Contig-U14731-1
Contig ID Contig-U14731-1
Contig update 2002.12.18
Contig sequence
>Contig-U14731-1 (Contig-U14731-1Q) /CSM_Contig/Contig-U14731-1Q.Seq.d
AATAAATTTCACACACATACAAAATCAATCAAAGAAATGGCTGGTCAATA
TTGGAGAGCTGCTGGTATCACTTATTTACAATACGCTAACATTTGCGGTA
CTCATGTCCGGTAATTGTTTAAAAGAACCATTCAGAGCTGCTGCTAAAAA
TAGAGAAGGTTTCATTTCAAATACTGTCATGTACCAAAATGGCAAAGAAT
CATCAACCATCATTTTAAATTCAGAATTACTCCAAAAAGAACTTTTAGTC
AAGAAAAACTAAATTAAATATTTAAAAATATAGAATATAGTAATATAATA
TTACGAGTGATTAAAATGTATACACACAAAAAAAAAAAAAAAAAAAGAAT
TATTAAATAAATCAATTTATAAAAGAAAAAATAAAGTTTTGAAATATATT
AAACAATAAAAAAAAAAAAAACAACAAATAATAATAATAGTACACCTTTT
TTTTTAGATTACATTTTATACACTATAAAAAAAAAAAAAAAA

Gap no gap
Contig length 492
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 6394207
End point 6393732
Strand (PLUS/MINUS) MINUS
Number of clones 10
Number of EST 15
Link to clone list U14731
List of clone(s)

est1=VHD555E,1,305
est2=VSF108F,10,380
est3=VSI188F,19,337
est4=VSI188Z,19,258
est5=VSC117E,20,470
est6=VSD351F,20,337
est7=VSD351Z,20,266
est8=VSF108Z,20,259
est9=VSF776F,22,337
est10=VSF776Z,22,282
est11=VSG719F,23,337
est12=VSH459F,32,337
est13=VSH459Z,32,259
est14=VSE739Z,59,493
est15=SSK319E,160,409
Translated Amino Acid sequence
INFTHIQNQSKKWLVNIGELLVSLIYNTLTFAVLMSGNCLKEPFRAAAKNREGFISNTVM
YQNGKESSTIILNSELLQKELLVKKN*ikylki*nivi*yye*lkcihtkkkkkkellnk
siykrknkvlkyikq*kkkkqqiiiivhlff*itfytl*kkkk


Translated Amino Acid sequence (All Frames)
Frame A:
nkfhthtksikemagqywraagitylqyanicgthvr*lfkrtiqscc*k*rrfhfkych
vpkwqriinhhfkfritpkrtfsqekln*ifknieysniilrvikmythkkkkkkriik*
inl*kkk*sfeiy*tikkkkttnnnnstpffldyilytikkkkk


Frame B:
INFTHIQNQSKKWLVNIGELLVSLIYNTLTFAVLMSGNCLKEPFRAAAKNREGFISNTVM
YQNGKESSTIILNSELLQKELLVKKN*ikylki*nivi*yye*lkcihtkkkkkkellnk
siykrknkvlkyikq*kkkkqqiiiivhlff*itfytl*kkkk


Frame C:
*ishtykinqrngwsilescwyhlftir*hlryscpviv*knhselllkiekvsfqilsc
tkmaknhqpsf*iqnyskknf*srktklni*kyri**ynitsd*nvytqkkkkkkny*in
qfikekikf*nilnnkkkknnk****ytfffrlhfihykkkkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U14731-1 (Contig-U14731-1Q)
/CSM_Contig/Contig-U14731-1Q.Seq.d
(492 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U14731-1 (Contig-U14731-1Q) /CSM_Contig/Conti... 648 0.0
Contig-U12123-1 (Contig-U12123-1Q) /CSM_Contig/Conti... 40 0.002
Contig-U09816-1 (Contig-U09816-1Q) /CSM_Contig/Conti... 38 0.009
Contig-U14745-1 (Contig-U14745-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U14434-1 (Contig-U14434-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U14380-1 (Contig-U14380-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U13992-1 (Contig-U13992-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U13845-1 (Contig-U13845-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U13530-1 (Contig-U13530-1Q) /CSM_Contig/Conti... 36 0.034
Contig-U12923-1 (Contig-U12923-1Q) /CSM_Contig/Conti... 36 0.034

>Contig-U14731-1 (Contig-U14731-1Q) /CSM_Contig/Contig-U14731-1Q.Seq.d
Length = 492

Score = 648 bits (327), Expect = 0.0
Identities = 327/327 (100%)
Strand = Plus / Plus


Query: 1 aataaatttcacacacatacaaaatcaatcaaagaaatggctggtcaatattggagagct 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 aataaatttcacacacatacaaaatcaatcaaagaaatggctggtcaatattggagagct 60


Query: 61 gctggtatcacttatttacaatacgctaacatttgcggtactcatgtccggtaattgttt 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 gctggtatcacttatttacaatacgctaacatttgcggtactcatgtccggtaattgttt 120


Query: 121 aaaagaaccattcagagctgctgctaaaaatagagaaggtttcatttcaaatactgtcat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aaaagaaccattcagagctgctgctaaaaatagagaaggtttcatttcaaatactgtcat 180


Query: 181 gtaccaaaatggcaaagaatcatcaaccatcattttaaattcagaattactccaaaaaga 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 gtaccaaaatggcaaagaatcatcaaccatcattttaaattcagaattactccaaaaaga 240


Query: 241 acttttagtcaagaaaaactaaattaaatatttaaaaatatagaatatagtaatataata 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 acttttagtcaagaaaaactaaattaaatatttaaaaatatagaatatagtaatataata 300


Query: 301 ttacgagtgattaaaatgtatacacac 327
|||||||||||||||||||||||||||
Sbjct: 301 ttacgagtgattaaaatgtatacacac 327


Score = 56.0 bits (28), Expect = 4e-08
Identities = 46/55 (83%)
Strand = Plus / Plus


Query: 422 caacaaataataataatagtacaccnnnnnnnnnagattacattttatacactat 476
||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 422 caacaaataataataatagtacacctttttttttagattacattttatacactat 476


>Contig-U12123-1 (Contig-U12123-1Q) /CSM_Contig/Contig-U12123-1Q.Seq.d
Length = 1410

Score = 40.1 bits (20), Expect = 0.002
Identities = 20/20 (100%)
Strand = Plus / Minus


Query: 198 aatcatcaaccatcatttta 217
||||||||||||||||||||
Sbjct: 1194 aatcatcaaccatcatttta 1175


Score = 32.2 bits (16), Expect = 0.53
Identities = 16/16 (100%)
Strand = Plus / Plus


Query: 427 aataataataatagta 442
||||||||||||||||
Sbjct: 708 aataataataatagta 723


>Contig-U09816-1 (Contig-U09816-1Q) /CSM_Contig/Contig-U09816-1Q.Seq.d
Length = 1222

Score = 38.2 bits (19), Expect = 0.009
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 424 acaaataataataatagta 442
|||||||||||||||||||
Sbjct: 44 acaaataataataatagta 62


Score = 36.2 bits (18), Expect = 0.034
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 422 caacaaataataataata 439
||||||||||||||||||
Sbjct: 807 caacaaataataataata 824


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


Query: 427 aataataataatagt 441
|||||||||||||||
Sbjct: 86 aataataataatagt 100


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: 19,511
Number of Sequences: 6905
Number of extensions: 19511
Number of successful extensions: 9011
Number of sequences better than 10.0: 1362
length of query: 492
length of database: 5,674,871
effective HSP length: 16
effective length of query: 476
effective length of database: 5,564,391
effective search space: 2648650116
effective search space used: 2648650116
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 2008.12.30
Homology vs DNA
Query= Contig-U14731-1 (Contig-U14731-1Q) /CSM_Contig/Contig-U14731-1Q.Seq.d
(492 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

(BJ438850) Dictyostelium discoideum cDNA clone:ddv38m13, 3' ... 283 e-131 2
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720... 218 e-127 5
(AU268292) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-121 2
(AU268293) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-121 2
(AU264720) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-120 2
(AU263890) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-120 2
(AU263891) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-120 2
(AU265775) Dictyostelium discoideum vegetative cDNA clone:VS... 442 e-120 1
(AU266750) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-118 2
(AU264721) Dictyostelium discoideum vegetative cDNA clone:VS... 278 e-118 2
(AU265774) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-117 2
(AU267480) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-113 2
(AU267481) Dictyostelium discoideum vegetative cDNA clone:VS... 283 e-113 2
(AU263336) Dictyostelium discoideum vegetative cDNA clone:VS... 278 e-108 4
(AU262342) Dictyostelium discoideum vegetative cDNA clone:VS... 226 e-103 3
(BJ420237) Dictyostelium discoideum cDNA clone:ddv38m13, 5' ... 218 1e-52 1
(C91471) Dictyostelium discoideum slug cDNA, clone SSK319. 186 5e-43 1
(FH125328) CHO_OF3315xn07f1.ab1 CHO_OF3 Nicotiana tabacum ge... 52 0.019 1
(ED681696) GM_WBb0014P16.r GM_WBb Glycine max genomic clone ... 46 0.13 2
(AC123796) Mus musculus BAC clone RP24-320P9 from chromosome... 48 0.30 1
(AC116731) Mus musculus chromosome 8, clone RP23-346D17, com... 48 0.30 1
(AL732515) Zebrafish DNA sequence from clone RP71-1K13 in li... 40 0.68 3
(AC102271) Mus musculus chromosome 7, clone RP24-281C4, comp... 46 1.2 1
(AC130753) Rattus norvegicus clone CH230-182D2, WORKING DRAF... 46 1.2 1
(AC095168) Rattus norvegicus clone CH230-8L12, *** SEQUENCIN... 46 1.2 1
(AC201387) Strongylocentrotus purpuratus clone R3-17G8, WORK... 46 1.2 1
(BU391455) 603510380F1 CSEQCHN57 Gallus gallus cDNA clone Ch... 46 1.2 1
(CG025237) ZMMBBc0563E05f ZMMBBc Zea mays subsp. mays genomi... 38 3.6 2
(AC153061) Bos taurus clone CH240-18J24, *** SEQUENCING IN P... 42 3.7 3
(CR933761) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 40 4.5 4
(CU466377) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 38 4.6 2
(AC176595) Strongylocentrotus purpuratus clone R3-3077O12, W... 44 4.6 1
(EC333049) GUTF089627D16 POSSUM_01-POSSUM-GUT-2KB Trichosuru... 44 4.6 1
(EC326387) GUTF089550P21 POSSUM_01-POSSUM-GUT-2KB Trichosuru... 44 4.6 1
(DY610018) IMMUNEF045823F18 POSSUM_01-C-POSSUM-IMMUNE-2KB Tr... 44 4.6 1
(DY593895) GUTF054259J17 POSSUM_01-POSSUM-GUT-2KB Trichosuru... 44 4.6 1
(DY592629) GUTF031292J5 POSSUM_01-POSSUM-GUT-2KB Trichosurus... 44 4.6 1
(CA152034) SCJFRZ2015B02.g RZ2 Saccharum officinarum cDNA cl... 44 4.6 1
(CU468342) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 42 5.2 2
(CG245595) OG4AL93TC ZM_0.7_1.5_KB Zea mays genomic clone ZM... 38 5.3 2
(CZ566954) p_bW013RE23Q_C12_046 WAG Gallus gallus genomic cl... 34 6.1 2
(AC177766) Strongylocentrotus purpuratus clone R3-1005H21, W... 42 6.2 3
(AC115682) Dictyostelium discoideum chromosome 2 map 4101105... 42 6.5 2
(BX511148) Zebrafish DNA sequence from clone DKEY-174N20 in ... 34 7.4 4
(AU073641) Dictyostelium discoideum slug cDNA, clone SSH723. 38 8.0 2
(AU072096) Dictyostelium discoideum slug cDNA, clone SSD414. 38 8.0 2
(AC103147) Rattus norvegicus clone CH230-36D10, *** SEQUENCI... 32 8.2 2
(AC111439) Rattus norvegicus clone CH230-181N11, *** SEQUENC... 32 8.2 2
(AF327988) Neon nelli cytochrome oxidase subunit I (COI) gen... 34 8.8 2

>(BJ438850) Dictyostelium discoideum cDNA clone:ddv38m13, 3' end,
single read.
Length = 304

Score = 283 bits (143), Expect(2) = e-131
Identities = 143/143 (100%)
Strand = Plus / Minus


Query: 111 gtaattgtttaaaagaaccattcagagctgctgctaaaaatagagaaggtttcatttcaa 170
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 195 gtaattgtttaaaagaaccattcagagctgctgctaaaaatagagaaggtttcatttcaa 136


Query: 171 atactgtcatgtaccaaaatggcaaagaatcatcaaccatcattttaaattcagaattac 230
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 135 atactgtcatgtaccaaaatggcaaagaatcatcaaccatcattttaaattcagaattac 76


Query: 231 tccaaaaagaacttttagtcaag 253
|||||||||||||||||||||||
Sbjct: 75 tccaaaaagaacttttagtcaag 53

Score = 218 bits (110), Expect(2) = e-131
Identities = 110/110 (100%)
Strand = Plus / Minus


Query: 1 aataaatttcacacacatacaaaatcaatcaaagaaatggctggtcaatattggagagct 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 304 aataaatttcacacacatacaaaatcaatcaaagaaatggctggtcaatattggagagct 245


Query: 61 gctggtatcacttatttacaatacgctaacatttgcggtactcatgtccg 110
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 244 gctggtatcacttatttacaatacgctaacatttgcggtactcatgtccg 195

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 419,177,660
Number of extensions: 30565869
Number of successful extensions: 5197881
Number of sequences better than 10.0: 49
Length of query: 492
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 469
Effective length of database: 93,106,754,628
Effective search space: 43667067920532
Effective search space used: 43667067920532
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.12
Homology vs Protein
Query= Contig-U14731-1 (Contig-U14731-1Q) /CSM_Contig/Contig-U14731-1Q.Seq.d
(492 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

CP001323_372(CP001323|pid:none) Micromonas sp. RCC299 chromosome... 32 0.004
AM443881_1(AM443881|pid:none) Vitis vinifera contig VV78X222712.... 40 0.030
EU963780_1(EU963780|pid:none) Zea mays clone 272605 ATP synthase... 40 0.039
(Q41898) RecName: Full=ATP synthase subunit epsilon, mitochondri... 39 0.051
EU976807_1(EU976807|pid:none) Zea mays clone 990677 ATP synthase... 39 0.051
EF145629_1(EF145629|pid:none) Populus trichocarpa clone WS0112_C... 38 0.15
EF146348_1(EF146348|pid:none) Populus trichocarpa clone WS0117_G... 38 0.15
EF148458_1(EF148458|pid:none) Populus trichocarpa x Populus delt... 38 0.15
AK243027_1(AK243027|pid:none) Oryza sativa Japonica Group cDNA, ... 37 0.20
AP005799_18(AP005799|pid:none) Oryza sativa Japonica Group genom... 37 0.20
AP008214_624(AP008214|pid:none) Oryza sativa (japonica cultivar-... 37 0.20
(Q96253) RecName: Full=ATP synthase subunit epsilon, mitochondri... 37 0.33
DQ413201_1(DQ413201|pid:none) Acyrthosiphon pisum isolate WHAP00... 36 0.43
AJ487471_1(AJ487471|pid:none) Cicer arietinum mRNA for putative ... 36 0.43
CR954207_206(CR954207|pid:none) Ostreococcus tauri strain OTTH05... 36 0.43
AE014298_2349(AE014298|pid:none) Drosophila melanogaster chromos... 34 1.7
AE014298_2350(AE014298|pid:none) Drosophila melanogaster chromos... 34 1.7
EU574833_1(EU574833|pid:none) Ornithodoros coriaceus clone OC-36... 34 2.2
BT078468_1(BT078468|pid:none) Lepeophtheirus salmonis Pacific fo... 33 2.8
DQ215179_1(DQ215179|pid:none) Taeniopygia guttata clone 0058P002... 33 4.8
BT081719_1(BT081719|pid:none) Rana catesbeiana clone rcat-evr-53... 32 6.3
(P56381) RecName: Full=ATP synthase subunit epsilon, mitochondri... 32 6.3
DQ215172_1(DQ215172|pid:none) Taeniopygia guttata clone 0064P001... 32 6.3
AY341883_1(AY341883|pid:none) Macaca mulatta H+ transporting F1 ... 32 6.3
(P05632) RecName: Full=ATP synthase subunit epsilon, mitochondri... 32 6.3
AY341874_1(AY341874|pid:none) Xenopus laevis H+ transporting F1 ... 32 6.3
PWBOE(S08239;S10042;C39566) H+-transporting two-sector ATPase (E... 32 6.3
EF191638_1(EF191638|pid:none) Taeniopygia guttata clone 0064P001... 32 6.3

>CP001323_372(CP001323|pid:none) Micromonas sp. RCC299 chromosome 2,
complete sequence.
Length = 74

Score = 32.0 bits (71), Expect(2) = 0.004
Identities = 11/24 (45%), Positives = 18/24 (75%)
Frame = +1

Query: 40 AGQYWRAAGITYLQYANICGTHVR 111
+ YWR AG++YL+Y+++C VR
Sbjct: 7 SASYWRIAGMSYLKYSSMCAEVVR 30

Score = 30.4 bits (67), Expect(2) = 0.004
Identities = 13/33 (39%), Positives = 18/33 (54%)
Frame = +2

Query: 116 CLKEPFRAAAKNREGFISNTVMYQNGKESSTII 214
CLKEPF AK RE +V + +GK ++
Sbjct: 32 CLKEPFLTKAKPREAVYFKSVKWTDGKPGKPVV 64

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: 565,216,849
Number of extensions: 9439298
Number of successful extensions: 16844
Number of sequences better than 10.0: 28
Number of HSP's gapped: 16843
Number of HSP's successfully gapped: 29
Length of query: 164
Length of database: 1,051,180,864
Length adjustment: 118
Effective length of query: 46
Effective length of database: 669,266,902
Effective search space: 30786277492
Effective search space used: 30786277492
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: 0.65 gvh: 0.61 alm: 0.32 top: 0.53 tms: 0.00 mit: 0.25 mip: 0.00
nuc: 0.00 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

32.0 %: nuclear
28.0 %: mitochondrial
24.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: vacuolar
4.0 %: peroxisomal
4.0 %: endoplasmic reticulum

>> prediction for Contig-U14731-1 is nuc

VS (DIR, S) 8
VH (FL, L) 1
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