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Dicty_cDB
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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-U05647-1
Contig ID Contig-U05647-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U05647-1 (Contig-U05647-1Q) /CSM_Contig/Contig-U05647-1Q.Seq.d
ACAAAACAAAAACCTTAAATAAAAATCAAAAAACTAAAACTTTAAAATGA
CTTTGTTATCCTCAATTTCTAAAATTGGCACAATTAAAAACGGTAATTCT
TTGAACGAAATTACCAGTACAATTTCTAACAATGAAGCTAAAGGATCACC
ATCATTTAGCGGAAATCAATCAACAAAATCTATAGGGGATTTATTACTTC
AAATTGCTATAATTACTAAAGCCACAACAAAAAATAAATAAGCCCATCTT
TTTCTCTAAAAAAAAAAAAAACAAAAATAAACAATTTATTTTTTTTTAAT
TCCAAAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 325
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4826014
End point 4825689
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05647
List of clone(s) 

est1=SSK208E,1,326
Translated Amino Acid sequence 
qnknlk*kskn*NFKMTLLSSISKIGTIKNGNSLNEITSTISNNEAKGSPSFSGNQSTKS
IGDLLLQIAIITKATTKNK*ahlfl*kkkkqk*tiyfflipkkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
tkqkp*ikikklkl*ndfvilnf*nwhn*kr*ffernyqynf*q*s*ritii*rksinki
yrgfitsncyny*shnkk*ispsfslkkkktkinnlfffnskkkkkkk


Frame B:
qnknlk*kskn*NFKMTLLSSISKIGTIKNGNSLNEITSTISNNEAKGSPSFSGNQSTKS
IGDLLLQIAIITKATTKNK*ahlfl*kkkkqk*tiyfflipkkkkkkk


Frame C:
ktktlnknqktktlk*lcypqflklaqlktvil*tklpvqfltmklkdhhhlaeinqqnl
*giyyfkll*llkpqqkinkpiffskkkknknkqfiff*fqkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05647-1 (Contig-U05647-1Q)
/CSM_Contig/Contig-U05647-1Q.Seq.d
         (325 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05647-1 (Contig-U05647-1Q) /CSM_Contig/Conti...   416  e-117
Contig-U05177-1 (Contig-U05177-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U14313-1 (Contig-U14313-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12644-1 (Contig-U12644-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12411-1 (Contig-U12411-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12401-1 (Contig-U12401-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12314-1 (Contig-U12314-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12110-1 (Contig-U12110-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U11970-1 (Contig-U11970-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U11296-1 (Contig-U11296-1Q) /CSM_Contig/Conti...    32  0.35

>Contig-U05647-1 (Contig-U05647-1Q) /CSM_Contig/Contig-U05647-1Q.Seq.d
          Length = 325

 Score =  416 bits (210), Expect = e-117
 Identities = 210/210 (100%)
 Strand = Plus / Plus

                                                                       
Query: 48  tgactttgttatcctcaatttctaaaattggcacaattaaaaacggtaattctttgaacg 107
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 48  tgactttgttatcctcaatttctaaaattggcacaattaaaaacggtaattctttgaacg 107

                                                                       
Query: 108 aaattaccagtacaatttctaacaatgaagctaaaggatcaccatcatttagcggaaatc 167
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 108 aaattaccagtacaatttctaacaatgaagctaaaggatcaccatcatttagcggaaatc 167

                                                                       
Query: 168 aatcaacaaaatctataggggatttattacttcaaattgctataattactaaagccacaa 227
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 168 aatcaacaaaatctataggggatttattacttcaaattgctataattactaaagccacaa 227

                                         
Query: 228 caaaaaataaataagcccatctttttctct 257
           ||||||||||||||||||||||||||||||
Sbjct: 228 caaaaaataaataagcccatctttttctct 257


>Contig-U05177-1 (Contig-U05177-1Q) /CSM_Contig/Contig-U05177-1Q.Seq.d
          Length = 320

 Score = 42.1 bits (21), Expect = 4e-04
 Identities = 39/45 (86%)
 Strand = Plus / Plus

                                                        
Query: 62  tcaatttctaaaattggcacaattaaaaacggtaattctttgaac 106
           ||||||||||  |||||  ||||| |||| |||||||||||||||
Sbjct: 55  tcaatttctagcattggttcaattcaaaatggtaattctttgaac 99


>Contig-U14313-1 (Contig-U14313-1Q) /CSM_Contig/Contig-U14313-1Q.Seq.d
          Length = 1491

 Score = 32.2 bits (16), Expect = 0.35
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 226  aacaaaaaataaataa 241
            ||||||||||||||||
Sbjct: 1431 aacaaaaaataaataa 1446


  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: 4201
Number of Sequences: 6905
Number of extensions: 4201
Number of successful extensions: 730
Number of sequences better than 10.0: 83
length of query: 325
length of database: 5,674,871
effective HSP length: 15
effective length of query: 310
effective length of database: 5,571,296
effective search space: 1727101760
effective search space used: 1727101760
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 2009. 8. 2
Homology vs DNA 
Query= Contig-U05647-1 (Contig-U05647-1Q) /CSM_Contig/Contig-U05647-1Q.Seq.d
         (325 letters)

Database: ddbj_B
           105,743,758 sequences; 104,622,809,269 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(C91289) Dictyostelium discoideum slug cDNA, clone SSK208.        416   e-112  1
(C84801) Dictyostelium discoideum slug cDNA, clone SSF862.         42   0.36   2
(DC584773) Diospyros kaki cDNA, clone: KA018_E05, 5' end, ex...    46   0.83   1
(AC093699) Homo sapiens BAC clone RP11-810C20 from 4, comple...    44   3.3    1
(AC087577) Homo sapiens chromosome 4 clone RP11-1035P1 map 4...    44   3.3    1
(AL079351) Human chromosome 4 DNA sequence *** IN PROGRESS *...    44   3.3    1
(BZ774142) mcv86e05.b1 HFOSMID007 Homo sapiens genomic, geno...    44   3.3    1
(CB652258) OSJNEc01P09.f OSJNEc Oryza sativa Japonica Group ...    44   3.3    1
(AC179751) Strongylocentrotus purpuratus clone R3-1018C02, W...    42   4.9    2
(ET809573) CHO_OF716xo16f1.ab1 CHO_OF Nicotiana tabacum geno...    32   7.7    2
(CU326343) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   8.2    4
(EY512788) CAPF10972.fwd CAPF Capitella sp. I ECS-2004 whole...    32   8.2    2
(EY512787) CAPF10972.rev CAPF Capitella sp. I ECS-2004 whole...    32   8.2    2
(ET973031) CHO_OF704xn20f1.ab1 CHO_OF Nicotiana tabacum geno...    32   9.0    2
(EJ488800) 1095403521199 Global-Ocean-Sampling_GS-28-01-01-1...    38   9.7    2

>(C91289) Dictyostelium discoideum slug cDNA, clone SSK208.
          Length = 326

 Score =  416 bits (210), Expect = e-112
 Identities = 210/210 (100%)
 Strand = Plus / Plus


Query: 48  tgactttgttatcctcaatttctaaaattggcacaattaaaaacggtaattctttgaacg 107
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 48  tgactttgttatcctcaatttctaaaattggcacaattaaaaacggtaattctttgaacg 107


Query: 108 aaattaccagtacaatttctaacaatgaagctaaaggatcaccatcatttagcggaaatc 167
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 108 aaattaccagtacaatttctaacaatgaagctaaaggatcaccatcatttagcggaaatc 167


Query: 168 aatcaacaaaatctataggggatttattacttcaaattgctataattactaaagccacaa 227
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 168 aatcaacaaaatctataggggatttattacttcaaattgctataattactaaagccacaa 227


Query: 228 caaaaaataaataagcccatctttttctct 257
           ||||||||||||||||||||||||||||||
Sbjct: 228 caaaaaataaataagcccatctttttctct 257

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 316,490,351
Number of extensions: 21870058
Number of successful extensions: 2050687
Number of sequences better than 10.0: 15
Length of query: 325
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 302
Effective length of database: 102,190,702,835
Effective search space: 30861592256170
Effective search space used: 30861592256170
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 8. 2
Homology vs Protein 
Query= Contig-U05647-1 (Contig-U05647-1Q) /CSM_Contig/Contig-U05647-1Q.Seq.d
         (325 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q86I06) RecName: Full=Probable serine/threonine-protein kinase ...    32   9.1
AC116979_32(AC116979|pid:none) Dictyostelium discoideum chromoso...    32   9.1

>(Q86I06) RecName: Full=Probable serine/threonine-protein kinase
           nek3;          EC=2.7.11.1; AltName: Full=Never in
           mitosis protein A-related protein kinase 3; AltName:
           Full=NimA-related protein kinase 3;
           &AC116305_132(AC116305|pid:none)
          Length = 1123

 Score = 31.6 bits (70), Expect = 9.1
 Identities = 21/60 (35%), Positives = 33/60 (55%)
 Frame = +2

Query: 59  SSISKIGTIKNGNSLNEITSTISNNEAKGSPSFSGNQSTKSIGDLLLQIAIITKATTKNK 238
           S  S I +  +GN+ N  T+T +NN    +P   G +STKS    +L+++  T  +T NK
Sbjct: 668 SGSSSISSSSSGNNSNSNTTT-NNNTTSTTPIRPGLKSTKS----MLELSTPTSISTSNK 722

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: 3268448
Number of Hits to DB: 341,490,362
Number of extensions: 5003127
Number of successful extensions: 13487
Number of sequences better than 10.0: 2
Number of HSP's gapped: 13473
Number of HSP's successfully gapped: 2
Length of query: 108
Length of database: 1,061,185,681
Length adjustment: 76
Effective length of query: 32
Effective length of database: 812,783,633
Effective search space: 26009076256
Effective search space used: 26009076256
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: 28 (15.4 bits)
PSORT 

 psg: 0.91  gvh: 0.44  alm: 0.43  top: 0.47  tms: 0.00  mit: 0.27  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 %: nuclear
	 32.0 %: cytoplasmic
	 16.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U05647-1 is nuc
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