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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U06279-1
Contig ID Contig-U06279-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U06279-1 (Contig-U06279-1Q) /CSM_Contig/Contig-U06279-1Q.Seq.d
AAATAAAATGCCTTGTTTATATATCTGTGGTGAATGTGGTGCTGAGCACG
AAATCAAACCAAAAGAACCAGTAAAATGCAAAGATTGCACTCATCGTATT
ATGTACAAAAAGAGAACCGATAAAATGATTCAATTCGAAGCAAGATAAAA
AAAAGAAAAAAAGAGAAAAAAGAAAAAAAAAAAAAACAAAACAAAATCAA
ATCAATTAAAATATACCAAAACACAACAATATACATAAAAAAAACTAAAA
AAAAACTAAAAAAAGAAAAGAAAAAAAAAAAATAGCTTAAAACAGCAACA
ACTTGTACACAGACCTTTAAATAAACAATTACCTTTTTTTTAAGTTAAAA
AAAAAAAAAA
Gap no gap
Contig length 360
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 588482
End point 588842
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 2
Link to clone list U06279
List of clone(s) 

est1=VSA574E,1,361
est2=VSK248Z,99,339
Translated Amino Acid sequence 
k*nalfiylw*mwc*arnqtkrtskmqrlhssyyvqkenr*NDSIRSKIKKRKKEKKEKK
KKQNKIKSIKIYQNTTIYIKKTKKKLKKEKKKKK*lktattctqtfk*titffls*kkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
k*nalfiylw*mwc*arnqtkrtskmqrlhssyyvqkenr*NDSIRSKIKKRKKEKKEKK
KKQNKIKSIKIYQNTTIYIKKTKKKLKKEKKKKK*lktattctqtfk*titffls*kkkk


Frame B:
nkmpclyicgecgaeheikpkepvkckdcthrimykkrtdkmiqfear*kkekkrkkkkk
knktksnqlkytktqqyt*kklkkn*kkkrkkknslkqqqlvhrplnkqlpff*vkkkk


Frame C:
ikclvyisvvnvvlstksnqknq*nakialivlctkrepik*fnskqdkkkkkrekrkkk
ktkqnqin*nipkhnnihkkn*kktkkrkekkkia*nsnnlytdl*innylffklkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06279-1 (Contig-U06279-1Q)
/CSM_Contig/Contig-U06279-1Q.Seq.d
         (360 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06279-1 (Contig-U06279-1Q) /CSM_Contig/Conti...   289  1e-78
Contig-U14764-1 (Contig-U14764-1Q) /CSM_Contig/Conti...    34  0.097
Contig-U14670-1 (Contig-U14670-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U13459-1 (Contig-U13459-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U13199-1 (Contig-U13199-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U11823-1 (Contig-U11823-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U11313-1 (Contig-U11313-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U11146-1 (Contig-U11146-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U10871-1 (Contig-U10871-1Q) /CSM_Contig/Conti...    32  0.39
Contig-U09336-1 (Contig-U09336-1Q) /CSM_Contig/Conti...    32  0.39

>Contig-U06279-1 (Contig-U06279-1Q) /CSM_Contig/Contig-U06279-1Q.Seq.d
          Length = 360

 Score =  289 bits (146), Expect = 1e-78
 Identities = 146/146 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aaataaaatgccttgtttatatatctgtggtgaatgtggtgctgagcacgaaatcaaacc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaataaaatgccttgtttatatatctgtggtgaatgtggtgctgagcacgaaatcaaacc 60

                                                                       
Query: 61  aaaagaaccagtaaaatgcaaagattgcactcatcgtattatgtacaaaaagagaaccga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaaagaaccagtaaaatgcaaagattgcactcatcgtattatgtacaaaaagagaaccga 120

                                     
Query: 121 taaaatgattcaattcgaagcaagat 146
           ||||||||||||||||||||||||||
Sbjct: 121 taaaatgattcaattcgaagcaagat 146


 Score =  101 bits (51), Expect = 5e-22
 Identities = 51/51 (100%)
 Strand = Plus / Plus

                                                              
Query: 283 tagcttaaaacagcaacaacttgtacacagacctttaaataaacaattacc 333
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 283 tagcttaaaacagcaacaacttgtacacagacctttaaataaacaattacc 333


 Score = 79.8 bits (40), Expect = 2e-15
 Identities = 40/40 (100%)
 Strand = Plus / Plus

                                                   
Query: 197 tcaaatcaattaaaatataccaaaacacaacaatatacat 236
           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 197 tcaaatcaattaaaatataccaaaacacaacaatatacat 236


>Contig-U14764-1 (Contig-U14764-1Q) /CSM_Contig/Contig-U14764-1Q.Seq.d
          Length = 1026

 Score = 34.2 bits (17), Expect = 0.097
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 120 ataaaatgattcaattc 136
           |||||||||||||||||
Sbjct: 398 ataaaatgattcaattc 382


>Contig-U14670-1 (Contig-U14670-1Q) /CSM_Contig/Contig-U14670-1Q.Seq.d
          Length = 825

 Score = 32.2 bits (16), Expect = 0.39
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 316 tttaaataaacaatta 331
           ||||||||||||||||
Sbjct: 362 tttaaataaacaatta 377


  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: 3305
Number of Sequences: 6905
Number of extensions: 3305
Number of successful extensions: 375
Number of sequences better than 10.0: 112
length of query: 360
length of database: 5,674,871
effective HSP length: 16
effective length of query: 344
effective length of database: 5,564,391
effective search space: 1914150504
effective search space used: 1914150504
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. 7
Homology vs DNA 
Query= Contig-U06279-1 (Contig-U06279-1Q) /CSM_Contig/Contig-U06279-1Q.Seq.d
         (360 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

(AU261576) Dictyostelium discoideum vegetative cDNA clone:VS...   289   e-105  2
(AU270877) Dictyostelium discoideum vegetative cDNA clone:VS...   113   4e-21  1
(X82444) S.pombe pmt1+ gene.                                       46   0.84   1
(U80217) Schizosaccharomyces pombe RNA polymerases I-III com...    46   0.84   1
(U20867) Schizosaccharomyces pombe RNA polymerase small Zn-b...    46   0.84   1
(D89634) Schizosaccharomyces pombe rpb12 gene for RNA polyme...    46   0.84   1
(CU329671) Schizosaccharomyces pombe chromosome II.                46   0.84   1
(AF027819) Schizosaccharomyces pombe RNA polymerases I, II a...    46   0.84   1
(AC166616) Oryctolagus cuniculus clone LB1-53C4, WORKING DRA...    44   2.6    2
(AC168959) Oryctolagus cuniculus clone LB1-274P2, WORKING DR...    44   3.1    2
(AC224186) Bos taurus clone CH240-447F22, WORKING DRAFT SEQU...    44   3.3    1
(AC209843) Zea mays chromosome 6 clone CH201-45B6; ZMMBBc004...    44   3.3    1
(EH016474) USDA-FP_188971 Lysiphlebus testaceipes adult whol...    44   3.3    1
(AP009694) Lotus japonicus genomic DNA, clone: LjT19D10, TM1...    40   5.4    2
(AC209275) Populus trichocarpa clone POP080-D18, complete se...    32   6.4    2

>(AU261576) Dictyostelium discoideum vegetative cDNA clone:VSA574,
           3' end single read.
          Length = 361

 Score =  289 bits (146), Expect(2) = e-105
 Identities = 146/146 (100%)
 Strand = Plus / Plus


Query: 1   aaataaaatgccttgtttatatatctgtggtgaatgtggtgctgagcacgaaatcaaacc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaataaaatgccttgtttatatatctgtggtgaatgtggtgctgagcacgaaatcaaacc 60


Query: 61  aaaagaaccagtaaaatgcaaagattgcactcatcgtattatgtacaaaaagagaaccga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaaagaaccagtaaaatgcaaagattgcactcatcgtattatgtacaaaaagagaaccga 120


Query: 121 taaaatgattcaattcgaagcaagat 146
           ||||||||||||||||||||||||||
Sbjct: 121 taaaatgattcaattcgaagcaagat 146

 Score =  127 bits (64), Expect(2) = e-105
 Identities = 64/64 (100%)
 Strand = Plus / Plus


Query: 283 tagcttaaaacagcaacaacttgtacacagacctttaaataaacaattacctttttttta 342
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 283 tagcttaaaacagcaacaacttgtacacagacctttaaataaacaattacctttttttta 342


Query: 343 agtt 346
           ||||
Sbjct: 343 agtt 346

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 350,505,036
Number of extensions: 17770136
Number of successful extensions: 1416783
Number of sequences better than 10.0: 15
Length of query: 360
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 337
Effective length of database: 93,106,754,628
Effective search space: 31376976309636
Effective search space used: 31376976309636
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06279-1 (Contig-U06279-1Q) /CSM_Contig/Contig-U06279-1Q.Seq.d
         (360 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BT056820_1(BT056820|pid:none) Salmo salar clone ssal-evd-509-226...    69   7e-11
BC072756_1(BC072756|pid:none) Xenopus laevis polymerase (RNA) II...    69   7e-11
(P53803) RecName: Full=DNA-directed RNA polymerases I, II, and I...    69   7e-11
AK018914_1(AK018914|pid:none) Mus musculus adult male testis cDN...    69   7e-11
AK008136_1(AK008136|pid:none) Mus musculus adult male small inte...    69   7e-11
BC150398_1(BC150398|pid:none) Danio rerio zgc:171795, mRNA (cDNA...    67   3e-10
BT077830_1(BT077830|pid:none) Lepeophtheirus salmonis clone lsal...    66   3e-10
BT077417_1(BT077417|pid:none) Lepeophtheirus salmonis clone lsal...    66   4e-10
BT070711_1(BT070711|pid:none) Picea sitchensis clone WS02745_N23...    66   4e-10
EU968496_1(EU968496|pid:none) Zea mays clone 321487 DNA-directed...    66   4e-10
EF081729_1(EF081729|pid:none) Picea sitchensis clone WS02722_K23...    66   4e-10
BT056447_1(BT056447|pid:none) Salmo salar clone ssal-evd-551-274...    65   7e-10
T21305(T21305) hypothetical protein F23B2.13 - Caenorhabditis el...    64   2e-09
(P48011) RecName: Full=DNA-directed RNA polymerases I, II, and I...    64   2e-09
BT056942_1(BT056942|pid:none) Salmo salar clone ssal-evf-550-105...    61   1e-08
EU958638_1(EU958638|pid:none) Zea mays clone 1706873 DNA-directe...    60   2e-08
AB010072_7(AB010072|pid:none) Arabidopsis thaliana genomic DNA, ...    60   2e-08
AM269972_30(AM269972|pid:none) Aspergillus niger contig An01c025...    60   3e-08
FN357325_20(FN357325|pid:none) Schistosoma mansoni genome sequen...    59   7e-08
CR380953_246(CR380953|pid:none) Candida glabrata strain CBS138 c...    58   9e-08
AE016819_259(AE016819|pid:none) Ashbya gossypii (= Eremothecium ...    56   3e-07
CR954202_273(CR954202|pid:none) Ostreococcus tauri strain OTTH05...    56   3e-07
CP000582_328(CP000582|pid:none) Ostreococcus lucimarinus CCE9901...    56   3e-07
AL158196_5(AL158196|pid:none) Human DNA sequence from clone RP11...    55   6e-07
AM910994_117(AM910994|pid:none) Plasmodium knowlesi strain H chr...    55   8e-07
BT057476_1(BT057476|pid:none) Salmo salar clone ssal-rgb2-584-29...    55   8e-07
(P40422) RecName: Full=DNA-directed RNA polymerases I, II, and I...    54   1e-06
CR382136_203(CR382136|pid:none) Debaryomyces hansenii strain CBS...    52   8e-06
CP000881_20(CP000881|pid:none) Hemiselmis andersenii chromosome ...    51   1e-05
AM920437_512(AM920437|pid:none) Penicillium chrysogenum Wisconsi...    49   4e-05
CR382129_749(CR382129|pid:none) Yarrowia lipolytica strain CLIB1...    49   7e-05
BT057241_1(BT057241|pid:none) Salmo salar clone ssal-evf-508-176...    49   7e-05
FN392319_470(FN392319|pid:none) Pichia pastoris GS115 chromosome...    49   7e-05
CR940352_21(CR940352|pid:none) Theileria annulata strain Ankara ...    48   9e-05
AJ010592_23(AJ010592|pid:none) Guillardia theta DNA for complete...    45   6e-04
AC024260_9(AC024260|pid:none) Arabidopsis thaliana chromosome 1 ...    45   8e-04
DQ158857_33(DQ158857|pid:none) Bigelowiella natans nucleomorph c...    42   0.007
AE004437_1606(AE004437|pid:none) Halobacterium sp. NRC-1, comple...    37   0.22
AM502238_73(AM502238|pid:none) Leishmania infantum chromosome 20.      34   1.8
CP001338_2400(CP001338|pid:none) Candidatus Methanosphaerula pal...    33   4.1
AX973026_1(AX973026|pid:none) Sequence 3829 from Patent EP1104808.     32   9.1

>BT056820_1(BT056820|pid:none) Salmo salar clone ssal-evd-509-226
           DNA-directed RNA polymerases I, II, and III subunit
           RPABC4 putative mRNA, complete cds.
          Length = 58

 Score = 68.6 bits (166), Expect = 7e-11
 Identities = 25/47 (53%), Positives = 39/47 (82%)
 Frame = +2

Query: 5   KMPCLYICGECGAEHEIKPKEPVKCKDCTHRIMYKKRTDKMIQFEAR 145
           + P +YICGEC  E+EIK ++P++C++C +RIMYKKRT +++ F+AR
Sbjct: 12  QQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

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: 271,395,730
Number of extensions: 3072117
Number of successful extensions: 7670
Number of sequences better than 10.0: 41
Number of HSP's gapped: 7661
Number of HSP's successfully gapped: 41
Length of query: 120
Length of database: 1,040,966,779
Length adjustment: 86
Effective length of query: 34
Effective length of database: 765,398,269
Effective search space: 26023541146
Effective search space used: 26023541146
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: 29 (15.8 bits)
PSORT 

 psg: 0.04  gvh: -0.06  alm: 0.65  top: 0.53  tms: 0.00  mit: 0.33  mip: 0.00
 nuc: 0.69  erl: 0.00  erm: 1.00  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 

	 64.0 %: nuclear
	 28.0 %: cytoplasmic
	  8.0 %: mitochondrial

>> prediction for Contig-U06279-1 is nuc
VS (DIR, S) 2
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) 0
FC-IC (SUB) 0