Contig-U13418-1
Contig ID Contig-U13418-1
Contig update 2002.12.18
Contig sequence
>Contig-U13418-1 (Contig-U13418-1Q) /CSM_Contig/Contig-U13418-1Q.Seq.d
TAAAAATCAAAAAAATAAAATTTTACCAAATACATTTTCACCAAATCTAC
AACCTCAACAACCATTGTCATCATCTTCATCAACAATAAATACACCATCA
TCACCAAATCAATTAAATTCACCCTCAATNGAGGATCAAATGGAGGAATA
TAAAAAAATTCATAGAGATAAATATA

Gap no gap
Contig length 176
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3470452
End point 3470276
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U13418
List of clone(s)

est1=SSH623F,1,177
Translated Amino Acid sequence
KNQKNKILPNTFSPNLQPQQPLSSSSSTINTPSSPNQLNSPSXEDQMEEYKKIHRDKY


Translated Amino Acid sequence (All Frames)
Frame A:
*kskk*nftkyiftksttsttiviifinnkytiitksikftlnxgsnggi*kns*r*i


Frame B:
KNQKNKILPNTFSPNLQPQQPLSSSSSTINTPSSPNQLNSPSXEDQMEEYKKIHRDKY


Frame C:
kikkikfyqihfhqiynlnnhchhlhqq*ihhhhqin*ihpqxrikwrnikkfieini


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13418-1 (Contig-U13418-1Q)
/CSM_Contig/Contig-U13418-1Q.Seq.d
(176 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U13418-1 (Contig-U13418-1Q) /CSM_Contig/Conti... 262 1e-70
Contig-U12860-1 (Contig-U12860-1Q) /CSM_Contig/Conti... 40 7e-04
Contig-U02015-1 (Contig-U02015-1Q) /CSM_Contig/Conti... 40 7e-04
Contig-U12751-1 (Contig-U12751-1Q) /CSM_Contig/Conti... 38 0.003
Contig-U06604-1 (Contig-U06604-1Q) /CSM_Contig/Conti... 38 0.003
Contig-U11567-1 (Contig-U11567-1Q) /CSM_Contig/Conti... 36 0.012
Contig-U11115-1 (Contig-U11115-1Q) /CSM_Contig/Conti... 36 0.012
Contig-U03468-1 (Contig-U03468-1Q) /CSM_Contig/Conti... 36 0.012
Contig-U12427-1 (Contig-U12427-1Q) /CSM_Contig/Conti... 34 0.046
Contig-U12346-1 (Contig-U12346-1Q) /CSM_Contig/Conti... 34 0.046

>Contig-U13418-1 (Contig-U13418-1Q) /CSM_Contig/Contig-U13418-1Q.Seq.d
Length = 176

Score = 262 bits (132), Expect = 1e-70
Identities = 149/156 (95%)
Strand = Plus / Plus


Query: 21 ttttaccaaatacattttcaccaaatctacaacctcaacaaccattgtcatcatcttcat 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21 ttttaccaaatacattttcaccaaatctacaacctcaacaaccattgtcatcatcttcat 80


Query: 81 caacaataaatacaccatcatcaccaaatcaattaaattcaccctcaatngaggatcaaa 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 81 caacaataaatacaccatcatcaccaaatcaattaaattcaccctcaatngaggatcaaa 140


Query: 141 tggaggaatatnnnnnnnttcatagagataaatata 176
||||||||||| ||||||||||||||||||
Sbjct: 141 tggaggaatataaaaaaattcatagagataaatata 176


>Contig-U12860-1 (Contig-U12860-1Q) /CSM_Contig/Contig-U12860-1Q.Seq.d
Length = 627

Score = 40.1 bits (20), Expect = 7e-04
Identities = 23/24 (95%)
Strand = Plus / Plus


Query: 83 acaataaatacaccatcatcacca 106
|||| |||||||||||||||||||
Sbjct: 282 acaacaaatacaccatcatcacca 305


>Contig-U02015-1 (Contig-U02015-1Q) /CSM_Contig/Contig-U02015-1Q.Seq.d
Length = 537

Score = 40.1 bits (20), Expect = 7e-04
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 93 caccatcatcaccaaatcaa 112
||||||||||||||||||||
Sbjct: 516 caccatcatcaccaaatcaa 535


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: 3778
Number of Sequences: 6905
Number of extensions: 3778
Number of successful extensions: 1491
Number of sequences better than 10.0: 279
length of query: 176
length of database: 5,674,871
effective HSP length: 15
effective length of query: 161
effective length of database: 5,571,296
effective search space: 896978656
effective search space used: 896978656
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. 9
Homology vs DNA
Query= Contig-U13418-1 (Contig-U13418-1Q) /CSM_Contig/Contig-U13418-1Q.Seq.d
(176 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

(AU073594) Dictyostelium discoideum slug cDNA, clone SSH623. 254 2e-68 2
(AC020895) Homo sapiens chromosome 19 clone CTC-312O10, comp... 40 0.016 2
(AC025278) Homo sapiens chromosome 19 clone RP11-1137G4, com... 40 0.016 2
(AC179133) Strongylocentrotus purpuratus clone R3-4011N21, W... 40 0.060 2
(BJ384409) Dictyostelium discoideum cDNA clone:ddc49i08, 3' ... 34 0.063 3
(AC103074) Rattus norvegicus clone CH230-174A13, *** SEQUENC... 48 0.097 1
(EJ650493) 1092953009319 Global-Ocean-Sampling_GS-30-02-01-1... 44 0.19 2
(CK283145) EST745867 Nicotiana benthamiana mixed tissue cDNA... 32 0.20 3
(AC168696) Strongylocentrotus purpuratus clone R3-3014G20, W... 36 0.22 2
(AC009492) Homo sapiens BAC clone RP11-423F9 from 2, complet... 36 0.22 2
(AC138475) Homo sapiens chromosome 16 clone CTD-3073N7, WORK... 36 0.22 2
(AC040167) Homo sapiens chromosome 16 clone RP11-457P5, WORK... 36 0.22 2
(AC092122) Homo sapiens chromosome 16 clone RP11-102F12, com... 36 0.22 2
(AC022195) Homo sapiens clone RP11-24P20, WORKING DRAFT SEQU... 36 0.22 2
(EK393270) 1095469509733 Global-Ocean-Sampling_GS-31-01-01-1... 44 0.23 2
(EK181907) 1095458126146 Global-Ocean-Sampling_GS-31-01-01-1... 44 0.26 2
(EJ685602) 1092955174843 Global-Ocean-Sampling_GS-30-02-01-1... 44 0.27 2
(CQ328278) Sequence 2372 from Patent WO0157275. 36 0.29 2
(CQ291161) Sequence 2266 from Patent WO0186003. 36 0.29 2
(CQ254150) Sequence 2411 from Patent WO0157277. 36 0.29 2
(CQ215557) Sequence 2396 from Patent WO0157273. 36 0.29 2
(CQ200076) Sequence 2353 from Patent WO0157271. 36 0.29 2
(CQ170925) Sequence 2321 from Patent WO0157274. 36 0.29 2
(CQ132360) Sequence 2382 from Patent WO0157276. 36 0.29 2
(CQ093586) Sequence 2445 from Patent WO0157272. 36 0.29 2
(CQ066540) Sequence 2340 from Patent WO0157278. 36 0.29 2
(CQ051492) Sequence 2312 from Patent WO0157270. 36 0.29 2
(AB137430) Homo sapiens DNA, STS on chromosome 16, D16S0175i... 36 0.29 2
(DJ469508) Method for analysing genome using microsatellite ... 36 0.29 2
(CV346289) MR1-TN0045-110900-007-a07 TN0045 Homo sapiens cDN... 36 0.29 2
(AC180315) Strongylocentrotus purpuratus clone R3-3119D02, W... 40 0.30 4
(CQ341000) Sequence 15094 from Patent WO0157275. 36 0.30 2
(CQ303669) Sequence 14774 from Patent WO0186003. 36 0.30 2
(CQ266718) Sequence 14979 from Patent WO0157277. 36 0.30 2
(CQ228562) Sequence 15401 from Patent WO0157273. 36 0.30 2
(CQ205183) Sequence 7460 from Patent WO0157271. 36 0.30 2
(CQ180806) Sequence 12202 from Patent WO0157274. 36 0.30 2
(CQ145368) Sequence 15390 from Patent WO0157276. 36 0.30 2
(CQ106714) Sequence 15573 from Patent WO0157272. 36 0.30 2
(CQ075733) Sequence 11533 from Patent WO0157278. 36 0.30 2
(CQ056467) Sequence 7287 from Patent WO0157270. 36 0.30 2
(AC189743) Gossypium hirsutum chromosome UNKNOWN clone ZMMBB... 46 0.38 1
(AC184642) Strongylocentrotus purpuratus clone R3-1031N8, WO... 46 0.38 1
(FH651640) CHO_OF4397xl19r2.ab1 CHO_OF4 Nicotiana tabacum ge... 46 0.38 1
(FH651556) CHO_OF4397xl19r1.ab1 CHO_OF4 Nicotiana tabacum ge... 46 0.38 1
(FH651446) CHO_OF4397xl19f1.ab1 CHO_OF4 Nicotiana tabacum ge... 46 0.38 1
(FH647037) CHO_OF4988xm09f1.ab1 CHO_OF4 Nicotiana tabacum ge... 46 0.38 1
(FH288047) CHO_OF4201xl16r1.ab1 CHO_OF4 Nicotiana tabacum ge... 46 0.38 1
(DX581105) SBA003_M05.f Sugar beet BAC library USH20 (Code S... 46 0.38 1
(AC114209) Rattus norvegicus clone CH230-198O21, WORKING DRA... 38 0.77 3
(DT483361) WS02522.B21_G03 PT-MB-N-A-15 Populus trichocarpa ... 38 0.78 2
(DT478293) WS02522.BR_G03 PT-MB-N-A-15 Populus trichocarpa c... 38 0.78 2
(AC106389) Rattus norvegicus clone CH230-140G24, WORKING DRA... 34 0.80 2
(AC195417) Pan troglodytes BAC clone CH251-141L7 from chromo... 36 0.81 2
(AC017047) Homo sapiens BAC clone RP11-323F10 from X, comple... 36 0.81 2
(AC021859) Homo sapiens chromosome UL clone RP11-585K14, WOR... 36 0.81 2
(AC213968) Sorex araneus clone SA_Ba-527P10, WORKING DRAFT S... 36 0.82 2
(AC209506) Sorex araneus clone SA_Ba-403I10, WORKING DRAFT S... 36 0.82 2
(AC107020) Homo sapiens 12 BAC RP11-271J4 (Roswell Park Canc... 34 0.83 2
(AC177040) Strongylocentrotus purpuratus clone R3-1038F06, W... 32 0.83 2
(AC119041) Homo sapiens X BAC RP11-585K14 (Roswell Park Canc... 36 0.84 2
(BZ164233) CH230-246O13.TJB CHORI-230 Segment 2 Rattus norve... 36 0.84 2
(AZ677864) ENTJG43TF Entamoeba histolytica Sheared DNA Entam... 34 0.93 2
(DQ696526) Mus musculus piRNA piR-111848, complete sequence. 44 1.5 1
(DQ691215) Mus musculus piRNA piR-106537, complete sequence. 44 1.5 1
(DQ689159) Mus musculus piRNA piR-104481, complete sequence. 44 1.5 1
(CT010485) Mouse DNA sequence from clone CH29-161F5 on chrom... 44 1.5 1
(AC144410) Mus musculus BAC clone RP23-479N14 from chromosom... 44 1.5 1
(AC125141) Mus musculus BAC clone RP24-333C3 from chromosome... 44 1.5 1
(AC149600) Medicago truncatula chromosome 2 clone mte1-41j24... 44 1.5 1
(AC096517) Rattus norvegicus clone CH230-16H15, WORKING DRAF... 44 1.5 1
(AC094818) Rattus norvegicus clone CH230-5J9, WORKING DRAFT ... 44 1.5 1
(AC179771) Strongylocentrotus purpuratus clone R3-1016G12, W... 44 1.5 1
(EK326396) 1095467008186 Global-Ocean-Sampling_GS-31-01-01-1... 44 1.5 1
(EL610360) mfcorj6c6 Medicago falcata SSH Library of cold-re... 44 1.5 1
(DW016599) EST1225560 MTY Medicago truncatula cDNA clone MTY... 44 1.5 1
(AM809520) Nicotiana tabacum EST, clone nt005043064. 44 1.5 1
(CX535183) s13dNF95C08MJ066_388543 Methyl Jasmonate-Elicited... 44 1.5 1
(CF450667) EST687012 normalized cDNA library of onion Allium... 44 1.5 1
(CF446303) EST682648 normalized cDNA library of onion Allium... 44 1.5 1
(CF442290) EST678635 normalized cDNA library of onion Allium... 44 1.5 1
(CF441532) EST677877 normalized cDNA library of onion Allium... 44 1.5 1
(BU725369) SJMCDD07 SJM Schistosoma japonicum cDNA, mRNA seq... 44 1.5 1
(BI269999) NF004A03FL1F1021 Developing flower Medicago trunc... 44 1.5 1
(BI263995) NF092E11PL1F1087 Phosphate starved leaf Medicago ... 44 1.5 1
(BI263561) NF087H10PL1F1092 Phosphate starved leaf Medicago ... 44 1.5 1
(BF642279) NF059C06IN1F1049 Insect herbivory Medicago trunca... 44 1.5 1
(BE323903) NF011A11PL1F1081 Phosphate starved leaf Medicago ... 44 1.5 1
(FD463129) LARVX40TR Haematobia irritans 1st Instar Larvae H... 44 1.5 1
(FD460561) LARVG09TR Haematobia irritans 1st Instar Larvae H... 44 1.5 1
(FD460560) LARVG09TF Haematobia irritans 1st Instar Larvae H... 44 1.5 1
(AW688186) NF004D09ST1F1000 Developing stem Medicago truncat... 44 1.5 1
(AW586765) EST318388 MHAM Medicago truncatula/Glomus versifo... 44 1.5 1
(EV255873) MTYCP88TF JCVI-MT1 Medicago truncatula cDNA 5', m... 44 1.5 1
(EU795096) Uncultured bacterium ARCTIC31_H_08 genomic sequence. 44 1.5 1
(CT572989) Mouse DNA sequence from clone RP24-176J14 on chro... 42 1.9 4
(FC593002) CAXP7337.fwd CAXP Lottia gigantea from head, foot... 34 2.6 2
(AC106661) Rattus norvegicus clone CH230-74C23, *** SEQUENCI... 32 2.8 2
(FC594766) CAXP8773.fwd CAXP Lottia gigantea from head, foot... 34 2.8 2
(AC114216) Rattus norvegicus clone CH230-315N24, *** SEQUENC... 30 2.8 2

>(AU073594) Dictyostelium discoideum slug cDNA, clone SSH623.
Length = 177

Score = 254 bits (128), Expect(2) = 2e-68
Identities = 131/131 (100%)
Strand = Plus / Plus


Query: 21 ttttaccaaatacattttcaccaaatctacaacctcaacaaccattgtcatcatcttcat 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 21 ttttaccaaatacattttcaccaaatctacaacctcaacaaccattgtcatcatcttcat 80


Query: 81 caacaataaatacaccatcatcaccaaatcaattaaattcaccctcaatngaggatcaaa 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 81 caacaataaatacaccatcatcaccaaatcaattaaattcaccctcaatngaggatcaaa 140


Query: 141 tggaggaatat 151
|||||||||||
Sbjct: 141 tggaggaatat 151

Score = 36.2 bits (18), Expect(2) = 2e-68
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 159 ttcatagagataaatata 176
||||||||||||||||||
Sbjct: 159 ttcatagagataaatata 176

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 182,857,717
Number of extensions: 12711803
Number of successful extensions: 3543038
Number of sequences better than 10.0: 286
Length of query: 176
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 154
Effective length of database: 93,199,600,587
Effective search space: 14352738490398
Effective search space used: 14352738490398
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7. 7
Homology vs Protein
Query= Contig-U13418-1 (Contig-U13418-1Q) /CSM_Contig/Contig-U13418-1Q.Seq.d
(176 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: 166,789,942
Number of extensions: 1975706
Number of successful extensions: 1590
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1590
Number of HSP's successfully gapped: 0
Length of query: 58
Length of database: 1,051,180,864
Length adjustment: 31
Effective length of query: 27
Effective length of database: 950,847,535
Effective search space: 25672883445
Effective search space used: 25672883445
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: 26 (14.6 bits)

PSORT

psg: 0.86 gvh: 0.42 alm: 0.67 top: 0.23 tms: 0.00 mit: 0.46 mip: 0.00
nuc: 0.00 erl: 0.00 erm: 0.20 pox: 0.00 px2: 0.00 vac: 0.33 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

32.0 %: nuclear
28.0 %: mitochondrial
24.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: Golgi
4.0 %: vacuolar
4.0 %: extracellular, including cell wall

>> prediction for Contig-U13418-1 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) 1
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