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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U13560-1
Contig ID Contig-U13560-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13560-1 (Contig-U13560-1Q) /CSM_Contig/Contig-U13560-1Q.Seq.d
NNNNNNNNNNTNATATGGTTTACCNACAANGATTTTCAGACCAGGNACAA
TNTTTAGTNANACCCAATTTGGNTTCAACAATCAAAATGATTCNATCGGN
TTAATAANTAAAGGNATCCTAGGNTNGAGTTCCTATCCAACTAAAAAAGA
TTACTTTAGTGGCGATTTAAATNTTTCNCCAGTTGATTGGGNATCATNTT
CAANGGNTTNTTTAANTAAGCATTTTCCNTTTTGGNGTAATAANACAAAA
ATTTATCATATGGNAAATGATAATNGTTTATCTTTANATTTGNTANGNCN
ATATATAAATAAANAAAAACNATTAGAAGAAATTAATTATTTNGATTGGA
TNGATGNTCAACTTAATTTTTCAAATAATCCNTTGTATTTTATTAAACNT
TTATTTAAAAANAATGATCGTTTCCCNATTGGTTTTCAGTCAATTAAAAA
TCCNAAAACTATTAAAGATTTANAATCNATTGGTGAACTTCAANGTCNAC
CNANATNNGATTCCC
Gap no gap
Contig length 515
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 U13560
List of clone(s) 

est1=VHB832Z,1,506
Translated Amino Acid sequence 
XXXXYGLPTXIFRPGTXFSXTQFGFNNQNDSIGLIXKGILGXSSYPTKKDYFSGDLNXSP
VDWXSXSXXXLXKHFPFWXNXTKIYHMXNDNXLSLXLXXXYINKXKXLEEINYXDWXDXQ
LNFSNNPLYFIKXLFKXNDRFPIGFQSIKNPKTIKDLXSIGELQXXPXXDS
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxiwftxxdfqtrxnx*xxpiwxqqsk*fxrxnx*rxprxeflsn*krll*wrfkxfx
s*lgixfxgxfx*afsxlx**xknlsygk**xfifxfxxxiyk*xktirrn*lfxldxxs
t*ffk*sxvfy*tfi*kx*sfpxwfsvn*ksxny*rfxixw*tsxstxxxf


Frame B:
XXXXYGLPTXIFRPGTXFSXTQFGFNNQNDSIGLIXKGILGXSSYPTKKDYFSGDLNXSP
VDWXSXSXXXLXKHFPFWXNXTKIYHMXNDNXLSLXLXXXYINKXKXLEEINYXDWXDXQ
LNFSNNPLYFIKXLFKXNDRFPIGFQSIKNPKTIKDLXSIGELQXXPXXDS


Frame C:
xxxxmvyxqxfsdqxqxlvxpnlxstikmixsx**xkxs*xxvpiqlkkitlvai*xfxq
ligxhxqxxx*xsifxfgvixqkfiiwxmixvylxixxxxi*ixknx*kkliixigxmxn
lifqiixcillnxylkxmivsxlvfsqlkixkllkixnxlvnfxvxxxxip
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13560-1 (Contig-U13560-1Q)
/CSM_Contig/Contig-U13560-1Q.Seq.d
         (515 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13560-1 (Contig-U13560-1Q) /CSM_Contig/Conti...   658  0.0
Contig-U09542-1 (Contig-U09542-1Q) /CSM_Contig/Conti...    38  0.009
Contig-U11288-1 (Contig-U11288-1Q) /CSM_Contig/Conti...    36  0.036
Contig-U10406-1 (Contig-U10406-1Q) /CSM_Contig/Conti...    36  0.036
Contig-U12503-1 (Contig-U12503-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U06069-1 (Contig-U06069-1Q) /CSM_Contig/Conti...    34  0.14
Contig-U14182-1 (Contig-U14182-1Q) /CSM_Contig/Conti...    32  0.56
Contig-U14136-1 (Contig-U14136-1Q) /CSM_Contig/Conti...    32  0.56
Contig-U12535-1 (Contig-U12535-1Q) /CSM_Contig/Conti...    32  0.56
Contig-U12285-1 (Contig-U12285-1Q) /CSM_Contig/Conti...    28  8.7

>Contig-U13560-1 (Contig-U13560-1Q) /CSM_Contig/Contig-U13560-1Q.Seq.d
          Length = 515

 Score =  658 bits (332), Expect = 0.0
 Identities = 495/503 (98%)
 Strand = Plus / Plus

                                                                       
Query: 13  atatggtttaccnacaangattttcagaccaggnacaatntttagtnanacccaatttgg 72
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 13  atatggtttaccnacaangattttcagaccaggnacaatntttagtnanacccaatttgg 72

                                                                       
Query: 73  nttcaacaatcaaaatgattcnatcggnttaataantaaaggnatcctaggntngagttc 132
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 73  nttcaacaatcaaaatgattcnatcggnttaataantaaaggnatcctaggntngagttc 132

                                                                       
Query: 133 ctatccaactaaaaaagattactttagtggcgatttaaatntttcnccagttgattgggn 192
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 133 ctatccaactaaaaaagattactttagtggcgatttaaatntttcnccagttgattgggn 192

                                                                       
Query: 193 atcatnttcaanggnttntttaantaagcattttccnttttggngtaataanacaaaaat 252
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 atcatnttcaanggnttntttaantaagcattttccnttttggngtaataanacaaaaat 252

                                                                       
Query: 253 ttatcatatggnaaatgataatngtttatctttanatttgntangncnatatataaatnn 312
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  
Sbjct: 253 ttatcatatggnaaatgataatngtttatctttanatttgntangncnatatataaataa 312

                                                                       
Query: 313 nnnnnnncnattagaagaaattaattatttngattggatngatgntcaacttaatttttc 372
            |     |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 313 anaaaaacnattagaagaaattaattatttngattggatngatgntcaacttaatttttc 372

                                                                       
Query: 373 aaataatccnttgtattttattaaacntttatttaaaaanaatgatcgtttcccnattgg 432
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 373 aaataatccnttgtattttattaaacntttatttaaaaanaatgatcgtttcccnattgg 432

                                                                       
Query: 433 ttttcagtcaattaaaaatccnaaaactattaaagatttanaatcnattggtgaacttca 492
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 433 ttttcagtcaattaaaaatccnaaaactattaaagatttanaatcnattggtgaacttca 492

                                  
Query: 493 angtcnaccnanatnngattccc 515
           |||||||||||||||||||||||
Sbjct: 493 angtcnaccnanatnngattccc 515


>Contig-U09542-1 (Contig-U09542-1Q) /CSM_Contig/Contig-U09542-1Q.Seq.d
          Length = 757

 Score = 38.2 bits (19), Expect = 0.009
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 245 acaaaaatttatcatatgg 263
           |||||||||||||||||||
Sbjct: 164 acaaaaatttatcatatgg 182


>Contig-U11288-1 (Contig-U11288-1Q) /CSM_Contig/Contig-U11288-1Q.Seq.d
          Length = 3111

 Score = 36.2 bits (18), Expect = 0.036
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 455  aaaactattaaagattta 472
            ||||||||||||||||||
Sbjct: 2251 aaaactattaaagattta 2268


  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: 4470
Number of Sequences: 6905
Number of extensions: 4470
Number of successful extensions: 385
Number of sequences better than 10.0: 103
length of query: 515
length of database: 5,674,871
effective HSP length: 16
effective length of query: 499
effective length of database: 5,564,391
effective search space: 2776631109
effective search space used: 2776631109
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 2008.12.11
Homology vs DNA 
Query= Contig-U13560-1 (Contig-U13560-1Q) /CSM_Contig/Contig-U13560-1Q.Seq.d
         (515 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

(BJ437499) Dictyostelium discoideum cDNA clone:ddv34p08, 3' ...   706   0.0    1
(EK265005) 1095462220224 Global-Ocean-Sampling_GS-31-01-01-1...    44   0.17   2
(AM464590) Vitis vinifera, whole genome shotgun sequence, co...    44   0.45   3
(ET288508) S0089K02_T7 CHORI-214 Salmo salar genomic clone S...    46   1.2    1
(AC097512) Homo sapiens BAC clone RP11-412P11 from 4, comple...    44   4.8    1
(AC119702) Rattus norvegicus clone CH230-123I18, *** SEQUENC...    44   4.8    1
(EJ589885) 1092961042750 Global-Ocean-Sampling_GS-29-01-01-1...    36   8.5    2
(AC229829) Monodelphis domestica clone VMRC18-581F22, WORKIN...    32   8.7    2
(EJ545662) 1092956084778 Global-Ocean-Sampling_GS-29-01-01-1...    36   9.2    2
(DQ927303) Tetrahymena malaccensis strain MP75 mitochondrion...    34   10.0   5

>(BJ437499) Dictyostelium discoideum cDNA clone:ddv34p08, 3' end,
           single read.
          Length = 506

 Score =  706 bits (356), Expect = 0.0
 Identities = 503/503 (100%)
 Strand = Plus / Minus


Query: 13  atatggtttaccnacaangattttcagaccaggnacaatntttagtnanacccaatttgg 72
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 504 atatggtttaccnacaangattttcagaccaggnacaatntttagtnanacccaatttgg 445


Query: 73  nttcaacaatcaaaatgattcnatcggnttaataantaaaggnatcctaggntngagttc 132
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 444 nttcaacaatcaaaatgattcnatcggnttaataantaaaggnatcctaggntngagttc 385


Query: 133 ctatccaactaaaaaagattactttagtggcgatttaaatntttcnccagttgattgggn 192
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 384 ctatccaactaaaaaagattactttagtggcgatttaaatntttcnccagttgattgggn 325


Query: 193 atcatnttcaanggnttntttaantaagcattttccnttttggngtaataanacaaaaat 252
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 324 atcatnttcaanggnttntttaantaagcattttccnttttggngtaataanacaaaaat 265


Query: 253 ttatcatatggnaaatgataatngtttatctttanatttgntangncnatatataaataa 312
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 264 ttatcatatggnaaatgataatngtttatctttanatttgntangncnatatataaataa 205


Query: 313 anaaaaacnattagaagaaattaattatttngattggatngatgntcaacttaatttttc 372
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 204 anaaaaacnattagaagaaattaattatttngattggatngatgntcaacttaatttttc 145


Query: 373 aaataatccnttgtattttattaaacntttatttaaaaanaatgatcgtttcccnattgg 432
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 144 aaataatccnttgtattttattaaacntttatttaaaaanaatgatcgtttcccnattgg 85


Query: 433 ttttcagtcaattaaaaatccnaaaactattaaagatttanaatcnattggtgaacttca 492
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 84  ttttcagtcaattaaaaatccnaaaactattaaagatttanaatcnattggtgaacttca 25


Query: 493 angtcnaccnanatnngattccc 515
           |||||||||||||||||||||||
Sbjct: 24  angtcnaccnanatnngattccc 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 353,652,122
Number of extensions: 22483464
Number of successful extensions: 1300116
Number of sequences better than 10.0: 10
Length of query: 515
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 492
Effective length of database: 93,106,754,628
Effective search space: 45808523276976
Effective search space used: 45808523276976
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 7
Homology vs Protein 
Query= Contig-U13560-1 (Contig-U13560-1Q) /CSM_Contig/Contig-U13560-1Q.Seq.d
         (515 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 427,522,236
Number of extensions: 6023155
Number of successful extensions: 3723
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3723
Number of HSP's successfully gapped: 0
Length of query: 171
Length of database: 1,051,180,864
Length adjustment: 119
Effective length of query: 52
Effective length of database: 666,030,343
Effective search space: 34633577836
Effective search space used: 34633577836
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: 30 (16.2 bits)
PSORT 

 psg: 0.86  gvh: 0.42  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.03
 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 

	 44.0 %: cytoplasmic
	 28.0 %: nuclear
	 12.0 %: mitochondrial
	  8.0 %: cytoskeletal
	  4.0 %: peroxisomal
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U13560-1 is cyt
VS (DIR, S) 0
VH (FL, L) 1
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