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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U10474-1
Contig ID Contig-U10474-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10474-1 (Contig-U10474-1Q) /CSM_Contig/Contig-U10474-1Q.Seq.d
NNNNNNNNNNAATGNNCTTTCNCATGGGGATATNGNAGCTAAAGNTANAA
AANATTTATCCNATGGNAAAAATNAAAACCCACNTGCNNAACATAAATTA
TTNCCCCCCATCNTTAGNCTATCCCTAGGNCCNAAAGATGGNTTAACNCC
AATTAATTCNAATTTNAATTTTGGNTCNTTTANATCNAGAATATTAAAAT
CCAATAATTTATTAATTAATAGNTTTNNAACCCCTTTTNATAATCCNGAA
CCCTTAAAAT
Gap no gap
Contig length 260
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U10474
List of clone(s) 

est1=VFL685Z,1,251
Translated Amino Acid sequence 
XXXNXLSHGDXXAKXXKXLSXGKNXNPXAXHKLXPPIXXLSLGPKDGLTPINSNXNFGSF
XSRILKSNNLLINXFXTPFXNPEPLK
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxxxfxwgyxs*xxkxfixwxkxkptcxt*iixphx*xiprxxrwxnxn*fxfxfwxx
xixnikiq*fin**xxnpfx*sxtlk


Frame B:
XXXNXLSHGDXXAKXXKXLSXGKNXNPXAXHKLXPPIXXLSLGPKDGLTPINSNXNFGSF
XSRILKSNNLLINXFXTPFXNPEPLK


Frame C:
xxxmxfxmgixxlkxxxiypmxkxkthxxninyxppslxyp*xxkmx*xqlixixilxxl
xxey*npiiy*lixxxplxiixnp*n
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10474-1 (Contig-U10474-1Q)
/CSM_Contig/Contig-U10474-1Q.Seq.d
         (260 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10474-1 (Contig-U10474-1Q) /CSM_Contig/Conti...   305  1e-83
Contig-U07084-1 (Contig-U07084-1Q) /CSM_Contig/Conti...    34  0.070
Contig-U06220-1 (Contig-U06220-1Q) /CSM_Contig/Conti...    34  0.070
Contig-U13639-1 (Contig-U13639-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U11170-1 (Contig-U11170-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U10742-1 (Contig-U10742-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U09419-1 (Contig-U09419-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U09012-1 (Contig-U09012-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U06805-1 (Contig-U06805-1Q) /CSM_Contig/Conti...    32  0.27
Contig-U06391-1 (Contig-U06391-1Q) /CSM_Contig/Conti...    32  0.27

>Contig-U10474-1 (Contig-U10474-1Q) /CSM_Contig/Contig-U10474-1Q.Seq.d
          Length = 260

 Score =  305 bits (154), Expect = 1e-83
 Identities = 244/244 (100%)
 Strand = Plus / Plus

                                                                       
Query: 17  ctttcncatggggatatngnagctaaagntanaaaanatttatccnatggnaaaaatnaa 76
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17  ctttcncatggggatatngnagctaaagntanaaaanatttatccnatggnaaaaatnaa 76

                                                                       
Query: 77  aacccacntgcnnaacataaattattnccccccatcnttagnctatccctaggnccnaaa 136
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 77  aacccacntgcnnaacataaattattnccccccatcnttagnctatccctaggnccnaaa 136

                                                                       
Query: 137 gatggnttaacnccaattaattcnaatttnaattttggntcntttanatcnagaatatta 196
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 137 gatggnttaacnccaattaattcnaatttnaattttggntcntttanatcnagaatatta 196

                                                                       
Query: 197 aaatccaataatttattaattaatagntttnnaaccccttttnataatccngaaccctta 256
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 197 aaatccaataatttattaattaatagntttnnaaccccttttnataatccngaaccctta 256

               
Query: 257 aaat 260
           ||||
Sbjct: 257 aaat 260


>Contig-U07084-1 (Contig-U07084-1Q) /CSM_Contig/Contig-U07084-1Q.Seq.d
          Length = 1017

 Score = 34.2 bits (17), Expect = 0.070
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 203 aataatttattaattaa 219
           |||||||||||||||||
Sbjct: 577 aataatttattaattaa 593


>Contig-U06220-1 (Contig-U06220-1Q) /CSM_Contig/Contig-U06220-1Q.Seq.d
          Length = 533

 Score = 34.2 bits (17), Expect = 0.070
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 203 aataatttattaattaa 219
           |||||||||||||||||
Sbjct: 407 aataatttattaattaa 423


 Score = 28.2 bits (14), Expect = 4.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 204 ataatttattaatt 217
           ||||||||||||||
Sbjct: 133 ataatttattaatt 120


  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: 1974
Number of Sequences: 6905
Number of extensions: 1974
Number of successful extensions: 720
Number of sequences better than 10.0: 95
length of query: 260
length of database: 5,674,871
effective HSP length: 15
effective length of query: 245
effective length of database: 5,571,296
effective search space: 1364967520
effective search space used: 1364967520
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 2008.11.20
Homology vs DNA 
Query= Contig-U10474-1 (Contig-U10474-1Q) /CSM_Contig/Contig-U10474-1Q.Seq.d
         (260 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

(BJ434751) Dictyostelium discoideum cDNA clone:ddv24i22, 3' ...   305   4e-79  1
(BJ432633) Dictyostelium discoideum cDNA clone:ddv19c08, 3' ...   200   2e-47  1
(BJ428536) Dictyostelium discoideum cDNA clone:ddv12h10, 3' ...   161   1e-35  1
(BJ432751) Dictyostelium discoideum cDNA clone:ddv19n13, 3' ...   133   3e-27  1
(ET933884) CHO_OF425xf24r1.ab1 CHO_OF Nicotiana tabacum geno...    44   2.3    1
(ET933824) CHO_OF425xf24f1.ab1 CHO_OF Nicotiana tabacum geno...    44   2.3    1
(ET933442) CHO_OF425xe23f1.ab1 CHO_OF Nicotiana tabacum geno...    44   2.3    1
(EK080956) 1092961104635 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.3    1
(EK026686) 1092955372259 Global-Ocean-Sampling_GS-31-01-01-1...    44   2.3    1
(ES386244) Blu_Testis_4_C13 Guppy pDNR_LIB Blue Testis Poeci...    44   2.3    1
(CT573421) M.truncatula DNA sequence from clone MTH2-27B10 o...    42   9.2    1
(AC009494) Homo sapiens BAC clone RP11-450B24 from Y, comple...    42   9.2    1
(AP010027) Lotus japonicus genomic DNA, clone: LjT04C06, TM0...    42   9.2    1
(AV401525) Bombyx mori cDNA clone:e96h0833.                        42   9.2    1
(EX849880) CBNC8169.rev CBNC Phycomyces blakesleeanus NRRL15...    42   9.2    1

>(BJ434751) Dictyostelium discoideum cDNA clone:ddv24i22, 3' end,
           single read.
          Length = 251

 Score =  305 bits (154), Expect = 4e-79
 Identities = 244/244 (100%)
 Strand = Plus / Minus


Query: 17  ctttcncatggggatatngnagctaaagntanaaaanatttatccnatggnaaaaatnaa 76
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 245 ctttcncatggggatatngnagctaaagntanaaaanatttatccnatggnaaaaatnaa 186


Query: 77  aacccacntgcnnaacataaattattnccccccatcnttagnctatccctaggnccnaaa 136
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 185 aacccacntgcnnaacataaattattnccccccatcnttagnctatccctaggnccnaaa 126


Query: 137 gatggnttaacnccaattaattcnaatttnaattttggntcntttanatcnagaatatta 196
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 125 gatggnttaacnccaattaattcnaatttnaattttggntcntttanatcnagaatatta 66


Query: 197 aaatccaataatttattaattaatagntttnnaaccccttttnataatccngaaccctta 256
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 65  aaatccaataatttattaattaatagntttnnaaccccttttnataatccngaaccctta 6


Query: 257 aaat 260
           ||||
Sbjct: 5   aaat 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 104,421,489
Number of extensions: 6932414
Number of successful extensions: 528621
Number of sequences better than 10.0: 16
Length of query: 260
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 237
Effective length of database: 93,106,754,628
Effective search space: 22066300846836
Effective search space used: 22066300846836
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.27
Homology vs Protein 
Query= Contig-U10474-1 (Contig-U10474-1Q) /CSM_Contig/Contig-U10474-1Q.Seq.d
         (260 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54NS9) RecName: Full=Apoptosis-inducing factor homolog A;     ...    97   2e-19
(Q54NS8) RecName: Full=Apoptosis-inducing factor homolog B;     ...    57   3e-07

>(Q54NS9) RecName: Full=Apoptosis-inducing factor homolog A;
            EC=1.-.-.-;
          Length = 408

 Score = 97.1 bits (240), Expect = 2e-19
 Identities = 52/83 (62%), Positives = 53/83 (63%)
 Frame = +2

Query: 11  NXLSHGDXXAKXXKXLSXGKNXNPXAXHKLXPPIXXLSLGPKDGLTPIXXXXXXXXXXXR 190
           N LSHG+  AK  K LS GKN N  A HKL PPI  LSLGPKDGLT I           R
Sbjct: 326 NALSHGNIVAKVIKDLSNGKNKNQLAKHKLLPPIISLSLGPKDGLTQINSNLNFGSFISR 385

Query: 191 ILKSNNLLINXFXTPFXNPEPLK 259
           ILKSNNLLIN F T F NPEPLK
Sbjct: 386 ILKSNNLLINRFQTHFNNPEPLK 408

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: 227,621,899
Number of extensions: 3931075
Number of successful extensions: 560
Number of sequences better than 10.0: 2
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 2
Length of query: 86
Length of database: 1,040,966,779
Length adjustment: 56
Effective length of query: 30
Effective length of database: 861,526,819
Effective search space: 25845804570
Effective search space used: 25845804570
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: 27 (15.0 bits)
PSORT 

 psg: 0.71  gvh: 0.38  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.14  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 

	 32.0 %: cytoplasmic
	 32.0 %: nuclear
	 16.0 %: mitochondrial
	 12.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U10474-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 1
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