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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-U04560-1
Contig ID Contig-U04560-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Contig-U04560-1Q.Seq.d
ATTTTATTAAATTATTTGTATATTTAAGAAAAAAAAAAAAAAAATATTAA
TAAATTTGATTTTTTTTTTTTTTTTTTCTCTTTAAAAACCAACAAACAAA
CCATTAATCTAAAAACAAAAATTATTTAAGCAACCNAAAAAAAAAANCAA
AAATAATTATTTATTTTATTTATTAATTTATCCAACACCAAATTATAAGA
AAAAAATTCTTTGCACCACACAATCAAAAAAAAAAAAAAAAAAAAAAAAA
AAAACATTAAATATAACTACTCCACAATATCACTACTCCACCCAATAAAA
AAAAAAATAAAAAAAAAATAAAATCAACAAATTCTATATTTAATAATATC
TATTAATATTCTCAAATTCTTTCAAAAAAAAAAAAAAAACAAAATAATAA
AATAAATATTTTTTAATAATAACACATTTATTTTTTCAACGTCAA
Gap no gap
Contig length 445
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 2487798
End point 2487352
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 2
Link to clone list U04560
List of clone(s) 

est1=SSK245E,1,446
est2=SSB466F,49,222
Translated Amino Acid sequence 
fy*iicifkkkkkkilinlifffffsl*kptnkpli*KQKLFKQPKKKXKNNYLFYLLIY
PTPNYKKKILCTTQSKKKKKKKKKTLNITTPQYHYSTQ*kkk*kknkinkfyi**yllif
snsfkkkkktk**nkyfliithlffqrq
Translated Amino Acid sequence (All Frames) 
Frame A:
illnylyi*ekkkkninkfdffffffslktnkqtinlktkii*atxkkxqk*lfilfinl
sntkl*eknslhhtikkkkkkkkknikynystisllhpikkkikkk*nqqilyliisini
lkffqkkkknkiik*iffnnntfifsts


Frame B:
fy*iicifkkkkkkilinlifffffsl*kptnkpli*KQKLFKQPKKKXKNNYLFYLLIY
PTPNYKKKILCTTQSKKKKKKKKKTLNITTPQYHYSTQ*kkk*kknkinkfyi**yllif
snsfkkkkktk**nkyfliithlffqrq


Frame C:
fiklfvylrkkkkky**i*fffffflfknqqtnh*sknknylsnxkkkxkiiiyfiy*fi
qhqiirkkffaphnqkkkkkkkkkh*i*llhnittppnkkknkkkikstnsifnniy*ys
qilskkkkkqnnkinif***hiyffnv
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04560-1 (Contig-U04560-1Q)
/CSM_Contig/Contig-U04560-1Q.Seq.d
         (445 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Conti...   100  2e-21
Contig-U11513-1 (Contig-U11513-1Q) /CSM_Contig/Conti...    36  0.031
Contig-U05787-1 (Contig-U05787-1Q) /CSM_Contig/Conti...    36  0.031
Contig-U14349-1 (Contig-U14349-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U06247-1 (Contig-U06247-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U14838-1 (Contig-U14838-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U14174-1 (Contig-U14174-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U13948-1 (Contig-U13948-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U13434-1 (Contig-U13434-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U12673-1 (Contig-U12673-1Q) /CSM_Contig/Conti...    32  0.48

>Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Contig-U04560-1Q.Seq.d
          Length = 445

 Score = 99.6 bits (50), Expect = 2e-21
 Identities = 50/50 (100%)
 Strand = Plus / Plus

                                                             
Query: 324 tcaacaaattctatatttaataatatctattaatattctcaaattctttc 373
           ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 324 tcaacaaattctatatttaataatatctattaatattctcaaattctttc 373


 Score = 83.8 bits (42), Expect = 1e-16
 Identities = 42/42 (100%)
 Strand = Plus / Plus

                                                     
Query: 255 cattaaatataactactccacaatatcactactccacccaat 296
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 255 cattaaatataactactccacaatatcactactccacccaat 296


 Score = 56.0 bits (28), Expect = 3e-08
 Identities = 28/28 (100%)
 Strand = Plus / Plus

                                      
Query: 1  attttattaaattatttgtatatttaag 28
          ||||||||||||||||||||||||||||
Sbjct: 1  attttattaaattatttgtatatttaag 28


 Score = 42.1 bits (21), Expect = 5e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 205 aattctttgcaccacacaatc 225
           |||||||||||||||||||||
Sbjct: 205 aattctttgcaccacacaatc 225


 Score = 30.2 bits (15), Expect = 1.9
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                         
Query: 45 tattaataaatttga 59
          |||||||||||||||
Sbjct: 45 tattaataaatttga 59


>Contig-U11513-1 (Contig-U11513-1Q) /CSM_Contig/Contig-U11513-1Q.Seq.d
          Length = 2108

 Score = 36.2 bits (18), Expect = 0.031
 Identities = 21/22 (95%)
 Strand = Plus / Minus

                                 
Query: 339 tttaataatatctattaatatt 360
           |||||||||||||| |||||||
Sbjct: 962 tttaataatatctaataatatt 941


>Contig-U05787-1 (Contig-U05787-1Q) /CSM_Contig/Contig-U05787-1Q.Seq.d
          Length = 620

 Score = 36.2 bits (18), Expect = 0.031
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 1   attttattaaattatttg 18
           ||||||||||||||||||
Sbjct: 478 attttattaaattatttg 461


  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: 3818
Number of Sequences: 6905
Number of extensions: 3818
Number of successful extensions: 398
Number of sequences better than 10.0: 112
length of query: 445
length of database: 5,674,871
effective HSP length: 16
effective length of query: 429
effective length of database: 5,564,391
effective search space: 2387123739
effective search space used: 2387123739
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. 6.24
Homology vs DNA 
Query= Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Contig-U04560-1Q.Seq.d
         (445 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

(C91435) Dictyostelium discoideum slug cDNA, clone SSK245.        100   6e-43  4
(AU074289) Dictyostelium discoideum slug cDNA, clone SSK245.       56   8e-12  3
(CT574574) Zebrafish DNA sequence from clone CH211-24C14 in ...    48   0.28   1
(DE152658) Bombyx mori genomic DNA, Fosmid clone:RO0294-D09_F.     48   0.28   1
(AL953858) Zebrafish DNA sequence from clone CH211-121H11 in...    42   0.97   2
(AC136105) Rattus norvegicus clone CH230-412E19, WORKING DRA...    46   1.1    1
(AC133799) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    46   1.1    1
(AC099084) Rattus norvegicus clone CH230-90E9, WORKING DRAFT...    46   1.1    1
(AC200943) Strongylocentrotus purpuratus clone R3-1036J5, WO...    46   1.1    1
(BH148963) ENTQG67TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AZ687855) ENTKI05TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AZ680011) ENTLZ16TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AZ678478) ENTHC77TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AZ673025) ENTHY29TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AZ541060) ENTER49TR Entamoeba histolytica Sheared DNA Entam...    46   1.1    1
(AE008589) Rickettsia conorii str. Malish 7, section 21 of 1...    36   1.4    2
(FC698764) CAXX7249.fwd CAXX Lottia gigantea from male gonad...    42   1.6    2
(BV339116) S230P6367FH8.T0 Rottweiler Canis familiaris STS g...    44   4.4    1
(CT826194) Pan troglodytes chromosome X clone CH251-206C06 m...    44   4.4    1
(CT573437) Pan troglodytes chromosome X clone PTB-152P08 map...    44   4.4    1
(AC193036) Pan troglodytes BAC clone CH251-550E10 from chrom...    44   4.4    1
(AC149571) Rhinolophus ferrumequinum clone VMRC7-305L23, com...    44   4.4    1
(AL139112) Human DNA sequence from clone GS1-103B18 on chrom...    44   4.4    1
(AL356366) Human DNA sequence *** SEQUENCING CANCELLED *** f...    44   4.4    1
(AC232207) Monodelphis domestica clone VMRC18-652N14, WORKIN...    44   4.4    1
(AC226474) Monodelphis domestica clone VMRC18-107B11, WORKIN...    44   4.4    1
(AC211522) Pongo abelii chromosome UNKNOWN clone CH276-526P8...    44   4.4    1
(AC173076) Bos taurus clone CH240-305D18, WORKING DRAFT SEQU...    44   4.4    1
(BH159678) ENTRR32TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(BH159346) ENTTK31TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(BH148798) ENTPH16TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(AZ687339) ENTLP36TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(AZ678643) ENTIY40TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(AZ530904) ENTCJ34TR Entamoeba histolytica Sheared DNA Entam...    44   4.4    1
(EI444239) PV_GBa0041E06.r PV_GBa Phaseolus vulgaris genomic...    44   4.4    1
(DU352048) 1098268380354 CHORI-243 Ovis aries genomic clone ...    44   4.4    1
(EE647225) CHEM7335.b1_M09.ab1 CHE(LMS) serpentine sunflower...    44   4.4    1
(AM828833) Nicotiana tabacum EST, clone nt005147042.               44   4.4    1
(BY943271) Bombyx mori cDNA, clone:E_FL_e100_08O21_R_0, 3' e...    44   4.4    1
(EV213288) 0185109 Brassica napus Leaf - drought Brassica na...    44   4.4    1
(EV205854) 0174561 Brassica napus Leaf - drought Brassica na...    44   4.4    1
(EV183276) 0157178 Brassica napus Etiolated seedlings (pSPOR...    44   4.4    1
(ES902051) BNARO1GH_T3_025_D08_23NOV2006_058 Brassica napus ...    44   4.4    1
(CP000107) Ehrlichia canis str. Jake, complete genome.             44   4.4    1

>(C91435) Dictyostelium discoideum slug cDNA, clone SSK245.
          Length = 402

 Score = 99.6 bits (50), Expect(4) = 6e-43
 Identities = 50/50 (100%)
 Strand = Plus / Plus


Query: 324 tcaacaaattctatatttaataatatctattaatattctcaaattctttc 373
           ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 280 tcaacaaattctatatttaataatatctattaatattctcaaattctttc 329

 Score = 83.8 bits (42), Expect(4) = 6e-43
 Identities = 42/42 (100%)
 Strand = Plus / Plus


Query: 255 cattaaatataactactccacaatatcactactccacccaat 296
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 211 cattaaatataactactccacaatatcactactccacccaat 252

 Score = 38.2 bits (19), Expect(4) = 6e-43
 Identities = 19/19 (100%)
 Strand = Plus / Plus


Query: 207 ttctttgcaccacacaatc 225
           |||||||||||||||||||
Sbjct: 163 ttctttgcaccacacaatc 181

 Score = 30.2 bits (15), Expect(4) = 6e-43
 Identities = 15/15 (100%)
 Strand = Plus / Plus


Query: 45 tattaataaatttga 59
          |||||||||||||||
Sbjct: 1  tattaataaatttga 15

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 213,447,551
Number of extensions: 14527939
Number of successful extensions: 1201823
Number of sequences better than 10.0: 49
Length of query: 445
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 422
Effective length of database: 99,442,330,388
Effective search space: 41964663423736
Effective search space used: 41964663423736
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04560-1 (Contig-U04560-1Q) /CSM_Contig/Contig-U04560-1Q.Seq.d
         (445 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: 242,243,485
Number of extensions: 1941676
Number of successful extensions: 1355
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1355
Number of HSP's successfully gapped: 0
Length of query: 148
Length of database: 1,061,185,681
Length adjustment: 110
Effective length of query: 38
Effective length of database: 701,656,401
Effective search space: 26662943238
Effective search space used: 26662943238
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: 29 (15.8 bits)
PSORT 

 psg: 0.62  gvh: 0.27  alm: 0.57  top: 0.53  tms: 0.00  mit: 0.53  mip: 0.00
 nuc: 0.83  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 

	 80.0 %: nuclear
	  8.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: cytoplasmic

>> prediction for Contig-U04560-1 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