Contig-U13435-1
Contig ID Contig-U13435-1
Contig update 2002.12.18
Contig sequence
>Contig-U13435-1 (Contig-U13435-1Q) /CSM_Contig/Contig-U13435-1Q.Seq.d
TTTATTTATAATACAATTTTAAATCATAAATATTTAACATCATTATCCAT
TACACATCGTTGTCCTGAAAGTTTTGAATTGAATCAGTTTTATACTGGTT
CTTATCAATCAAGTTCAACATCGATATCGAGGGAATTTATTGAGAATTTC
GGTTCAATGATTTTAAATAATCAATCAATAAAGTCATTAAGATTATCTGG
ATTTCATACACCTTCACTATTTGAATATGTTATGGCAAATAAAAGAATAA
TAAAGTATAAATCGGAATTCATTGATACTTTAAATAATTCAAAATATTAT
ATTGACACAATTAGTAATTTATTAAAAATTAATCCAACAATTATTAAATT
TCATTTACATGAAATTAGTTTCACTGGTGATTATATAAGGAAAAACTATT
TAACATTTAAATGTTTTTATAATAAATCAATTAAAAATTAAATAAAATTG
AATCCATATTGTGATTTCAAAAAAAAAAAATAAAAAAAAAAAAAAATAAA
ATGAAAAATAAAAAAAAAA

Gap no gap
Contig length 519
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4934948
End point 4935467
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13435
List of clone(s)

est1=SSK139Z,1,520
Translated Amino Acid sequence
FIYNTILNHKYLTSLSITHRCPESFELNQFYTGSYQSSSTSISREFIENFGSMILNNQSI
KSLRLSGFHTPSLFEYVMANKRIIKYKSEFIDTLNNSKYYIDTISNLLKINPTIIKFHLH
EISFTGDYIRKNYLTFKCFYNKSIKN*iklnpycdfkkkk*kkkkik*kikkk


Translated Amino Acid sequence (All Frames)
Frame A:
FIYNTILNHKYLTSLSITHRCPESFELNQFYTGSYQSSSTSISREFIENFGSMILNNQSI
KSLRLSGFHTPSLFEYVMANKRIIKYKSEFIDTLNNSKYYIDTISNLLKINPTIIKFHLH
EISFTGDYIRKNYLTFKCFYNKSIKN*iklnpycdfkkkk*kkkkik*kikkk


Frame B:
lfiiqf*iini*hhyplhivvlkvln*isfilvlinqvqhryrgnllrisvq*f*iinq*
sh*dyldfihlhylnmlwqike**sinrnslil*iiqniiltqlviy*kliqqllnfiym
klvslvii*gkti*hlnvfiinqlkik*n*ihiviskkknkkkkk*nek*kk


Frame C:
yl*ynfks*ifniiihytsls*kf*iesvlywflsikfnidiegiy*efrfndfk*sink
vikiiwisytfti*icygk*knnkv*igih*yfk*fkily*hn**fikn*snny*isft*
n*fhw*lykeklfni*mfl**in*klnkiesil*fqkkkikkkknkmknkkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13435-1 (Contig-U13435-1Q)
/CSM_Contig/Contig-U13435-1Q.Seq.d
(519 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U13435-1 (Contig-U13435-1Q) /CSM_Contig/Conti... 773 0.0
Contig-U06782-1 (Contig-U06782-1Q) /CSM_Contig/Conti... 38 0.009
Contig-U13824-1 (Contig-U13824-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U12236-1 (Contig-U12236-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U11902-1 (Contig-U11902-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U11366-1 (Contig-U11366-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U11106-1 (Contig-U11106-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U10639-1 (Contig-U10639-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U10403-1 (Contig-U10403-1Q) /CSM_Contig/Conti... 36 0.036
Contig-U05003-1 (Contig-U05003-1Q) /CSM_Contig/Conti... 36 0.036

>Contig-U13435-1 (Contig-U13435-1Q) /CSM_Contig/Contig-U13435-1Q.Seq.d
Length = 519

Score = 773 bits (390), Expect = 0.0
Identities = 390/390 (100%)
Strand = Plus / Plus


Query: 1 tttatttataatacaattttaaatcataaatatttaacatcattatccattacacatcgt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 tttatttataatacaattttaaatcataaatatttaacatcattatccattacacatcgt 60


Query: 61 tgtcctgaaagttttgaattgaatcagttttatactggttcttatcaatcaagttcaaca 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tgtcctgaaagttttgaattgaatcagttttatactggttcttatcaatcaagttcaaca 120


Query: 121 tcgatatcgagggaatttattgagaatttcggttcaatgattttaaataatcaatcaata 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcgatatcgagggaatttattgagaatttcggttcaatgattttaaataatcaatcaata 180


Query: 181 aagtcattaagattatctggatttcatacaccttcactatttgaatatgttatggcaaat 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aagtcattaagattatctggatttcatacaccttcactatttgaatatgttatggcaaat 240


Query: 241 aaaagaataataaagtataaatcggaattcattgatactttaaataattcaaaatattat 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aaaagaataataaagtataaatcggaattcattgatactttaaataattcaaaatattat 300


Query: 301 attgacacaattagtaatttattaaaaattaatccaacaattattaaatttcatttacat 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 attgacacaattagtaatttattaaaaattaatccaacaattattaaatttcatttacat 360


Query: 361 gaaattagtttcactggtgattatataagg 390
||||||||||||||||||||||||||||||
Sbjct: 361 gaaattagtttcactggtgattatataagg 390


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


Query: 449 tgaatccatattgtgatttc 468
||||||||||||||||||||
Sbjct: 449 tgaatccatattgtgatttc 468


>Contig-U06782-1 (Contig-U06782-1Q) /CSM_Contig/Contig-U06782-1Q.Seq.d
Length = 316

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


Query: 236 caaataaaagaataataaa 254
|||||||||||||||||||
Sbjct: 29 caaataaaagaataataaa 47


>Contig-U13824-1 (Contig-U13824-1Q) /CSM_Contig/Contig-U13824-1Q.Seq.d
Length = 1010

Score = 36.2 bits (18), Expect = 0.036
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 5 tttataatacaattttaa 22
||||||||||||||||||
Sbjct: 120 tttataatacaattttaa 103


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: 10,280
Number of Sequences: 6905
Number of extensions: 10280
Number of successful extensions: 1232
Number of sequences better than 10.0: 407
length of query: 519
length of database: 5,674,871
effective HSP length: 16
effective length of query: 503
effective length of database: 5,564,391
effective search space: 2798888673
effective search space used: 2798888673
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-U13435-1 (Contig-U13435-1Q) /CSM_Contig/Contig-U13435-1Q.Seq.d
(519 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

(C91373) Dictyostelium discoideum slug cDNA, clone SSK139. 559 e-175 3
(AL929354) Plasmodium falciparum strain 3D7, chromosome 5, s... 52 0.020 1
(AC095893) Rattus norvegicus clone CH230-10N8, *** SEQUENCIN... 42 0.044 3
(CU914642) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 50 0.079 1
(BH457128) BOHAR94TF BOHA Brassica oleracea genomic clone BO... 50 0.079 1
(BZ460819) BONMW30TR BO_1.6_2_KB_tot Brassica oleracea genom... 50 0.079 1
(FG607144) stem_S019_C11.SEQ Opium poppy stem cDNA library P... 48 0.31 1
(FG603382) PF_T3_51R_F04_14Aug2003_022 Opium poppy root cDNA... 48 0.31 1
(FF635596) G825P572FH2.T0 Acorn worm normalized gastrula pEx... 40 1.1 2
(BX005125) Zebrafish DNA sequence from clone CH211-127I16 in... 46 1.2 1
(BV615955) S217P60439RB3.T0 Noemie Pan troglodytes troglodyt... 46 1.2 1
(AL356866) Human DNA sequence from clone RP11-211D10 on chro... 46 1.2 1
(AC069510) Homo sapiens 3 BAC RP11-395P20 (Roswell Park Canc... 46 1.2 1
(AC149240) Muntiacus muntjak vaginalis clone CH244-83P16, WO... 46 1.2 1
(AC182219) Bos taurus clone CH240-515C3, WORKING DRAFT SEQUE... 46 1.2 1
(EK382943) 1095469469290 Global-Ocean-Sampling_GS-31-01-01-1... 46 1.2 1
(EK374305) 1095469432041 Global-Ocean-Sampling_GS-31-01-01-1... 46 1.2 1
(AC180531) Strongylocentrotus purpuratus clone R3-3098G20, W... 42 1.3 2
(FF667231) G826P5361FH6.T0 Acorn worm normalized juvenile pE... 40 1.4 2
(FF635898) G825P575FD11.T0 Acorn worm normalized gastrula pE... 40 1.5 2
(FF505758) G709P5200FH9.T0 Acorn worm normalized neurula pEx... 40 1.5 2
(FF615419) G825P5186FE10.T0 Acorn worm normalized gastrula p... 40 1.6 2
(AC179079) Strongylocentrotus purpuratus clone R3-4009H20, W... 42 1.6 2
(FF513793) G709P569FE7.T0 Acorn worm normalized neurula pExp... 40 1.7 2
(AC180146) Strongylocentrotus purpuratus clone R3-4004B14, W... 42 1.7 2
(AC181503) Strongylocentrotus purpuratus clone R3-58G5, WORK... 42 1.8 2
(CP000942) Ureaplasma parvum serovar 3 str. ATCC 27815, comp... 38 2.2 8
(BX005151) Zebrafish DNA sequence from clone CH211-11M20. 34 2.5 2
(AL935049) Zebrafish DNA sequence from clone CH211-185K2 in ... 40 2.5 3
(BJ336448) Dictyostelium discoideum cDNA clone:dda53o19, 5' ... 36 3.0 2
(BJ334137) Dictyostelium discoideum cDNA clone:dda45c11, 5' ... 36 3.0 2
(BJ393869) Dictyostelium discoideum cDNA clone:dds32m23, 5' ... 36 3.2 2
(CZ929558) 246976 Tomato EcoRI BAC Library Solanum lycopersi... 34 3.2 2
(AC015905) Homo sapiens clone RP11-44A10, WORKING DRAFT SEQU... 38 3.7 3
(CU861902) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 38 3.8 4
(AL732482) Mouse DNA sequence from clone RP23-199C21 on chro... 42 4.1 4
(AC116957) Dictyostelium discoideum chromosome 2 map 1685067... 38 4.5 7
(CR382301) Zebrafish DNA sequence from clone CH211-257P1 in ... 44 4.9 1
(BX649440) Zebrafish DNA sequence from clone CH211-198M12 in... 44 4.9 1
(BX119901) Zebrafish DNA sequence from clone CH211-194D7 in ... 44 4.9 1
(CR382138) Debaryomyces hansenii chromosome F of strain CBS7... 44 4.9 1
(AC189617) Brassica rapa subsp. pekinensis clone KBrH102A07,... 44 4.9 1
(AC152843) Muntiacus muntjak vaginalis clone CH244-547G20, W... 44 4.9 1
(AC112008) Rattus norvegicus clone CH230-236B13, WORKING DRA... 44 4.9 1
(AC108637) Rattus norvegicus clone CH230-276G19, *** SEQUENC... 44 4.9 1
(CU467779) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 44 4.9 1
(AC212632) Solanum lycopersicum chromosome 7 clone C07HBa012... 44 4.9 1
(AC181066) Strongylocentrotus purpuratus clone R3-3050C22, W... 44 4.9 1
(AC178116) Strongylocentrotus purpuratus clone R3-3074C01, W... 44 4.9 1
(AC176548) Strongylocentrotus purpuratus clone R3-114H03, WO... 44 4.9 1
(AC168700) Strongylocentrotus purpuratus clone R3-3014D17, W... 44 4.9 1
(AC165372) Muntiacus reevesi clone CH245-186H24, WORKING DRA... 44 4.9 1
(AM678170) Entamoeba terrapinae GSS, clone terra161d08.q1k. 44 4.9 1
(AM676767) Entamoeba terrapinae GSS, clone terra122f05.p1k. 44 4.9 1
(ED730588) GM_WBb0087H23.r GM_WBb Glycine max genomic clone ... 44 4.9 1
(AL438817) T3 end of clone XBC0AA002F05 of library XBC0AA fr... 44 4.9 1
(AL436488) T3 end of clone BC0AA003F03 of library BC0AA from... 44 4.9 1
(AG987967) Hemicentrotus pulcherrimus BAC clone: BUB1-11B24_... 44 4.9 1
(BZ164025) CH230-276D16.TJB CHORI-230 Segment 2 Rattus norve... 44 4.9 1
(BX227980) Danio rerio genomic clone DKEY-245K1, genomic sur... 44 4.9 1
(BH734515) BOMOT94TR BO_2_3_KB Brassica oleracea genomic clo... 44 4.9 1
(AI731095) BNLGHi8663 Six-day Cotton fiber Gossypium hirsutu... 44 4.9 1
(AI730686) BNLGHi7677 Six-day Cotton fiber Gossypium hirsutu... 44 4.9 1
(DX542332) GH_MBb0030B10f GH_MBb Gossypium hirsutum genomic ... 32 5.0 3
(FF635665) G825P573FD11.T0 Acorn worm normalized gastrula pE... 38 5.5 2
(AC102418) Mus musculus chromosome 3, clone RP24-499L10, com... 38 6.1 2
(EL502820) E02_PFLAB1-LARGE-PLATE11B.AB1 Blood stage Plasmod... 40 7.7 2
(AC130928) Rattus norvegicus clone CH230-24G1, *** SEQUENCIN... 30 8.6 2
(AC111340) Rattus norvegicus clone CH230-239C23, *** SEQUENC... 30 8.7 2
(BX005431) Zebrafish DNA sequence from clone CH211-214G2 in ... 32 8.7 2
(AL161897) Human DNA sequence from clone RP11-262G14 on chro... 36 8.8 4
(DU944336) 364705 Tomato EcoRI BAC Library Solanum lycopersi... 38 9.6 2
(CT573396) Zebrafish DNA sequence from clone DKEY-88N10 in l... 32 9.9 2

>(C91373) Dictyostelium discoideum slug cDNA, clone SSK139.
Length = 520

Score = 559 bits (282), Expect(3) = e-175
Identities = 282/282 (100%)
Strand = Plus / Plus


Query: 1 tttatttataatacaattttaaatcataaatatttaacatcattatccattacacatcgt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 tttatttataatacaattttaaatcataaatatttaacatcattatccattacacatcgt 60


Query: 61 tgtcctgaaagttttgaattgaatcagttttatactggttcttatcaatcaagttcaaca 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tgtcctgaaagttttgaattgaatcagttttatactggttcttatcaatcaagttcaaca 120


Query: 121 tcgatatcgagggaatttattgagaatttcggttcaatgattttaaataatcaatcaata 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcgatatcgagggaatttattgagaatttcggttcaatgattttaaataatcaatcaata 180


Query: 181 aagtcattaagattatctggatttcatacaccttcactatttgaatatgttatggcaaat 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aagtcattaagattatctggatttcatacaccttcactatttgaatatgttatggcaaat 240


Query: 241 aaaagaataataaagtataaatcggaattcattgatacttta 282
||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aaaagaataataaagtataaatcggaattcattgatacttta 282

Score = 79.8 bits (40), Expect(3) = e-175
Identities = 40/40 (100%)
Strand = Plus / Plus


Query: 351 tcatttacatgaaattagtttcactggtgattatataagg 390
||||||||||||||||||||||||||||||||||||||||
Sbjct: 351 tcatttacatgaaattagtttcactggtgattatataagg 390

Score = 38.2 bits (19), Expect(3) = e-175
Identities = 19/19 (100%)
Strand = Plus / Plus


Query: 450 gaatccatattgtgatttc 468
|||||||||||||||||||
Sbjct: 450 gaatccatattgtgatttc 468

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 433,542,148
Number of extensions: 27281816
Number of successful extensions: 2289929
Number of sequences better than 10.0: 74
Length of query: 519
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 496
Effective length of database: 93,106,754,628
Effective search space: 46180950295488
Effective search space used: 46180950295488
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7. 7
Homology vs Protein
Query= Contig-U13435-1 (Contig-U13435-1Q) /CSM_Contig/Contig-U13435-1Q.Seq.d
(519 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

AC115584_8(AC115584|pid:none) Dictyostelium discoideum chromosom... 45 0.001
EF203088_47(EF203088|pid:none) Gryllus bimaculatus nudivirus, co... 39 0.077
CP000716_380(CP000716|pid:none) Thermosipho melanesiensis BI429,... 34 1.9
AM180355_370(AM180355|pid:none) Clostridium difficile 630 comple... 33 3.2
CP000393_2230(CP000393|pid:none) Trichodesmium erythraeum IMS101... 33 5.5
AJ749949_232(AJ749949|pid:none) Francisella tularensis subsp. tu... 32 7.2
AY967090_1(AY967090|pid:none) Synthetic construct isolate FTT023... 32 7.2
AC153123_34(AC153123|pid:none) Medicago truncatula clone mte1-72... 32 7.2
AE009951_1552(AE009951|pid:none) Fusobacterium nucleatum subsp. ... 32 9.4
CP000939_3168(CP000939|pid:none) Clostridium botulinum B1 str. O... 32 9.4
AC117075_27(AC117075|pid:none) Dictyostelium discoideum chromoso... 32 9.4
CR940347_912(CR940347|pid:none) Theileria annulata strain Ankara... 32 9.4

>AC115584_8(AC115584|pid:none) Dictyostelium discoideum chromosome 2
map complement(3622543-3568102) strain AX4, complete
sequence.
Length = 604

Score = 45.1 bits (105), Expect = 0.001
Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 4/124 (3%)
Frame = +1

Query: 16 ILNHKYLTSLSITHRCPESFELNQFYTGXXXXXXXXXXREFIENFGSMILNNQSIKSLRL 195
I NH L SL I C E+ E+ +F F++ FGSMI + ++ L +
Sbjct: 447 IENHNSLESLHIGQECKENGEVMEF--SQRKQRSIKLSNAFVKEFGSMISSIAPLRKLSI 504

Query: 196 SGFHTPSLFEYVMA-NKRIIKYKSEFIDTLNNSKYYID---TISNLLKINPTIIKFHLHE 363
G ++ L Y+ + NK+I KY +++ Y D TI ++L NP I +
Sbjct: 505 LGLNSDQLIRYISSINKKITKY-FHVESIMDDGSYAHDDTPTIQSILVDNPQITDLKHTK 563

Query: 364 ISFT 375
FT
Sbjct: 564 FVFT 567

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: 652,196,991
Number of extensions: 11497613
Number of successful extensions: 23888
Number of sequences better than 10.0: 12
Number of HSP's gapped: 23879
Number of HSP's successfully gapped: 12
Length of query: 173
Length of database: 1,051,180,864
Length adjustment: 120
Effective length of query: 53
Effective length of database: 662,793,784
Effective search space: 35128070552
Effective search space used: 35128070552
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: 0.39 alm: 0.50 top: 0.60 tms: 0.00 mit: 0.41 mip: 0.05
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

40.0 %: mitochondrial
24.0 %: cytoplasmic
24.0 %: nuclear
8.0 %: vacuolar
4.0 %: peroxisomal

>> prediction for Contig-U13435-1 is mit

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