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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-U07539-1
Contig ID Contig-U07539-1
Contig update 2002. 5. 9
Contig sequence 
>Contig-U07539-1 (Contig-U07539-1Q) /CSM_Contig/Contig-U07539-1Q.Seq.d
ACAAATACATACATCAAAACAACAAACACATACATACTACACATACAATG
TCATCAGNATAGTTCATTTGCATTATATATTCATAGAGAAAGAAGATTAA
TTGATATTGTTGATAATAATTGGGAACAAGAAACTTTACCACAAGAATTA
ATTAGACATCCAACTATAAATGAAAATATAACTTTAAATGAAGAATTTGA
AGAGTTACAAAGACAACAATGTAAGAAAGAAAAAGCATGGAATGAATTAG
CTTTAAATAGTTTCAATTAATTTGTGTATATTAGAAAAAAAAATAAAAAT
AAATAAGTGTTGTAATTGTCAATTTTACAAAATCAAAATTATTTCAATAA
TACATTGTAAAAAATGAAATAAAATGAAATGAAATAAAATAAAAGTGATT
GAAGCTATAATTTTAAAATATTTTAAAATATTAGTTCAAAATTATATATA
TTAATTAAAAAAAAAAAAAAAAAAAAAAAACCCCTGGGCCGGGNNNNNNN
NN
Gap no gap
Contig length 502
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 184998
End point 185457
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 1
Link to clone list U07539
List of clone(s) 

est1=FC-IC1640F,1,493
Translated Amino Acid sequence 
TNTYIKTTNTYILHIQCHQXSSFALYIHRERRLIDIVDNNWEQETLPQELIRHPTINENI
TLNEEFEELQRQQCKKEKAWNELALNSFN*fvyirkknknk*vl*lsilqnqnyfnntl*
kmk*nemk*nksd*synfkif*nissklyilikkkkkkkkplgrxxx
Translated Amino Acid sequence (All Frames) 
Frame A:
TNTYIKTTNTYILHIQCHQXSSFALYIHRERRLIDIVDNNWEQETLPQELIRHPTINENI
TLNEEFEELQRQQCKKEKAWNELALNSFN*fvyirkknknk*vl*lsilqnqnyfnntl*
kmk*nemk*nksd*synfkif*nissklyilikkkkkkkkplgrxxx


Frame B:
qihtskqqthtyytynvixivhlhyifieked*lilliiignkklyhkn*ldiql*mki*
l*mknlksykdnnvrkkkhgmn*l*ivsinlcilekkikinkccncqfykikiisiihck
k*nkmk*nkikvieaiilkyfkilvqnyiy*lkkkkkkknpwagxxx


Frame C:
kyihqnnkhihtthtmssx*ficiiys*rkkin*yc***lgtrnfttrin*tsnyk*kyn
fk*ri*rvtkttm*erksme*isfk*fqlicvy*kkk*k*isvvivnftksklfq*yivk
neik*neik*k*lkl*f*nilky*fkiiyin*kkkkkkktpgpgxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07539-1 (Contig-U07539-1Q)
/CSM_Contig/Contig-U07539-1Q.Seq.d
         (502 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07539-1 (Contig-U07539-1Q) /CSM_Contig/Conti...   464  e-131
Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U10744-1 (Contig-U10744-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U04491-1 (Contig-U04491-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U04373-1 (Contig-U04373-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U14880-1 (Contig-U14880-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U13956-1 (Contig-U13956-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U11925-1 (Contig-U11925-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U09199-1 (Contig-U09199-1Q) /CSM_Contig/Conti...    36  0.035
Contig-U05305-1 (Contig-U05305-1Q) /CSM_Contig/Conti...    36  0.035

>Contig-U07539-1 (Contig-U07539-1Q) /CSM_Contig/Contig-U07539-1Q.Seq.d
          Length = 502

 Score =  464 bits (234), Expect = e-131
 Identities = 237/237 (100%)
 Strand = Plus / Plus

                                                                       
Query: 48  atgtcatcagnatagttcatttgcattatatattcatagagaaagaagattaattgatat 107
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 48  atgtcatcagnatagttcatttgcattatatattcatagagaaagaagattaattgatat 107

                                                                       
Query: 108 tgttgataataattgggaacaagaaactttaccacaagaattaattagacatccaactat 167
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 108 tgttgataataattgggaacaagaaactttaccacaagaattaattagacatccaactat 167

                                                                       
Query: 168 aaatgaaaatataactttaaatgaagaatttgaagagttacaaagacaacaatgtaagaa 227
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 168 aaatgaaaatataactttaaatgaagaatttgaagagttacaaagacaacaatgtaagaa 227

                                                                    
Query: 228 agaaaaagcatggaatgaattagctttaaatagtttcaattaatttgtgtatattag 284
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 228 agaaaaagcatggaatgaattagctttaaatagtttcaattaatttgtgtatattag 284


 Score =  123 bits (62), Expect = 2e-28
 Identities = 62/62 (100%)
 Strand = Plus / Plus

                                                                       
Query: 395 gtgattgaagctataattttaaaatattttaaaatattagttcaaaattatatatattaa 454
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 395 gtgattgaagctataattttaaaatattttaaaatattagttcaaaattatatatattaa 454

             
Query: 455 tt 456
           ||
Sbjct: 455 tt 456


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

                               
Query: 410 attttaaaatattttaaaat 429
           ||||||||||||||||||||
Sbjct: 429 attttaaaatattttaaaat 410


 Score = 32.2 bits (16), Expect = 0.54
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                           
Query: 417 aatattttaaaatatt 432
           ||||||||||||||||
Sbjct: 432 aatattttaaaatatt 417


>Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Contig-U11185-1Q.Seq.d
          Length = 961

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

                              
Query: 188 atgaagaatttgaagagtt 206
           |||||||||||||||||||
Sbjct: 693 atgaagaatttgaagagtt 675


>Contig-U10744-1 (Contig-U10744-1Q) /CSM_Contig/Contig-U10744-1Q.Seq.d
          Length = 1335

 Score = 38.2 bits (19), Expect = 0.009
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                  
Query: 408 taattttaaaatattttaaaata 430
           |||||||||| ||||||||||||
Sbjct: 71  taattttaaattattttaaaata 93


 Score = 32.2 bits (16), Expect = 0.54
 Identities = 19/20 (95%)
 Strand = Plus / Minus

                               
Query: 410 attttaaaatattttaaaat 429
           ||||||||||| ||||||||
Sbjct: 92  attttaaaataatttaaaat 73


  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: 8262
Number of Sequences: 6905
Number of extensions: 8262
Number of successful extensions: 1186
Number of sequences better than 10.0: 345
length of query: 502
length of database: 5,674,871
effective HSP length: 16
effective length of query: 486
effective length of database: 5,564,391
effective search space: 2704294026
effective search space used: 2704294026
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 2008.11.11
Homology vs DNA 
Query= Contig-U07539-1 (Contig-U07539-1Q) /CSM_Contig/Contig-U07539-1Q.Seq.d
         (502 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

(AU275148) Dictyostelium discoideum gamete cDNA clone:FC-IC1...   462   e-126  1
(CU468531) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    56   0.001  1
(AC106707) Homo sapiens 3 BAC RP11-538P18 (Roswell Park Canc...    44   0.10   4
(AC012027) Homo sapiens chromosome 3 clone RP11-91L9, WORKIN...    44   0.18   4
(AC089988) Homo sapiens chromosome 3 clone RP11-600P22, WORK...    44   0.27   4
(AC223278) Bos taurus clone CH240-424E23, WORKING DRAFT SEQU...    48   0.30   1
(AC223177) Bos taurus clone CH240-427D22, WORKING DRAFT SEQU...    48   0.30   1
(FH002168) CHO_OF276xd22f2.ab1 CHO_OF Nicotiana tabacum geno...    34   0.84   2
(AC068393) Homo sapiens chromosome 3 clone RP11-538P18 map 3...    44   0.93   3
(AL359539) Human DNA sequence from clone RP11-719E16 on chro...    40   0.94   2
(AC213132) Oryza glaberrima clone OG_BBa0037K02, *** SEQUENC...    44   1.1    4
(EU153401) Felis catus FLA extended class II, class II, clas...    46   1.2    1
(DQ020489) Sus scrofa clone BAC KNP_992H3, complete sequence.      46   1.2    1
(AC060775) Homo sapiens chromosome 8, clone RP11-678D18, com...    46   1.2    1
(AC102949) Homo sapiens clone RP11-12K13, LOW-PASS SEQUENCE ...    46   1.2    1
(CU856282) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   1.2    1
(ET057936) MUGQ_CH252P351N21T7_CP658_083 CHORI-252 Vervet Mo...    46   1.2    1
(EK129853) 1093004301894 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.2    1
(EK114587) 1092963187067 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.2    1
(DX097474) AU_BAC014A1F03_T7 CHORI212 Ictalurus punctatus ge...    46   1.2    1
(ES528821) BIG_AF_36642 Brine Shrimp embryos, 15 hours after...    46   1.2    1
(ES521817) BIG_AF_29636 Brine Shrimp embryos, 15 hours after...    46   1.2    1
(AC023128) Homo sapiens BAC clone RP11-357J9 from 2, complet...    44   1.3    2
(AC196357) Dasypus novemcinctus clone VMRC5-310I8, WORKING D...    42   1.9    3
(AC192256) Gallus gallus BAC clone CH261-75J22 from chromoso...    38   4.1    4
(CQ337345) Sequence 11439 from Patent WO0157275.                   44   4.7    1
(CQ300109) Sequence 11214 from Patent WO0186003.                   44   4.7    1
(CQ263076) Sequence 11337 from Patent WO0157277.                   44   4.7    1
(CQ225055) Sequence 11894 from Patent WO0157273.                   44   4.7    1
(CQ177362) Sequence 8758 from Patent WO0157274.                    44   4.7    1
(CQ141768) Sequence 11790 from Patent WO0157276.                   44   4.7    1
(CQ102891) Sequence 11750 from Patent WO0157272.                   44   4.7    1
(CQ072198) Sequence 7998 from Patent WO0157278.                    44   4.7    1
(BD055618) Sequence tag and encoded human protein.                 44   4.7    1
(AX920085) Sequence 35948 from Patent EP1033401.                   44   4.7    1
(AR981479) Sequence 35948 from patent US 7115416.                  44   4.7    1
(AR755879) Sequence 35948 from patent US 6783961.                  44   4.7    1
(CU207325) Wallaby DNA sequence from clone MEKBa-538M1.            44   4.7    1
(EF173377) Aedes aegypti clone BAC ND56P6, complete sequence.      44   4.7    1
(AL021997) Human DNA sequence from clone RP5-874C20 on chrom...    44   4.7    1
(AC149798) Aedes aegypti clone NDL.56P6, *** SEQUENCING IN P...    44   4.7    1
(AC123091) Rattus norvegicus clone CH230-189A17, *** SEQUENC...    44   4.7    1
(AC119769) Rattus norvegicus clone CH230-443C8, *** SEQUENCI...    44   4.7    1
(CU582900) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.7    1
(AC196825) Sorghum bicolor clone SB_BBc0044I10, WORKING DRAF...    44   4.7    1
(AC196819) Sorghum bicolor clone SB_BBc0007H11, WORKING DRAF...    44   4.7    1
(EK346031) 1095467510486 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.7    1
(AM612799) Entamoeba invadens IP1 GSS, clone inv030b06.q1k.        44   4.7    1
(DU914845) 326313 Tomato EcoRI BAC Library Solanum lycopersi...    44   4.7    1
(CZ955868) 272032 Tomato EcoRI BAC Library Solanum lycopersi...    44   4.7    1
(CR891424) Sus scrofa BES.                                         44   4.7    1
(DN564676) 90826090 Sea Urchin primary mesenchyme cell cDNA ...    44   4.7    1
(BP830490) Arabidopsis thaliana cDNA clone:RAFL22-85-I12, 5'...    44   4.7    1
(BM299762) MCR052G04_24052 Ice plant Lambda Uni-Zap XR expre...    44   4.7    1
(FE244260) CAPG8099.fwd CAPG Naegleria gruberi amoeba stage ...    44   4.7    1
(CP001078) Clostridium botulinum E3 str. Alaska E43, complet...    44   4.7    1
(CP001056) Clostridium botulinum B str. Eklund 17B, complete...    44   4.7    1
(CP000361) Arcobacter butzleri RM4018, complete genome.            44   4.7    1
(AC023670) Homo sapiens BAC clone RP11-457M7 from Xq23, comp...    42   7.0    2
(BH166223) ENTRF41TF Entamoeba histolytica Sheared DNA Entam...    36   7.3    2
(CU618341) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   7.5    3
(AC138085) Homo sapiens X BAC RP11-146D5 (Roswell Park Cance...    42   8.6    2

>(AU275148) Dictyostelium discoideum gamete cDNA clone:FC-IC1640, 5'
           end single read.
          Length = 493

 Score =  462 bits (233), Expect = e-126
 Identities = 236/236 (100%)
 Strand = Plus / Plus


Query: 49  tgtcatcagnatagttcatttgcattatatattcatagagaaagaagattaattgatatt 108
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 49  tgtcatcagnatagttcatttgcattatatattcatagagaaagaagattaattgatatt 108


Query: 109 gttgataataattgggaacaagaaactttaccacaagaattaattagacatccaactata 168
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 109 gttgataataattgggaacaagaaactttaccacaagaattaattagacatccaactata 168


Query: 169 aatgaaaatataactttaaatgaagaatttgaagagttacaaagacaacaatgtaagaaa 228
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 169 aatgaaaatataactttaaatgaagaatttgaagagttacaaagacaacaatgtaagaaa 228


Query: 229 gaaaaagcatggaatgaattagctttaaatagtttcaattaatttgtgtatattag 284
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 229 gaaaaagcatggaatgaattagctttaaatagtttcaattaatttgtgtatattag 284

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 354,634,854
Number of extensions: 23615577
Number of successful extensions: 2127273
Number of sequences better than 10.0: 62
Length of query: 502
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 479
Effective length of database: 93,106,754,628
Effective search space: 44598135466812
Effective search space used: 44598135466812
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07539-1 (Contig-U07539-1Q) /CSM_Contig/Contig-U07539-1Q.Seq.d
         (502 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC149038_10(AC149038|pid:none) Medicago truncatula chromosome 7 ...    38   0.12
AY088589_1(AY088589|pid:none) Arabidopsis thaliana clone 8189 mR...    35   1.00
U48508_1(U48508|pid:none) Human skeletal muscle ryanodine recept...    33   2.9
AY268935_1(AY268935|pid:none) Mus musculus ryanodine receptor (R...    33   2.9
X69465_1(X69465|pid:none) S.scrofa gene for skeletal muscle ryan...    33   2.9
I46646(I46646;I46645;S31395;I47133;S26624;A37105;I47212;) ryanod...    33   2.9
(P16960) RecName: Full=Ryanodine receptor 1;          Short=RYR-...    33   2.9
(P21817) RecName: Full=Ryanodine receptor 1;          Short=RYR-...    33   2.9
CP001330_477(CP001330|pid:none) Micromonas sp. RCC299 chromosome...    33   4.9
DQ904331_1(DQ904331|pid:none) Homo sapiens lung specific F-box a...    32   6.5
AK304425_1(AK304425|pid:none) Homo sapiens cDNA FLJ50042 complet...    32   6.5
(Q17YZ8) RecName: Full=Elongation factor Ts;          Short=EF-T...    32   8.4
CR380958_490(CR380958|pid:none) Candida glabrata strain CBS138 c...    32   8.4

>AC149038_10(AC149038|pid:none) Medicago truncatula chromosome 7
           clone mth2-29a5, complete sequence.
          Length = 63

 Score = 38.1 bits (87), Expect = 0.12
 Identities = 22/53 (41%), Positives = 32/53 (60%)
 Frame = +1

Query: 97  LIDIVDNNWEQETLPQELIRHPTINENITLNEEFEELQRQQCKKEKAWNELAL 255
           LIDIVD +W ++TLPQ+ +  P      T + E    + QQ  K+ AW++LAL
Sbjct: 9   LIDIVDEDWMRDTLPQDDLPLPPTLVVRTDDTEDSNQEAQQVNKD-AWHDLAL 60

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: 424,161,151
Number of extensions: 5542087
Number of successful extensions: 14272
Number of sequences better than 10.0: 13
Number of HSP's gapped: 14267
Number of HSP's successfully gapped: 13
Length of query: 167
Length of database: 1,040,966,779
Length adjustment: 119
Effective length of query: 48
Effective length of database: 659,656,864
Effective search space: 31663529472
Effective search space used: 31663529472
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: 0.88  gvh: 0.46  alm: 0.51  top: 0.50  tms: 0.00  mit: 0.41  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 %: mitochondrial
	 32.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum
	  4.0 %: peroxisomal

>> prediction for Contig-U07539-1 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) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 1
FC-IC (SUB) 1