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Dicty_cDB
Contig List | Clone List | cDNA Library List
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U05770-1
Contig ID Contig-U05770-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U05770-1 (Contig-U05770-1Q) /CSM_Contig/Contig-U05770-1Q.Seq.d
AACAAATTATGAAAATCAAAGATTTAATAATTCAAACTGTTGTAGAAGGT
GGTGAAATTTTAGATGATTCTGCTTGTGATTTATTGGAATTCTTAAAAGA
AGTTGCATCAAAACAAGAATTACAAAAANCTAAAGAAAGACAAAGACTTC
AAGAAGAAAAAGAAAATAAAGCCAAAAATTCTGTATTCTTTAAATTCTCC
TCAAAATTCTCTTCAAAAAGGAGATCCAAAGATGGAAAAAATCAACCACT
CTCTCCACCATTATCATCACAAAATAGTCAACAAGAAAAAGATTCTCCAA
ATTCTGGTGCAGCATTATCTTTAAATAATTAATTTAAAAAAAAAAAAAAA
AAAAAAAAGAAAAACAATTAAAAACAATTAAAAACTTGTACATATAATAT
TATATATATATTTTTTTTTATGCACTGTATAACAAAGAAAAAAAAGAATA
AATAATTTAAAAAAAAAAATAAAA
Gap no gap
Contig length 474
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 1664755
End point 1665230
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U05770
List of clone(s) 

est1=SSL446E,1,475
Translated Amino Acid sequence 
QIMKIKDLIIQTVVEGGEILDDSACDLLEFLKEVASKQELQKXKERQRLQEEKENKAKNS
VFFKFSSKFSSKRRSKDGKNQPLSPPLSSQNSQQEKDSPNSGAALSLNN*fkkkkkkkkk
nn*kqlktctyniiyifffmhcitkkkknk*fkkknk
Translated Amino Acid sequence (All Frames) 
Frame A:
nkl*kski**fkll*kvvkf*millviywns*kklhqnknykxlkkdkdfkkkkkikpki
lyslnspqnslqkgdpkmekinhslhhyhhkivnkkkilqilvqhyl*iinlkkkkkkkr
ktiknn*klvhiilyiyfflctv*qrkkrinnlkkkik


Frame B:
tnyenqrfnnsnccrrw*nfr*fcl*figilkrsciktritkx*rktktsrrkrk*sqkf
cil*illkilfkkeiqrwkksttlstiiitk*strkrfskfwcsiifk*li*kkkkkkke
kqlktiknlyi*yyiyiffyalynkekke*ii*kkk*


Frame C:
QIMKIKDLIIQTVVEGGEILDDSACDLLEFLKEVASKQELQKXKERQRLQEEKENKAKNS
VFFKFSSKFSSKRRSKDGKNQPLSPPLSSQNSQQEKDSPNSGAALSLNN*fkkkkkkkkk
nn*kqlktctyniiyifffmhcitkkkknk*fkkknk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05770-1 (Contig-U05770-1Q)
/CSM_Contig/Contig-U05770-1Q.Seq.d
         (474 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05770-1 (Contig-U05770-1Q) /CSM_Contig/Conti...   311  4e-85
Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Conti...    44  1e-04
Contig-U14828-1 (Contig-U14828-1Q) /CSM_Contig/Conti...    36  0.033
Contig-U10771-1 (Contig-U10771-1Q) /CSM_Contig/Conti...    36  0.033
Contig-U08908-1 (Contig-U08908-1Q) /CSM_Contig/Conti...    36  0.033
Contig-U01808-1 (Contig-U01808-1Q) /CSM_Contig/Conti...    36  0.033
Contig-U01196-1 (Contig-U01196-1Q) /CSM_Contig/Conti...    36  0.033
Contig-U12030-1 (Contig-U12030-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11282-1 (Contig-U11282-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11267-1 (Contig-U11267-1Q) /CSM_Contig/Conti...    34  0.13

>Contig-U05770-1 (Contig-U05770-1Q) /CSM_Contig/Contig-U05770-1Q.Seq.d
          Length = 474

 Score =  311 bits (157), Expect = 4e-85
 Identities = 157/157 (100%)
 Strand = Plus / Plus

                                                                       
Query: 179 ttctgtattctttaaattctcctcaaaattctcttcaaaaaggagatccaaagatggaaa 238
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179 ttctgtattctttaaattctcctcaaaattctcttcaaaaaggagatccaaagatggaaa 238

                                                                       
Query: 239 aaatcaaccactctctccaccattatcatcacaaaatagtcaacaagaaaaagattctcc 298
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 239 aaatcaaccactctctccaccattatcatcacaaaatagtcaacaagaaaaagattctcc 298

                                                
Query: 299 aaattctggtgcagcattatctttaaataattaattt 335
           |||||||||||||||||||||||||||||||||||||
Sbjct: 299 aaattctggtgcagcattatctttaaataattaattt 335


 Score =  254 bits (128), Expect = 7e-68
 Identities = 128/128 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aacaaattatgaaaatcaaagatttaataattcaaactgttgtagaaggtggtgaaattt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aacaaattatgaaaatcaaagatttaataattcaaactgttgtagaaggtggtgaaattt 60

                                                                       
Query: 61  tagatgattctgcttgtgatttattggaattcttaaaagaagttgcatcaaaacaagaat 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tagatgattctgcttgtgatttattggaattcttaaaagaagttgcatcaaaacaagaat 120

                   
Query: 121 tacaaaaa 128
           ||||||||
Sbjct: 121 tacaaaaa 128


 Score = 52.0 bits (26), Expect = 6e-07
 Identities = 26/26 (100%)
 Strand = Plus / Plus

                                     
Query: 385 cttgtacatataatattatatatata 410
           ||||||||||||||||||||||||||
Sbjct: 385 cttgtacatataatattatatatata 410


 Score = 28.2 bits (14), Expect = 8.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 392 atataatattatat 405
           ||||||||||||||
Sbjct: 405 atataatattatat 392


>Contig-U12399-1 (Contig-U12399-1Q) /CSM_Contig/Contig-U12399-1Q.Seq.d
          Length = 1368

 Score = 44.1 bits (22), Expect = 1e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                  
Query: 107  atcaaaacaagaattacaaaaa 128
            ||||||||||||||||||||||
Sbjct: 1073 atcaaaacaagaattacaaaaa 1094


 Score = 32.2 bits (16), Expect = 0.51
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 110  aaaacaagaattacaa 125
            ||||||||||||||||
Sbjct: 1097 aaaacaagaattacaa 1112


>Contig-U14828-1 (Contig-U14828-1Q) /CSM_Contig/Contig-U14828-1Q.Seq.d
          Length = 112

 Score = 36.2 bits (18), Expect = 0.033
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 392 atataatattatatatat 409
           ||||||||||||||||||
Sbjct: 6   atataatattatatatat 23


 Score = 28.2 bits (14), Expect = 8.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 392 atataatattatat 405
           ||||||||||||||
Sbjct: 19  atataatattatat 6


  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: 7283
Number of Sequences: 6905
Number of extensions: 7283
Number of successful extensions: 912
Number of sequences better than 10.0: 303
length of query: 474
length of database: 5,674,871
effective HSP length: 16
effective length of query: 458
effective length of database: 5,564,391
effective search space: 2548491078
effective search space used: 2548491078
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. 6
Homology vs DNA 
Query= Contig-U05770-1 (Contig-U05770-1Q) /CSM_Contig/Contig-U05770-1Q.Seq.d
         (474 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

(AU038760) Dictyostelium discoideum slug cDNA, clone SSL446.      200   6e-58  3
(AU074649) Dictyostelium discoideum slug cDNA, clone SSL446.      186   1e-48  2
(AC203845) Zea mays chromosome 1 clone CH201-248I12; ZMMBBc0...    48   0.28   1
(AC200879) Zea mays chromosome 1 clone CH201-257M2; ZMMBBc02...    48   0.28   1
(CG129935) PUIAI82TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    48   0.28   1
(CG129933) PUIAI82TB ZM_0.6_1.0_KB Zea mays genomic clone ZM...    48   0.28   1
(CC982334) ZUAF465TH ZM_3.0_4.0_KB Zea mays genomic clone ZM...    48   0.28   1
(AC182850) Bos taurus clone CH240-330N20, WORKING DRAFT SEQU...    42   0.35   2
(AC124649) Homo sapiens chromosome 8, clone RP11-23I8, compl...    44   0.36   2
(AC016756) Homo sapiens chromosome 8 clone RP11-521M14, WORK...    44   0.39   2
(AC090150) Homo sapiens chromosome 8, clone RP11-521M14, com...    44   0.39   2
(AE001401) Plasmodium falciparum 3D7 chromosome 2 section 38...    40   0.41   2
(AM457502) Vitis vinifera contig VV78X187425.3, whole genome...    44   0.69   2
(AC157311) Bos taurus clone CH240-67D7, WORKING DRAFT SEQUEN...    40   0.77   4
(FC268533) CAGN17745.rev CAGN Nematostella vectensis Nemve m...    36   0.80   2
(FC314223) CAIC4286.fwd CAIC Nematostella vectensis Nemve wh...    36   0.80   2
(FC317959) CAIC6480.rev CAIC Nematostella vectensis Nemve wh...    36   0.80   2
(AC170496) Bos taurus clone CH240-226E16, WORKING DRAFT SEQU...    40   0.88   3
(BX293991) Zebrafish DNA sequence from clone CH211-261I24 in...    40   0.94   3
(AC219942) Bos taurus clone CH240-318F11, WORKING DRAFT SEQU...    40   0.95   3
(AC185074) Bos taurus clone CH240-190B2, WORKING DRAFT SEQUE...    36   1.1    3
(BB201854) Mus musculus 0 day neonate thymus cDNA, RIKEN ful...    46   1.1    1
(EY487757) CBBP16003.fwd CBBP Hirudo medicinalis hermaphrodi...    46   1.1    1
(AC220443) Bos taurus clone CH240-358F6, WORKING DRAFT SEQUE...    40   1.5    3
(CT192253) Sus scrofa genomic clone PigE-94M11, genomic surv...    34   1.9    2
(AC069574) Homo sapiens chromosome 4 clone RP11-267H10 map 4...    44   2.1    3
(AC094715) Rattus norvegicus clone CH230-5M5, *** SEQUENCING...    32   2.2    2
(AC128539) Rattus norvegicus clone CH230-382F1, WORKING DRAF...    32   2.3    2
(AC145202) Medicago truncatula clone mth2-15e9, complete seq...    38   2.8    3
(CC453768) BARC-Sat_229 Size-selected soybean genomic Glycin...    36   2.9    2
(BH289892) CH230-77K20.TV CHORI-230 Segment 1 Rattus norvegi...    32   3.0    2
(AM477619) Vitis vinifera contig VV78X218366.13, whole genom...    42   3.4    2
(AC022771) Homo sapiens clone RP11-368G6, WORKING DRAFT SEQU...    38   4.3    2
(BG453163) NF091H03LF1F1029 Developing leaf Medicago truncat...    36   4.4    2
(AC024667) Homo sapiens chromosome 4 clone RP11-700J17 map 4...    40   4.4    2
(AC024539) Homo sapiens chromosome 6 clone RP11-426L17 map 6...    42   4.4    2
(BX649293) Mouse DNA sequence from clone RP23-360N18 on chro...    44   4.4    1
(AC165342) Mus musculus BAC clone RP23-472O23 from chromosom...    44   4.4    1
(AC154368) Mus musculus BAC clone RP23-137J22 from chromosom...    44   4.4    1
(AC154317) Mus musculus BAC clone RP23-346H4 from chromosome...    44   4.4    1
(AC131758) Mus musculus BAC clone RP24-211E5 from chromosome...    44   4.4    1
(AC109503) Mus musculus chromosome 12, clone RP23-427N7, com...    44   4.4    1
(AM474896) Vitis vinifera contig VV79X001698.3, whole genome...    44   4.4    1
(AM452390) Vitis vinifera contig VV78X169623.2, whole genome...    44   4.4    1
(AM449431) Vitis vinifera, whole genome shotgun sequence, co...    44   4.4    1
(AM439517) Vitis vinifera contig VV78X187425.8, whole genome...    44   4.4    1
(AC003672) Arabidopsis thaliana chromosome 2 clone F16B22 ma...    44   4.4    1
(AC002388) Arabidopsis thaliana chromosome 2 clone T13E15 ma...    44   4.4    1
(AL031745) Plasmodium falciparum DNA from MAL1P2.                  44   4.4    1
(AE014832) Plasmodium falciparum 3D7 chromosome 10 section 4...    44   4.4    1
(AE014828) Plasmodium falciparum 3D7 chromosome 14 section 1...    44   4.4    1
(AE014816) Plasmodium falciparum 3D7 chromosome 14 section 1...    44   4.4    1
(AL353143) Human DNA sequence from clone RP11-383F12 on chro...    44   4.4    1
(AC130416) Homo sapiens 3 BAC RP11-771O11 (Roswell Park Canc...    44   4.4    1
(AC108019) Homo sapiens BAC clone RP11-5K16 from 4, complete...    44   4.4    1
(AC093842) Homo sapiens BAC clone RP11-443J23 from 4, comple...    44   4.4    1
(AC117172) Rattus norvegicus clone CH230-33D19, *** SEQUENCI...    44   4.4    1
(AC108823) Mus musculus clone RP23-76L13, WORKING DRAFT SEQU...    44   4.4    1
(AC108294) Rattus norvegicus clone CH230-277A22, *** SEQUENC...    44   4.4    1
(CU633768) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   4.4    1
(CU633426) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.4    1
(AC094051) Rattus norvegicus clone CH230-89D20, *** SEQUENCI...    44   4.4    1
(AC087626) Homo sapiens chromosome 8 clone RP11-545M12 map 8...    44   4.4    1
(AY331134) Homo sapiens chromosome 3 clone PAC_821N7, *** SE...    44   4.4    1
(AL844509) Plasmodium falciparum chromosome 13.                    44   4.4    1
(AC230793) Bos taurus clone CH240-498J2, WORKING DRAFT SEQUE...    44   4.4    1
(AC230587) Bos taurus clone CH240-504C12, WORKING DRAFT SEQU...    44   4.4    1
(AC213939) Equus caballus clone CH241-302C6, WORKING DRAFT S...    44   4.4    1
(AC025490) Homo sapiens chromosome 4 clone RP11-69O1 map 4, ...    44   4.4    1
(AC011710) Homo sapiens chromosome 15 clone RP11-363G8 map 1...    44   4.4    1
(AC011055) Homo sapiens clone RP11-10M16, WORKING DRAFT SEQU...    44   4.4    1
(AQ473812) CITBI-E1-2583D6.TR CITBI-E1 Homo sapiens genomic ...    44   4.4    1
(ER575918) 1093015811536 Global-Ocean-Sampling_GS-36-01-01-2...    44   4.4    1
(EK117973) 1092963267244 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.4    1
(EK108280) 1092963075316 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.4    1
(DX525799) GH_MBb0072K06r GH_MBb Gossypium hirsutum genomic ...    44   4.4    1
(DU391623) 1098268365352 CHORI-243 Ovis aries genomic clone ...    44   4.4    1
(AJ303952) Plasmodium chabaudi genome survey sequence, clone...    44   4.4    1
(DH335052) Oryzias latipes Fosmid clone:GOLWFno702_a17, forw...    44   4.4    1
(CU740687) A BAC library has been constructed from PN40024 g...    44   4.4    1
(CU191885) Equus caballus GSS, BAC clone CH241-350L20, T7 en...    44   4.4    1
(BZ145874) CH230-503L9.TJ CHORI-230 Segment 2 Rattus norvegi...    44   4.4    1
(CF585857) AGENCOURT_8793932_updated NIH_MGC_137 Mus musculu...    44   4.4    1
(CF344502) AGENCOURT_15222299 NICHD_XGC_Swb1 Xenopus (Silura...    44   4.4    1
(CD497050) CDA25-F12.y1d-s SHGC-CDA Gasterosteus aculeatus c...    44   4.4    1
(AL381428) Medicago truncatula EST MtBC01A03R2 : T7 end of c...    36   4.5    2
(CX523342) s13dNF1TD05VI046_472488 Virus-Infected Leaves Med...    36   4.5    2
(AC184197) Strongylocentrotus purpuratus clone R3-3093K17, W...    36   4.5    3
(AC026892) Homo sapiens chromosome 1 clone RP11-286E4, WORKI...    38   4.8    2
(CL382397) RPCI44_324G1.f RPCI-44 Sus scrofa genomic clone R...    34   5.4    2
(CV829927) ID0ACC14AD11RM1 ID0ACC Acyrthosiphon pisum cDNA c...    40   5.8    2
(CV829695) ID0ACC13BG06RM1 ID0ACC Acyrthosiphon pisum cDNA c...    40   5.8    2
(DH605734) Rattus norvegicus DNA, BAC clone: RNB1-133E06, 3'...    38   6.1    2
(FI088149) CHO_OF7122xd06f1.ab1 CHO_OF7 Nicotiana tabacum ge...    40   6.4    2
(CP000025) Campylobacter jejuni RM1221, complete genome.           32   6.8    2
(CP000538) Campylobacter jejuni subsp. jejuni 81-176, comple...    32   6.9    2
(AC096586) Homo sapiens chromosome 4 clone RP11-700J17, comp...    40   8.8    3
(AC009391) Drosophila melanogaster clone BACR21I23, complete...    38   9.9    3

>(AU038760) Dictyostelium discoideum slug cDNA, clone SSL446.
          Length = 241

 Score =  200 bits (101), Expect(3) = 6e-58
 Identities = 101/101 (100%)
 Strand = Plus / Plus


Query: 235 gaaaaaatcaaccactctctccaccattatcatcacaaaatagtcaacaagaaaaagatt 294
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gaaaaaatcaaccactctctccaccattatcatcacaaaatagtcaacaagaaaaagatt 60


Query: 295 ctccaaattctggtgcagcattatctttaaataattaattt 335
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ctccaaattctggtgcagcattatctttaaataattaattt 101

 Score = 52.0 bits (26), Expect(3) = 6e-58
 Identities = 26/26 (100%)
 Strand = Plus / Plus


Query: 385 cttgtacatataatattatatatata 410
           ||||||||||||||||||||||||||
Sbjct: 151 cttgtacatataatattatatatata 176

 Score = 28.2 bits (14), Expect(3) = 6e-58
 Identities = 14/14 (100%)
 Strand = Plus / Plus


Query: 420 atgcactgtataac 433
           ||||||||||||||
Sbjct: 186 atgcactgtataac 199

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 389,355,458
Number of extensions: 25692805
Number of successful extensions: 2346594
Number of sequences better than 10.0: 99
Length of query: 474
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 451
Effective length of database: 93,106,754,628
Effective search space: 41991146337228
Effective search space used: 41991146337228
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.20
Homology vs Protein 
Query= Contig-U05770-1 (Contig-U05770-1Q) /CSM_Contig/Contig-U05770-1Q.Seq.d
         (474 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: 387,801,785
Number of extensions: 3892636
Number of successful extensions: 11835
Number of sequences better than 10.0: 0
Number of HSP's gapped: 11706
Number of HSP's successfully gapped: 0
Length of query: 158
Length of database: 1,040,966,779
Length adjustment: 118
Effective length of query: 40
Effective length of database: 662,861,149
Effective search space: 26514445960
Effective search space used: 26514445960
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: 0.79  gvh: 0.47  alm: 0.50  top: 0.53  tms: 0.00  mit: 0.19  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: 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 %: cytoplasmic
	 32.0 %: nuclear
	 12.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U05770-1 is cyt
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