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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-U04961-1
Contig ID Contig-U04961-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04961-1 (Contig-U04961-1Q) /CSM_Contig/Contig-U04961-1Q.Seq.d
TTTTTTTAATTTTTTTTTTTTCCATTAATTTAGTTTACTAACATTTTTAT
TCTTATAGAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAACCA
AAATTTTGTCAATAAGGATTATTTCTTTAAATATTTTTTTTTTTTTTTAA
AAAAAAAAAAAAAAAAAAATCTCCAAAAATATTTCACCACCAGAGGCCAT
TATTTGATTGTTT
Gap no gap
Contig length 213
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 196053
End point 195840
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 2
Link to clone list U04961
List of clone(s) 

est1=SSG290F,-1,214
est2=SSE222F,27,168
Translated Amino Acid sequence 
flifffsinlvy*HFYSYRNKKKKKKKKKKQNQNFVNKDYFFKYFFFFLKKKKKKNLQKY
FTTRGHYLIV
Translated Amino Acid sequence (All Frames) 
Frame A:
ff*ffffpli*ftnifilieikkkkkkkkknktkilsiriislniffff*kkkkkkiskn
isppeaii*lf


Frame B:
ffnffffh*fslltflfl*k*kkkkkkkkktkpkfcq*glfl*ifffffkkkkkkkspki
fhhqrplfdc


Frame C:
flifffsinlvy*HFYSYRNKKKKKKKKKKQNQNFVNKDYFFKYFFFFLKKKKKKNLQKY
FTTRGHYLIV
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04961-1 (Contig-U04961-1Q)
/CSM_Contig/Contig-U04961-1Q.Seq.d
         (213 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04961-1 (Contig-U04961-1Q) /CSM_Contig/Conti...    88  4e-18
Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Conti...    34  0.056
Contig-U14067-1 (Contig-U14067-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U13529-1 (Contig-U13529-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U12830-1 (Contig-U12830-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U12446-1 (Contig-U12446-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U12147-1 (Contig-U12147-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U11890-1 (Contig-U11890-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U11442-1 (Contig-U11442-1Q) /CSM_Contig/Conti...    30  0.88
Contig-U11424-1 (Contig-U11424-1Q) /CSM_Contig/Conti...    30  0.88

>Contig-U04961-1 (Contig-U04961-1Q) /CSM_Contig/Contig-U04961-1Q.Seq.d
          Length = 213

 Score = 87.7 bits (44), Expect = 4e-18
 Identities = 44/44 (100%)
 Strand = Plus / Plus

                                                       
Query: 170 tctccaaaaatatttcaccaccagaggccattatttgattgttt 213
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 170 tctccaaaaatatttcaccaccagaggccattatttgattgttt 213


 Score = 81.8 bits (41), Expect = 3e-16
 Identities = 41/41 (100%)
 Strand = Plus / Plus

                                                    
Query: 93  caaaaccaaaattttgtcaataaggattatttctttaaata 133
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 93  caaaaccaaaattttgtcaataaggattatttctttaaata 133


 Score = 81.8 bits (41), Expect = 3e-16
 Identities = 41/41 (100%)
 Strand = Plus / Plus

                                                   
Query: 22 ccattaatttagtttactaacatttttattcttatagaaat 62
          |||||||||||||||||||||||||||||||||||||||||
Sbjct: 22 ccattaatttagtttactaacatttttattcttatagaaat 62


>Contig-U04879-1 (Contig-U04879-1Q) /CSM_Contig/Contig-U04879-1Q.Seq.d
          Length = 562

 Score = 34.2 bits (17), Expect = 0.056
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 38  ctaacatttttattctt 54
           |||||||||||||||||
Sbjct: 111 ctaacatttttattctt 95


>Contig-U14067-1 (Contig-U14067-1Q) /CSM_Contig/Contig-U14067-1Q.Seq.d
          Length = 1279

 Score = 30.2 bits (15), Expect = 0.88
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                          
Query: 199 attatttgattgttt 213
           |||||||||||||||
Sbjct: 41  attatttgattgttt 27


  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: 2251
Number of Sequences: 6905
Number of extensions: 2251
Number of successful extensions: 662
Number of sequences better than 10.0: 61
length of query: 213
length of database: 5,674,871
effective HSP length: 15
effective length of query: 198
effective length of database: 5,571,296
effective search space: 1103116608
effective search space used: 1103116608
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. 7. 5
Homology vs DNA 
Query= Contig-U04961-1 (Contig-U04961-1Q) /CSM_Contig/Contig-U04961-1Q.Seq.d
         (213 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(AU073163) Dictyostelium discoideum slug cDNA, clone SSG290.       88   5e-51  3
(AU072337) Dictyostelium discoideum slug cDNA, clone SSE222.       82   2e-27  2
(B75168) RPCI11-13N3.TV RPCI-11 Homo sapiens genomic clone R...    44   0.018  2
(CR392341) Zebrafish DNA sequence from clone CH211-222E20 in...    46   0.51   1
(BX296525) Zebrafish DNA sequence from clone CH211-252F24 in...    46   0.51   1
(AC146681) Medicago truncatula clone mth2-77o10, complete se...    46   0.51   1
(AC133341) Medicago truncatula clone mth2-28i3, complete seq...    46   0.51   1
(AC191508) Spermophilus tridecemlineatus clone VMRC20-392L9,...    46   0.51   1
(CR759898) Human DNA sequence from clone XX-NCIH2171_7O06.         44   2.0    1
(AL589684) Human DNA sequence from clone RP11-437J19 on chro...    44   2.0    1
(AL135744) Human chromosome 14 DNA sequence BAC R-524O1 of l...    44   2.0    1
(CU928863) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   2.0    1
(AL391275) Human DNA sequence *** SEQUENCING CANCELLED *** f...    44   2.0    1
(ED365434) AUAC-aah59d05.g1 Ascaris suum whole genome shotgu...    44   2.0    1
(AI480316) tm26h09.x1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA ...    44   2.0    1
(H71625) ys10a09.s1 Soares fetal liver spleen 1NFLS Homo sap...    44   2.0    1
(EK105436) 1092963045042 Global-Ocean-Sampling_GS-31-01-01-1...    32   2.2    3
(AC167558) Mus musculus chromosome 15, clone wi1-2677E14, co...    42   7.9    1
(AC103672) Mus musculus chromosome 15, clone RP24-351G3, com...    42   7.9    1
(AC120051) Homo sapiens chromosome 8, clone RP11-809L8, comp...    42   7.9    1
(AC093769) Homo sapiens BAC clone RP11-114I18 from 2, comple...    42   7.9    1
(AC135165) Homo sapiens chromosome 8 clone CTD-2522F10 map 8...    42   7.9    1
(AC120755) Rattus norvegicus clone CH230-49L18, *** SEQUENCI...    42   7.9    1
(AC095171) Rattus norvegicus clone CH230-7K10, WORKING DRAFT...    42   7.9    1
(CU856476) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   7.9    1
(AC090148) Homo sapiens chromosome 8 clone RP11-412E20 map 8...    42   7.9    1
(AC173864) Bos taurus clone CH240-253N1, WORKING DRAFT SEQUE...    42   7.9    1
(AC163435) Mus musculus chromosome 15 clone RP24-231O24 map ...    42   7.9    1
(AC025648) Homo sapiens chromosome 8 clone RP11-809L8 map 8,...    42   7.9    1
(AC024238) Homo sapiens chromosome 8 clone RP11-412E20, WORK...    42   7.9    1
(CW327508) 104_823_11478787_116_35975_076 Sorghum methylatio...    42   7.9    1
(DN305530) PL05008B2C12 cDNA from sexually mature hermaphodi...    42   7.9    1
(DN296868) PL04007B1B10 cDNA from sexually mature hermaphodi...    42   7.9    1
(BU930829) AGENCOURT_10425415 NIH_MGC_83 Homo sapiens cDNA c...    42   7.9    1
(FE966345) PLATE_T3_026_D10_02DEC2004_074 Opium poppy elicit...    42   7.9    1

>(AU073163) Dictyostelium discoideum slug cDNA, clone SSG290.
          Length = 216

 Score = 87.7 bits (44), Expect(3) = 5e-51
 Identities = 44/44 (100%)
 Strand = Plus / Plus


Query: 170 tctccaaaaatatttcaccaccagaggccattatttgattgttt 213
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 172 tctccaaaaatatttcaccaccagaggccattatttgattgttt 215

 Score = 81.8 bits (41), Expect(3) = 5e-51
 Identities = 41/41 (100%)
 Strand = Plus / Plus


Query: 22 ccattaatttagtttactaacatttttattcttatagaaat 62
          |||||||||||||||||||||||||||||||||||||||||
Sbjct: 24 ccattaatttagtttactaacatttttattcttatagaaat 64

 Score = 81.8 bits (41), Expect(3) = 5e-51
 Identities = 41/41 (100%)
 Strand = Plus / Plus


Query: 93  caaaaccaaaattttgtcaataaggattatttctttaaata 133
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 95  caaaaccaaaattttgtcaataaggattatttctttaaata 135

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 206,319,826
Number of extensions: 13797988
Number of successful extensions: 3584436
Number of sequences better than 10.0: 35
Length of query: 213
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 190
Effective length of database: 99,442,330,388
Effective search space: 18894042773720
Effective search space used: 18894042773720
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.31
Homology vs Protein 
Query= Contig-U04961-1 (Contig-U04961-1Q) /CSM_Contig/Contig-U04961-1Q.Seq.d
         (213 letters)

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

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

 ***** No hits found ******

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: 100,795,401
Number of extensions: 825763
Number of successful extensions: 402
Number of sequences better than 10.0: 0
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 0
Length of query: 71
Length of database: 1,061,185,681
Length adjustment: 42
Effective length of query: 29
Effective length of database: 923,910,865
Effective search space: 26793415085
Effective search space used: 26793415085
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: 0.12  gvh: 0.10  alm: 0.57  top: 0.53  tms: 0.00  mit: 0.30  mip: 0.00
 nuc: 0.65  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 

	 72.0 %: nuclear
	 12.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U04961-1 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) 2
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