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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-U12624-1
Contig ID Contig-U12624-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12624-1 (Contig-U12624-1Q) /CSM_Contig/Contig-U12624-1Q.Seq.d
NNNNNNNNNNGTCATTATANTTCAGAATNNGTAGCTTGCCGTAANTGTNA
NAGTNCAAACNCTGTNNTGGAAANAAACNACCGTTTAAACTTTTTANGTT
GTAATGCTTGNAACTNTCAAAAATCCGTNNCNGTCATTAANAAAGGNTTG
GAANGGNCCCGNAAAAAA
Gap no gap
Contig length 168
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 U12624
List of clone(s) 

est1=AHA450Z,1,159
Translated Amino Acid sequence 
XXXXHYXSEXVACRXCXSXNXVXEXNXRLNFLXCNAXNXQKSVXVIXKGLEXXRKK
Translated Amino Acid sequence (All Frames) 
Frame A:
XXXXHYXSEXVACRXCXSXNXVXEXNXRLNFLXCNAXNXQKSVXVIXKGLEXXRKK


Frame B:
xxxviixqnx*lavxvxvqtlxwkxttv*tfxvvmlxtxknpxxslxkxwxgpxk


Frame C:
xxxslxfrxxslp*xxxxkxcxgxkxpfklfxl*clxlskirxxh*xrxgxxpxk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12624-1 (Contig-U12624-1Q)
/CSM_Contig/Contig-U12624-1Q.Seq.d
         (168 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12624-1 (Contig-U12624-1Q) /CSM_Contig/Conti...   176  5e-45
Contig-U14770-1 (Contig-U14770-1Q) /CSM_Contig/Conti...    28  2.7
Contig-U04795-1 (Contig-U04795-1Q) /CSM_Contig/Conti...    28  2.7

>Contig-U12624-1 (Contig-U12624-1Q) /CSM_Contig/Contig-U12624-1Q.Seq.d
          Length = 168

 Score =  176 bits (89), Expect = 5e-45
 Identities = 158/158 (100%)
 Strand = Plus / Plus

                                                                       
Query: 11  gtcattatanttcagaatnngtagcttgccgtaantgtnanagtncaaacnctgtnntgg 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  gtcattatanttcagaatnngtagcttgccgtaantgtnanagtncaaacnctgtnntgg 70

                                                                       
Query: 71  aaanaaacnaccgtttaaactttttangttgtaatgcttgnaactntcaaaaatccgtnn 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  aaanaaacnaccgtttaaactttttangttgtaatgcttgnaactntcaaaaatccgtnn 130

                                                 
Query: 131 cngtcattaanaaaggnttggaanggncccgnaaaaaa 168
           ||||||||||||||||||||||||||||||||||||||
Sbjct: 131 cngtcattaanaaaggnttggaanggncccgnaaaaaa 168


>Contig-U14770-1 (Contig-U14770-1Q) /CSM_Contig/Contig-U14770-1Q.Seq.d
          Length = 614

 Score = 28.2 bits (14), Expect = 2.7
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 83  gtttaaacttttta 96
           ||||||||||||||
Sbjct: 171 gtttaaacttttta 184


>Contig-U04795-1 (Contig-U04795-1Q) /CSM_Contig/Contig-U04795-1Q.Seq.d
          Length = 616

 Score = 28.2 bits (14), Expect = 2.7
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 83  gtttaaacttttta 96
           ||||||||||||||
Sbjct: 452 gtttaaacttttta 439


  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: 232
Number of Sequences: 6905
Number of extensions: 232
Number of successful extensions: 88
Number of sequences better than 10.0: 3
length of query: 168
length of database: 5,674,871
effective HSP length: 15
effective length of query: 153
effective length of database: 5,571,296
effective search space: 852408288
effective search space used: 852408288
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 2008.12. 2
Homology vs DNA 
Query= Contig-U12624-1 (Contig-U12624-1Q) /CSM_Contig/Contig-U12624-1Q.Seq.d
         (168 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

(BJ347896) Dictyostelium discoideum cDNA clone:dda31d14, 3' ...   174   6e-40  1
(C94209) Dictyostelium discoideum slug cDNA, clone SSK543.        139   3e-29  1
(BJ347504) Dictyostelium discoideum cDNA clone:dda27e12, 3' ...    60   1e-10  2

>(BJ347896) Dictyostelium discoideum cDNA clone:dda31d14, 3' end,
           single read.
          Length = 159

 Score =  174 bits (88), Expect = 6e-40
 Identities = 157/157 (100%)
 Strand = Plus / Minus


Query: 12  tcattatanttcagaatnngtagcttgccgtaantgtnanagtncaaacnctgtnntgga 71
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 158 tcattatanttcagaatnngtagcttgccgtaantgtnanagtncaaacnctgtnntgga 99


Query: 72  aanaaacnaccgtttaaactttttangttgtaatgcttgnaactntcaaaaatccgtnnc 131
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 98  aanaaacnaccgtttaaactttttangttgtaatgcttgnaactntcaaaaatccgtnnc 39


Query: 132 ngtcattaanaaaggnttggaanggncccgnaaaaaa 168
           |||||||||||||||||||||||||||||||||||||
Sbjct: 38  ngtcattaanaaaggnttggaanggncccgnaaaaaa 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 32,025,911
Number of extensions: 1663130
Number of successful extensions: 310983
Number of sequences better than 10.0: 3
Length of query: 168
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 146
Effective length of database: 93,199,600,587
Effective search space: 13607141685702
Effective search space used: 13607141685702
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 4
Homology vs Protein 
Query= Contig-U12624-1 (Contig-U12624-1Q) /CSM_Contig/Contig-U12624-1Q.Seq.d
         (168 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54T27) RecName: Full=Eukaryotic translation initiation factor ...    64   2e-09
AE017345_81(AE017345|pid:none) Cryptococcus neoformans var. neof...    34   1.4
AK222455_1(AK222455|pid:none) Ciona intestinalis mRNA for transl...    34   1.4
(A6NK07) RecName: Full=Eukaryotic translation initiation factor ...    34   1.8
CR382131_1303(CR382131|pid:none) Yarrowia lipolytica strain CLIB...    33   3.1
BC122609_1(BC122609|pid:none) Bos taurus eukaryotic translation ...    33   4.0
AB169578_1(AB169578|pid:none) Macaca fascicularis brain cDNA, cl...    33   4.0
A31226(A31226) translation initiation factor eIF-2 beta chain - ...    33   4.0
JC2329(JC2329;PC2209;S38536)translation initiation factor eIF-2 ...    33   4.0
BC007888_1(BC007888|pid:none) Homo sapiens eukaryotic translatio...    33   4.0
AJ294707_1(AJ294707|pid:none) Gallus gallus mRNA for eukaryote i...    33   4.0
(P20042) RecName: Full=Eukaryotic translation initiation factor ...    33   4.0
BT073720_1(BT073720|pid:none) Oncorhynchus mykiss clone omyk-evo...    33   4.0
AY071253_1(AY071253|pid:none) Drosophila melanogaster RE29270 fu...    32   5.3
CR382124_365(CR382124|pid:none) Kluyveromyces lactis strain NRRL...    32   6.9
(P56329) RecName: Full=Probable eukaryotic translation initiatio...    32   9.0
FN392319_902(FN392319|pid:none) Pichia pastoris GS115 chromosome...    32   9.0
T39024(T39024) probable eukaryotic translation initiation factor...    32   9.0

>(Q54T27) RecName: Full=Eukaryotic translation initiation factor 2
           subunit 2; AltName: Full=Eukaryotic translation
           initiation factor 2 subunit beta;
           Short=eIF-2-beta;
          Length = 317

 Score = 63.5 bits (153), Expect = 2e-09
 Identities = 32/52 (61%), Positives = 34/52 (65%)
 Frame = +1

Query: 13  HYXSEXVACRXCXSXNXVXEXNXRLNFLXCNAXNXQKSVXVIXKGLEXXRKK 168
           HY SE VACR C S N V E N RL FL CNA N ++SV VI KGLE   KK
Sbjct: 260 HYISEYVACRNCKSPNTVLERNNRLYFLCCNACNSKRSVAVIKKGLEGAGKK 311

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: 3236559
Number of Hits to DB: 95,199,616
Number of extensions: 1208846
Number of successful extensions: 119
Number of sequences better than 10.0: 18
Number of HSP's gapped: 119
Number of HSP's successfully gapped: 18
Length of query: 56
Length of database: 1,051,180,864
Length adjustment: 29
Effective length of query: 27
Effective length of database: 957,320,653
Effective search space: 25847657631
Effective search space used: 25847657631
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: 26 (14.6 bits)
PSORT 

 psg: 0.76  gvh: 0.45  alm: 0.55  top: 0.53  tms: 0.00  mit: 0.26  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 

	 52.0 %: nuclear
	 24.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U12624-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
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