NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U01944-1
Contig ID Contig-U01944-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01944-1 (Contig-U01944-1Q) /CSM_Contig/Contig-U01944-1Q.Seq.d
TTAACAAATAAAAATAAAAAAATTAAACACAAATAATAATAACAATAATA
TTTATTTTTTATTTTAATTTTTCTAAACATATACCAATTATAATTATATT
TTTTTTATTATAAATAAAATAAAAAAAAAAAAAAAAAAAAATTTTTTTAT
TTCCAAATCACAAAATCAATTTTAAAAAAATAATTTACTAAATACTTTTT
TTTCTAAAAAAAACTTTACTTAAAAAAACTTCAAAAACTAAAAATGGAAT
CTAAAAGTGAAATTAATTTTATCTTAAATAAAACCAAAGTTCCACCAGTC
ATTTTCGGAGGAATCTTTTCAACATTTGGAGTTGATAAAAATATGGATTA
TTATTATAACTATAGTGATTACCAAAATAAAAATAATAATAATAATGATA
GAAACTATACAAAAAATAATAAAATAATCAATAGTTGTCAAACTGTTCAA
TGTAATAATTTATCATACTTATTACACTAAAATTAAAAAAAAA-------
---AATCTTGCTTTGTAAATAANGAAATATAAAAAAAAAAAAAAAAAATA
TGGATTGTACATAACTAATATCATCAACTGATATATATATATAAGAAATA
CGCCAAAACGATACTCTAAGAGTAAAATTAAAAATTTTAATAAAAATAAA
TTTATAATTT
Gap gap included
Contig length 650
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 801700
End point 802351
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 4
Link to clone list U01944
List of clone(s) 

est1=SSL422F,1,280
est2=VSK450F,241,494
est3=VSK450Z,241,471
est4=SSL422Z,495,652
Translated Amino Acid sequence 
*qikikklntnnnnnniyflf*ff*tytnynyiffiinkikkkkkknffisksqnqf*kn
nllntffskknft*knfkn*kwnlkvklils*ikpkfhqsfseesfqhlelikiwiiiit
ivitkikiiiimietiqkiik*SIVVKLFNVIIYHTYYTKIKKK---

---SCFVNXEI*kkkkkiwivhn*yhqliyiykkyaktil*e*n*kf**k*iyn
Translated Amino Acid sequence (All Frames) 
Frame A:
ltnknkkikhk***q*ylffiliflniyql*lyffyyk*nkkkkkkkffyfqitksilkk
*ftkyfff*kklylkklqklkmeskseinfilnktkvppvifggifstfgvdknmdyyyn
ysdyqnknnnnndrnytknnkiinscqtvqcnnlsyllh*n*kk---

---nlal*ixkykkkkkkyglyitniin*yiyirntpkryskskiknfnknkfii

Frame B:
*qikikklntnnnnnniyflf*ff*tytnynyiffiinkikkkkkknffisksqnqf*kn
nllntffskknft*knfkn*kwnlkvklils*ikpkfhqsfseesfqhlelikiwiiiit
ivitkikiiiimietiqkiik*SIVVKLFNVIIYHTYYTKIKKK---

---illck*xnikkkkknmdct*lisstdiyi*eirqndtlrvklkilikinl*f

Frame C:
nk*k*kn*tqiiitiififyfnfskhipiiiiffll*ik*kkkkkkiflfpnhkinfkki
iy*ilfflkktllkktsktkngi*k*n*fylk*nqsstshfrrnlfniws**kyglll*l
**lpk*k******klykk**nnq*lsncsm**fiilitlklkk---

---SCFVNXEI*kkkkkiwivhn*yhqliyiykkyaktil*e*n*kf**k*iyn
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U01944-1 (Contig-U01944-1Q)
/CSM_Contig/Contig-U01944-1Q.Seq.d
         (660 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01944-1 (Contig-U01944-1Q) /CSM_Contig/Conti...   256  3e-68
Contig-U10802-1 (Contig-U10802-1Q) /CSM_Contig/Conti...    36  0.046
Contig-U14818-1 (Contig-U14818-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U14185-1 (Contig-U14185-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U13879-1 (Contig-U13879-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U13416-1 (Contig-U13416-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U13371-1 (Contig-U13371-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U13341-1 (Contig-U13341-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U12368-1 (Contig-U12368-1Q) /CSM_Contig/Conti...    34  0.18
Contig-U12185-1 (Contig-U12185-1Q) /CSM_Contig/Conti...    34  0.18

>Contig-U01944-1 (Contig-U01944-1Q) /CSM_Contig/Contig-U01944-1Q.Seq.d
          Length = 660

 Score =  256 bits (129), Expect = 3e-68
 Identities = 129/129 (100%)
 Strand = Plus / Plus

                                                                       
Query: 245 tggaatctaaaagtgaaattaattttatcttaaataaaaccaaagttccaccagtcattt 304
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 245 tggaatctaaaagtgaaattaattttatcttaaataaaaccaaagttccaccagtcattt 304

                                                                       
Query: 305 tcggaggaatcttttcaacatttggagttgataaaaatatggattattattataactata 364
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 305 tcggaggaatcttttcaacatttggagttgataaaaatatggattattattataactata 364

                    
Query: 365 gtgattacc 373
           |||||||||
Sbjct: 365 gtgattacc 373


 Score =  111 bits (56), Expect = 1e-24
 Identities = 56/56 (100%)
 Strand = Plus / Plus

                                                                   
Query: 429 caatagttgtcaaactgttcaatgtaataatttatcatacttattacactaaaatt 484
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 429 caatagttgtcaaactgttcaatgtaataatttatcatacttattacactaaaatt 484


 Score = 63.9 bits (32), Expect = 2e-10
 Identities = 32/32 (100%)
 Strand = Plus / Plus

                                           
Query: 549 tatggattgtacataactaatatcatcaactg 580
           ||||||||||||||||||||||||||||||||
Sbjct: 549 tatggattgtacataactaatatcatcaactg 580


 Score = 61.9 bits (31), Expect = 8e-10
 Identities = 31/31 (100%)
 Strand = Plus / Plus

                                          
Query: 142 tttttttatttccaaatcacaaaatcaattt 172
           |||||||||||||||||||||||||||||||
Sbjct: 142 tttttttatttccaaatcacaaaatcaattt 172


 Score = 58.0 bits (29), Expect = 1e-08
 Identities = 29/29 (100%)
 Strand = Plus / Plus

                                        
Query: 594 agaaatacgccaaaacgatactctaagag 622
           |||||||||||||||||||||||||||||
Sbjct: 594 agaaatacgccaaaacgatactctaagag 622


 Score = 52.0 bits (26), Expect = 8e-07
 Identities = 26/26 (100%)
 Strand = Plus / Plus

                                    
Query: 73 ctaaacatataccaattataattata 98
          ||||||||||||||||||||||||||
Sbjct: 73 ctaaacatataccaattataattata 98


 Score = 48.1 bits (24), Expect = 1e-05
 Identities = 27/27 (100%)
 Strand = Plus / Plus

                                      
Query: 504 aatcttgctttgtaaataangaaatat 530
           |||||||||||||||||||||||||||
Sbjct: 504 aatcttgctttgtaaataangaaatat 530


>Contig-U10802-1 (Contig-U10802-1Q) /CSM_Contig/Contig-U10802-1Q.Seq.d
          Length = 1447

 Score = 36.2 bits (18), Expect = 0.046
 Identities = 21/22 (95%)
 Strand = Plus / Minus

                                  
Query: 259  gaaattaattttatcttaaata 280
            ||||||||||||||||| ||||
Sbjct: 1313 gaaattaattttatcttcaata 1292


>Contig-U14818-1 (Contig-U14818-1Q) /CSM_Contig/Contig-U14818-1Q.Seq.d
          Length = 819

 Score = 34.2 bits (17), Expect = 0.18
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 323 catttggagttgataaa 339
           |||||||||||||||||
Sbjct: 749 catttggagttgataaa 733


  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: 19,275
Number of Sequences: 6905
Number of extensions: 19275
Number of successful extensions: 1063
Number of sequences better than 10.0: 87
length of query: 660
length of database: 5,674,871
effective HSP length: 16
effective length of query: 644
effective length of database: 5,564,391
effective search space: 3583467804
effective search space used: 3583467804
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2009. 5.10
Homology vs DNA 
Query= Contig-U01944-1 (Contig-U01944-1Q) /CSM_Contig/Contig-U01944-1Q.Seq.d
         (660 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

(AU271219) Dictyostelium discoideum vegetative cDNA clone:VS...   119   6e-43  2
(AU271220) Dictyostelium discoideum vegetative cDNA clone:VS...    92   6e-30  2
(AU038740) Dictyostelium discoideum slug cDNA, clone SSL422.       64   2e-26  3
(AC158103) Bos taurus clone CH240-50H2, WORKING DRAFT SEQUEN...    50   0.11   1
(AC051638) Mus musculus chromosome 6, clone RP23-177J17, com...    48   0.43   1
(AC114689) Homo sapiens chromosome 18, clone RP11-638L3, com...    48   0.43   1
(AC021561) Homo sapiens chromosome 18, clone RP11-766D3, com...    48   0.43   1
(AC142275) Mus musculus chromosome UNK clone RP23-203J13, WO...    48   0.43   1
(CU469024) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    48   0.43   1
(CU041332) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    48   0.43   1
(AC025002) Homo sapiens chromosome 1 clone RP11-204L3 map 1,...    48   0.43   1
(AK041046) Mus musculus adult male aorta and vein cDNA, RIKE...    48   0.43   1
(BB221670) Mus musculus adult male aorta and vein cDNA, RIKE...    48   0.43   1
(AC204741) Rhesus Macaque  BAC CH250-97L14 () complete seque...    46   1.7    1
(BD452915) Diagnosis of Diseases Associated with tumor suppr...    46   1.7    1
(AX344845) Sequence 270 from Patent WO0200927.                     46   1.7    1
(AX251394) Sequence 362 from Patent WO0168912.                     46   1.7    1
(ER509619) 1093015436004 Global-Ocean-Sampling_GS-35-01-01-1...    46   1.7    1
(EK435552) 1095521031172 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EK431595) 1095516156510 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EK367176) 1095469402448 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EK099910) 1092963008556 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EK098822) 1092962061115 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EK097850) 1092962050287 Global-Ocean-Sampling_GS-31-01-01-1...    46   1.7    1
(EJ549980) 1092959434451 Global-Ocean-Sampling_GS-29-01-01-1...    46   1.7    1
(EJ526896) 1092955190838 Global-Ocean-Sampling_GS-29-01-01-1...    46   1.7    1
(AM481104) Vitis vinifera contig VV78X081683.12, whole genom...    44   3.0    2
(AC217333) Solanum lycopersicum chromosome 12 clone LE_HBa-2...    38   5.4    2
(AC212272) Macaca mulatta  BAC CH250-329N3 (Children's Hospi...    44   6.7    1
(AC199586) Rhesus Macaque  BAC CH250-101H7 () complete seque...    44   6.7    1
(AM484168) Vitis vinifera contig VV78X070909.8, whole genome...    44   6.7    1
(AM470314) Vitis vinifera contig VV78X136923.3, whole genome...    44   6.7    1
(AM449544) Vitis vinifera contig VV78X116525.3, whole genome...    44   6.7    1
(AM429392) Vitis vinifera contig VV78X075405.5, whole genome...    44   6.7    1
(AC212306) Solanum lycopersicum cv. Heinz 1706, chromosome 0...    44   6.7    1
(AL445188) Human DNA sequence from clone RP11-260E14 on chro...    44   6.7    1
(AE014305) Homo sapiens chromosome 13q34 schizophrenia regio...    44   6.7    1
(AC148141) Bos taurus clone RP42-335C16, WORKING DRAFT SEQUE...    44   6.7    1
(AC112279) Rattus norvegicus clone CH230-30O5, *** SEQUENCIN...    44   6.7    1
(AC097170) Rattus norvegicus clone CH230-84O1, WORKING DRAFT...    44   6.7    1
(CU914283) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   6.7    1
(AC172033) Bos taurus clone CH240-309E20, WORKING DRAFT SEQU...    44   6.7    1
(DU916799) 324297 Tomato EcoRI BAC Library Solanum lycopersi...    44   6.7    1
(DU899294) 411960 Tomato HindIII BAC Library Solanum lycoper...    44   6.7    1
(DU894807) 415556 Tomato HindIII BAC Library Solanum lycoper...    44   6.7    1
(CZ987738) 202442 Tomato MboI BAC Library Solanum lycopersic...    44   6.7    1
(CZ960695) 306407 Tomato EcoRI BAC Library Solanum lycopersi...    44   6.7    1
(CZ941111) 323121 Tomato EcoRI BAC Library Solanum lycopersi...    44   6.7    1
(CC581765) CH240_376N22.TARBAC13P2 CHORI-240 Bos taurus geno...    44   6.7    1
(BZ771556) mct77g11.b6 HFOSMID004 Homo sapiens genomic, geno...    44   6.7    1
(EL915577) INIT2_92_E06.g2_A006 G5 trophont cDNA (INIT2) Ich...    44   6.7    1
(EL915017) INIT2_85_E11.g1_A006 G5 trophont cDNA (INIT2) Ich...    44   6.7    1
(EV759654) AGENCOURT_109125313 NIH_ZGC_30 Danio rerio cDNA c...    44   6.7    1
(AC212512) Macaca mulatta  BAC CH250-350L8 (Children's Hospi...    36   7.1    3

>(AU271219) Dictyostelium discoideum vegetative cDNA clone:VSK450,
           5' end single read.
          Length = 254

 Score =  119 bits (60), Expect(2) = 6e-43
 Identities = 60/60 (100%)
 Strand = Plus / Plus


Query: 434 gttgtcaaactgttcaatgtaataatttatcatacttattacactaaaattaaaaaaaaa 493
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 194 gttgtcaaactgttcaatgtaataatttatcatacttattacactaaaattaaaaaaaaa 253

 Score = 91.7 bits (46), Expect(2) = 6e-43
 Identities = 46/46 (100%)
 Strand = Plus / Plus


Query: 289 gttccaccagtcattttcggaggaatcttttcaacatttggagttg 334
           ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 49  gttccaccagtcattttcggaggaatcttttcaacatttggagttg 94

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 351,424,992
Number of extensions: 22196774
Number of successful extensions: 2247048
Number of sequences better than 10.0: 55
Length of query: 660
Length of database: 101,790,757,118
Length adjustment: 24
Effective length of query: 636
Effective length of database: 99,340,224,878
Effective search space: 63180383022408
Effective search space used: 63180383022408
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01944-1 (Contig-U01944-1Q) /CSM_Contig/Contig-U01944-1Q.Seq.d
         (660 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: 369,337,370
Number of extensions: 2959256
Number of successful extensions: 16822
Number of sequences better than 10.0: 0
Number of HSP's gapped: 16822
Number of HSP's successfully gapped: 0
Length of query: 220
Length of database: 1,051,180,864
Length adjustment: 124
Effective length of query: 96
Effective length of database: 649,847,548
Effective search space: 62385364608
Effective search space used: 62385364608
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: 31 (16.5 bits)
PSORT 

 psg: 0.82  gvh: 0.14  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.35  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 

	 44.0 %: nuclear
	 36.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: Golgi
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U01944-1 is nuc
VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 1
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