DRAFT... 42 8.1 1
(AC187185) Callicebus moloch clone LB5-257J5, WORKING DRAFT ... 42 8.1 1
(AC186454) Callithrix jacchus clone CH259-22L17, WORKING DRA... 42 8.1 1
(AC184464) Strongylocentrotus purpuratus clone R3-4003I7, WO... 42 8.1 1
(AC182122) Bos taurus clone CH240-496L3, WORKING DRAFT SEQUE... 42 8.1 1
(AC171786) Bos taurus clone CH240-302O24, WORKING DRAFT SEQU... 42 8.1 1
(AC169831) Macaca mulatta clone CH250-34J20, WORKING DRAFT S... 42 8.1 1
(AC169828) Macaca mulatta clone CH250-13E3, WORKING DRAFT SE... 42 8.1 1
(AC025235) Homo sapiens chromosome 11 clone RP11-405K6, WORK... 42 8.1 1
(BH251792) SALK_012140 Arabidopsis thaliana TDNA insertion l... 42 8.1 1
(FH558798) CHO_OF4477xd14r1.ab1 CHO_OF4 Nicotiana tabacum ge... 42 8.1 1
(ET207199) MUGQ_CH252P406M18T7_CP774_067 CHORI-252 Vervet Mo... 42 8.1 1
(ET018388) MUGQ_CH252P324I09Sp6_CP606_039 CHORI-252 Vervet M... 42 8.1 1
(EK230696) 1095460178535 Global-Ocean-Sampling_GS-31-01-01-1... 42 8.1 1
(ED572737) SALK_012140.44.00.x Arabidopsis thaliana TDNA ins... 42 8.1 1
(DU068476) 139008 Tomato HindIII BAC Library Solanum lycoper... 42 8.1 1
(CW773037) OG_BBa0090J08.r OG_BBa Oryza glaberrima genomic c... 42 8.1 1
(CL799037) OR_CBa0010B13.r OR_CBa Oryza rufipogon genomic cl... 42 8.1 1
(CL727380) OR_BBa0058A21.f OR_BBa Oryza nivara genomic clone... 42 8.1 1
(CL719686) OR_BBa0047I01.f OR_BBa Oryza nivara genomic clone... 42 8.1 1
(CL492244) SAIL_564_G08.v1 SAIL Collection Arabidopsis thali... 42 8.1 1
(BX148282) Danio rerio genomic clone DKEY-108M7, genomic sur... 42 8.1 1
(DV288944) NAAHI26TF Aedes aegypti - Fat Bodies Normalized (... 42 8.1 1
(DV242102) A2FM916TV Aedes aegypti full length cDNA library,... 42 8.1 1
(DV242032) A2FM916TO Aedes aegypti full length cDNA library,... 42 8.1 1
(DT879658) AGENCOURT_58679162 NIH_ZGC_9 Danio rerio cDNA clo... 42 8.1 1
(CN758094) ID0AAA21BC01RM1 ApMS Acyrthosiphon pisum cDNA clo... 42 8.1 1
(CN757722) ID0AAA20BB01RM1 ApMS Acyrthosiphon pisum cDNA clo... 42 8.1 1
(CK176582) EST765902 BEA Rhipicephalus microplus cDNA clone ... 42 8.1 1
(CJ979859) Bursaphelenchus xylophilus cDNA clone: Bx_K1_15B0... 42 8.1 1
(CF920732) gmrhRww3-01_A03_1_031 Soybean root hair subtracte... 42 8.1 1

>(CU928627) Pig DNA sequence *** SEQUENCING IN PROGRESS *** from clone
CH242-204D4.
Length = 180361

Score = 38.2 bits (19), Expect(3) = 0.025
Identities = 22/23 (95%)
Strand = Plus / Plus


Query: 14 aaaactttgtaaatccaattgaa 36
|||||||||||||| ||||||||
Sbjct: 178708 aaaactttgtaaattcaattgaa 178730

Score = 36.2 bits (18), Expect(3) = 0.025
Identities = 21/22 (95%)
Strand = Plus / Plus


Query: 173 atatatacattaaataataatt 194
||||||||||||||| ||||||
Sbjct: 180158 atatatacattaaattataatt 180179

Score = 32.2 bits (16), Expect(3) = 0.025
Identities = 19/20 (95%)
Strand = Plus / Plus


Query: 2 gtattaatattcaaaacttt 21
|||||||| |||||||||||
Sbjct: 121489 gtattaatcttcaaaacttt 121508

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 98226423
Number of Hits to DB: 199,378,009
Number of extensions: 14272528
Number of successful extensions: 4236628
Number of sequences better than 10.0: 114
Length of query: 216
Length of database: 98,766,808,389
Length adjustment: 23
Effective length of query: 193
Effective length of database: 100,802,567,956
Effective search space: 19454895615508
Effective search space used: 19454895615508
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.15
Homology vs Protein
Query= Contig-U15233-1 (Contig-U15233-1Q) /CSM_Contig/Contig-U15233-1Q.Seq.d
(216 letters)

Database: nrp_B
3,236,559 sequences; 1,051,180,864 total letters

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

Score E
Sequences producing significant alignments: (bits) Value

(Q54U89) RecName: Full=Metabotropic glutamate receptor-like prot... 47 3e-04

>(Q54U89) RecName: Full=Metabotropic glutamate receptor-like protein
J; Flags: Precursor;
Length = 708

Score = 46.6 bits (109), Expect = 3e-04
Identities = 22/22 (100%), Positives = 22/22 (100%)
Frame = +1

Query: 4 INIQNFVNPIEASSRAAAQNDN 69
INIQNFVNPIEASSRAAAQNDN
Sbjct: 687 INIQNFVNPIEASSRAAAQNDN 708

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: 172,840,038
Number of extensions: 1716452
Number of successful extensions: 1823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1823
Number of HSP's successfully gapped: 1
Length of query: 72
Length of database: 1,051,180,864
Length adjustment: 43
Effective length of query: 29
Effective length of database: 912,008,827
Effective search space: 26448255983
Effective search space used: 26448255983
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: 0.68 gvh: 0.01 alm: 0.70 top: 0.53 tms: 0.00 mit: 0.36 mip: 0.00
nuc: 0.73 erl: 0.00 erm: 0.40 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

84.0 %: nuclear
12.0 %: cytoplasmic
4.0 %: mitochondrial

>> prediction for Contig-U15233-1 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) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 1
FC (DIR, S) 1
FC-IC (SUB) 0