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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-U03099-1
Contig ID Contig-U03099-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U03099-1 (Contig-U03099-1Q) /CSM_Contig/Contig-U03099-1Q.Seq.d
TCTTTTCAAAAGGTCAANATAATTTGGAATCATTTGATGNCAACTACGTG
ANACTAAATTTGGATAATGATCAATGAAAATATCCAATAAACGTAATGAA
TNTAAACGGATGGTTGTCTTTAAATGNGTNNNACCGGAATTAATGTAAAC
TNAAAACAATGGNATGAATGGTGAA
Gap no gap
Contig length 175
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 3007539
End point 3007714
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U03099
List of clone(s) 

est1=CFB404Z,1,176
Translated Amino Acid sequence 
lfkrsx*fgii*xqlrxtkfg**SMKISNKRNEXKRMVVFKXVXPELM*txnngmnge
Translated Amino Acid sequence (All Frames) 
Frame A:
sfqkvxiiwnhlmxtt*x*iwimineniq*t**x*tdgcl*mxxtginvnxkqwxew*


Frame B:
lfkrsx*fgii*xqlrxtkfg**SMKISNKRNEXKRMVVFKXVXPELM*txnngmnge


Frame C:
fskgqxnlesfdxnyvxlnldndq*kypinvmnxngwlslnxxxrn*cklktmx*mv
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U03099-1 (Contig-U03099-1Q)
/CSM_Contig/Contig-U03099-1Q.Seq.d
         (175 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U03099-1 (Contig-U03099-1Q) /CSM_Contig/Conti...   287  2e-78
Contig-U14015-1 (Contig-U14015-1Q) /CSM_Contig/Conti...    36  0.011
Contig-U01513-1 (Contig-U01513-1Q) /CSM_Contig/Conti...    32  0.18
Contig-U14541-1 (Contig-U14541-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U13959-1 (Contig-U13959-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U12372-1 (Contig-U12372-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U12327-1 (Contig-U12327-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U10627-1 (Contig-U10627-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U10338-1 (Contig-U10338-1Q) /CSM_Contig/Conti...    30  0.71
Contig-U09230-1 (Contig-U09230-1Q) /CSM_Contig/Conti...    30  0.71

>Contig-U03099-1 (Contig-U03099-1Q) /CSM_Contig/Contig-U03099-1Q.Seq.d
          Length = 175

 Score =  287 bits (145), Expect = 2e-78
 Identities = 175/175 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   tcttttcaaaaggtcaanataatttggaatcatttgatgncaactacgtganactaaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   tcttttcaaaaggtcaanataatttggaatcatttgatgncaactacgtganactaaatt 60

                                                                       
Query: 61  tggataatgatcaatgaaaatatccaataaacgtaatgaatntaaacggatggttgtctt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tggataatgatcaatgaaaatatccaataaacgtaatgaatntaaacggatggttgtctt 120

                                                                  
Query: 121 taaatgngtnnnaccggaattaatgtaaactnaaaacaatggnatgaatggtgaa 175
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taaatgngtnnnaccggaattaatgtaaactnaaaacaatggnatgaatggtgaa 175


>Contig-U14015-1 (Contig-U14015-1Q) /CSM_Contig/Contig-U14015-1Q.Seq.d
          Length = 1405

 Score = 36.2 bits (18), Expect = 0.011
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 75  tgaaaatatccaataaac 92
           ||||||||||||||||||
Sbjct: 674 tgaaaatatccaataaac 657


>Contig-U01513-1 (Contig-U01513-1Q) /CSM_Contig/Contig-U01513-1Q.Seq.d
          Length = 686

 Score = 32.2 bits (16), Expect = 0.18
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                           
Query: 55  taaatttggataatga 70
           ||||||||||||||||
Sbjct: 584 taaatttggataatga 569


  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: 1335
Number of Sequences: 6905
Number of extensions: 1335
Number of successful extensions: 379
Number of sequences better than 10.0: 37
length of query: 175
length of database: 5,674,871
effective HSP length: 15
effective length of query: 160
effective length of database: 5,571,296
effective search space: 891407360
effective search space used: 891407360
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. 5.25
Homology vs DNA 
Query= Contig-U03099-1 (Contig-U03099-1Q) /CSM_Contig/Contig-U03099-1Q.Seq.d
         (175 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

(BJ373437) Dictyostelium discoideum cDNA clone:ddc3h02, 3' e...   287   6e-74  1
(ED134078) AUAC-aaa80c05.g1 Ascaris suum whole genome shotgu...    36   1.1    2
(GH264637) EST_eluc_evq_996445 elucevq mixed_tissue Esox luc...    32   4.1    2
(GH264638) EST_eluc_evq_1007197 elucevq mixed_tissue Esox lu...    32   4.2    2
(AC181892) Strongylocentrotus purpuratus clone R3-1016M05, W...    38   4.9    2
(CR381585) Zebrafish DNA sequence from clone DKEY-27P7 in li...    42   6.4    1
(AL928705) Mouse DNA sequence from clone RP23-200K17 on chro...    42   6.4    1
(AM450641) Vitis vinifera contig VV78X054074.3, whole genome...    42   6.4    1
(AC136119) Rattus norvegicus clone CH230-525F3, *** SEQUENCI...    42   6.4    1
(AC133678) Rattus norvegicus clone CH230-178A18, *** SEQUENC...    42   6.4    1
(AC129128) Rattus norvegicus clone CH230-275F7, WORKING DRAF...    42   6.4    1
(AC094304) Rattus norvegicus clone CH230-3I10, *** SEQUENCIN...    42   6.4    1
(BX005433) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    42   6.4    1
(AC232868) Medicago truncatula clone mth2-79c11, WORKING DRA...    42   6.4    1
(AC229688) Medicago truncatula clone mth2-151o9, WORKING DRA...    42   6.4    1
(DX443371) BE1031_A05_R IASMA L1 HindIII BAC library Vitis v...    42   6.4    1
(CT523365) A BAC library has been constructed from cultivar ...    42   6.4    1

>(BJ373437) Dictyostelium discoideum cDNA clone:ddc3h02, 3' end,
           single read.
          Length = 176

 Score =  287 bits (145), Expect = 6e-74
 Identities = 175/175 (100%)
 Strand = Plus / Minus


Query: 1   tcttttcaaaaggtcaanataatttggaatcatttgatgncaactacgtganactaaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 176 tcttttcaaaaggtcaanataatttggaatcatttgatgncaactacgtganactaaatt 117


Query: 61  tggataatgatcaatgaaaatatccaataaacgtaatgaatntaaacggatggttgtctt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 116 tggataatgatcaatgaaaatatccaataaacgtaatgaatntaaacggatggttgtctt 57


Query: 121 taaatgngtnnnaccggaattaatgtaaactnaaaacaatggnatgaatggtgaa 175
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 56  taaatgngtnnnaccggaattaatgtaaactnaaaacaatggnatgaatggtgaa 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 142,333,129
Number of extensions: 8055921
Number of successful extensions: 1789135
Number of sequences better than 10.0: 17
Length of query: 175
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 153
Effective length of database: 99,544,435,898
Effective search space: 15230298692394
Effective search space used: 15230298692394
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.22
Homology vs Protein 
Query= Contig-U03099-1 (Contig-U03099-1Q) /CSM_Contig/Contig-U03099-1Q.Seq.d
         (175 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AK132870_1(AK132870|pid:none) Mus musculus adult male testis cDN...    48   9e-05
(Q803M3) RecName: Full=Testis-expressed sequence 10 protein homo...    48   9e-05
AK302619_1(AK302619|pid:none) Homo sapiens cDNA FLJ57815 complet...    45   8e-04
AK304869_1(AK304869|pid:none) Homo sapiens cDNA FLJ50387 complet...    45   8e-04
BC112672_1(BC112672|pid:none) Bos taurus testis expressed 10, mR...    45   8e-04
(Q5RDK1) RecName: Full=Testis-expressed sequence 10 protein;  &C...    45   8e-04
BC030652_1(BC030652|pid:none) Homo sapiens testis expressed 10, ...    45   8e-04
(Q5ZM41) RecName: Full=Testis-expressed sequence 10 protein homo...    43   0.004
BC006867_1(BC006867|pid:none) Mus musculus testis expressed gene...    35   0.62
AB006700_11(AB006700|pid:none) Arabidopsis thaliana genomic DNA,...    32   5.2
(A3M0B1) RecName: Full=Pre-rRNA-processing protein IPI1;  &CP000...    32   6.8

>AK132870_1(AK132870|pid:none) Mus musculus adult male testis cDNA,
           RIKEN full-length enriched library, clone:4930467H04
           product:testis expressed gene 10, full insert sequence.
           &AK141288_1(AK141288|pid:none)
           &AL807247_3(AL807247|pid:none)
           &BC151176_1(BC151176|pid:none)
           &BC151177_1(BC151177|pid:none)
           &BC156481_1(BC156481|pid:none)
           &BC172695_1(BC172695|pid:none)
          Length = 928

 Score = 48.1 bits (113), Expect = 9e-05
 Identities = 20/56 (35%), Positives = 36/56 (64%)
 Frame = -2

Query: 174 SPFXPLFXVYINSGXTHLKTTIRLXSLRLLDIFIDHYPNLVSRSXHQMIPNYXDLL 7
           SPF PL   +++S  TH+   I+  SL++LDI ++HYP L++     ++ N+ +L+
Sbjct: 135 SPFFPLVSAHLSSAMTHITEGIQEDSLKVLDILLEHYPALITGRSSILLKNFVELI 190

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: 212,108,458
Number of extensions: 2922666
Number of successful extensions: 2451
Number of sequences better than 10.0: 11
Number of HSP's gapped: 2451
Number of HSP's successfully gapped: 11
Length of query: 58
Length of database: 1,051,180,864
Length adjustment: 31
Effective length of query: 27
Effective length of database: 950,847,535
Effective search space: 25672883445
Effective search space used: 25672883445
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: 0.57  gvh: 0.10  alm: 0.63  top: 0.53  tms: 0.00  mit: 0.34  mip: 0.00
 nuc: 0.12  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 

	 68.0 %: nuclear
	 12.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U03099-1 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) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 1
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0