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Dicty_cDB
Contig List | Clone List | cDNA Library List
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U01815-1
Contig ID Contig-U01815-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01815-1 (Contig-U01815-1Q) /CSM_Contig/Contig-U01815-1Q.Seq.d
CCAATGTTTGATAATGGATCATGTAATTATATACCAAAACAAATTTTACC
ACCACAAACTGCAGACTCATTAATTCAAATTTGTGTTGGTAAAATTGTAC
AAAACATTCATTCTTTAACATCAGTAAAAGGTACAACAATACCAGAGGAA
ATCTTACAAAAGATTATTACATTATTAATTAGTCAAGATAAAATTAAGGG
TGGTAGTAATGATCCAATAACCAATCAATTGGATGATAGTTTATTAGCAA
GATTATTAAGTCCATTCATGCAATCATTAGATTTAGAGGGTGCAAAATTC
TTATCGACAATATCATTGAAAACCA
Gap no gap
Contig length 325
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 6763954
End point 6764262
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U01815
List of clone(s) 

est1=SSH796F,1,326
Translated Amino Acid sequence 
PMFDNGSCNYIPKQILPPQTADSLIQICVGKIVQNIHSLTSVKGTTIPEEILQKIITLLI
SQDKIKGGSNDPITNQLDDSLLARLLSPFMQSLDLEGAKFLSTISLKT
Translated Amino Acid sequence (All Frames) 
Frame A:
PMFDNGSCNYIPKQILPPQTADSLIQICVGKIVQNIHSLTSVKGTTIPEEILQKIITLLI
SQDKIKGGSNDPITNQLDDSLLARLLSPFMQSLDLEGAKFLSTISLKT


Frame B:
qclimdhviiyqnkfyhhklqth*fkfvlvklyktfil*hq*kvqqyqrksykrllhy*l
vkiklrvvvmiq*pinwmivy*qdy*vhscnh*i*rvqnsyrqyh*kp


Frame C:
nv**wim*lytktnftttncrlinsnlcw*nctkhsffniskrynntrgnltkdyyiin*
sr*n*gw***snnqsig**fiskiiksihaiirfrgckilidniien
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01815-1 (Contig-U01815-1Q)
/CSM_Contig/Contig-U01815-1Q.Seq.d
         (325 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01815-1 (Contig-U01815-1Q) /CSM_Contig/Conti...   644  0.0
Contig-U11530-1 (Contig-U11530-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U02377-1 (Contig-U02377-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U14787-1 (Contig-U14787-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U13368-1 (Contig-U13368-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U11958-1 (Contig-U11958-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U11331-1 (Contig-U11331-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U09329-1 (Contig-U09329-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U06634-1 (Contig-U06634-1Q) /CSM_Contig/Conti...    32  0.48
Contig-U02155-1 (Contig-U02155-1Q) /CSM_Contig/Conti...    32  0.48

>Contig-U01815-1 (Contig-U01815-1Q) /CSM_Contig/Contig-U01815-1Q.Seq.d
          Length = 325

 Score =  644 bits (325), Expect = 0.0
 Identities = 325/325 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ccaatgtttgataatggatcatgtaattatataccaaaacaaattttaccaccacaaact 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ccaatgtttgataatggatcatgtaattatataccaaaacaaattttaccaccacaaact 60

                                                                       
Query: 61  gcagactcattaattcaaatttgtgttggtaaaattgtacaaaacattcattctttaaca 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gcagactcattaattcaaatttgtgttggtaaaattgtacaaaacattcattctttaaca 120

                                                                       
Query: 121 tcagtaaaaggtacaacaataccagaggaaatcttacaaaagattattacattattaatt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcagtaaaaggtacaacaataccagaggaaatcttacaaaagattattacattattaatt 180

                                                                       
Query: 181 agtcaagataaaattaagggtggtagtaatgatccaataaccaatcaattggatgatagt 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 agtcaagataaaattaagggtggtagtaatgatccaataaccaatcaattggatgatagt 240

                                                                       
Query: 241 ttattagcaagattattaagtccattcatgcaatcattagatttagagggtgcaaaattc 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 ttattagcaagattattaagtccattcatgcaatcattagatttagagggtgcaaaattc 300

                                    
Query: 301 ttatcgacaatatcattgaaaacca 325
           |||||||||||||||||||||||||
Sbjct: 301 ttatcgacaatatcattgaaaacca 325


>Contig-U11530-1 (Contig-U11530-1Q) /CSM_Contig/Contig-U11530-1Q.Seq.d
          Length = 1393

 Score = 34.2 bits (17), Expect = 0.12
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                 
Query: 37   aaacaaattttaccaccacaa 57
            ||||||||| |||||||||||
Sbjct: 1179 aaacaaattctaccaccacaa 1199


>Contig-U02377-1 (Contig-U02377-1Q) /CSM_Contig/Contig-U02377-1Q.Seq.d
          Length = 1831

 Score = 34.2 bits (17), Expect = 0.12
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 37   aaacaaattttaccacc 53
            |||||||||||||||||
Sbjct: 1486 aaacaaattttaccacc 1502


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 6988
Number of Sequences: 8361
Number of extensions: 6988
Number of successful extensions: 738
Number of sequences better than 10.0: 218
length of query: 325
length of database: 7,895,291
effective HSP length: 16
effective length of query: 309
effective length of database: 7,761,515
effective search space: 2398308135
effective search space used: 2398308135
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. 8
Homology vs DNA 
Query= Contig-U01815-1 (Contig-U01815-1Q) /CSM_Contig/Contig-U01815-1Q.Seq.d
         (325 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

(AC114261) Dictyostelium discoideum chromosome 2 map 126059-...   644   0.0    1
(AU073674) Dictyostelium discoideum slug cDNA, clone SSH796.      476   e-130  1
(AC181770) Strongylocentrotus purpuratus clone R3-1034O05, W...    34   0.61   4
(BX294160) Zebrafish DNA sequence from clone CH211-285I13 in...    46   0.80   1
(CZ932296) 252420 Tomato EcoRI BAC Library Solanum lycopersi...    46   0.80   1
(CT393638) Sus scrofa genomic clone CH242-456C12, genomic su...    34   0.84   2
(EX476517) EST_lsal_evj_796861 lsalevj mixed_tissue_mixed_st...    34   2.2    2
(CK797859) AGENCOURT_18792772 NICHD_XGC_Te2N Xenopus laevis ...    32   2.2    3
(AL744998) Danio rerio genomic clone DKEY-6B10, genomic surv...    40   2.4    2
(AC180969) Strongylocentrotus purpuratus clone R3-3059A22, W...    34   2.8    4
(AB081348) Human enterovirus 71 gene for polyprotein, partia...    44   3.2    1
(AC187318) Canis Familiaris chromosome 34, clone XX-67L19, c...    44   3.2    1
(EU100917) Apis dorsata isolate Dors55Maly complementary sex...    44   3.2    1
(DQ325041) Apis dorsata complementary sex determiner (csd) g...    44   3.2    1
(DQ325040) Apis dorsata complementary sex determiner (csd) g...    44   3.2    1
(AC113719) Rattus norvegicus clone CH230-115M23, WORKING DRA...    44   3.2    1
(AC112573) Rattus norvegicus clone CH230-243G7, *** SEQUENCI...    44   3.2    1
(AC108344) Rattus norvegicus clone CH230-297C3, WORKING DRAF...    44   3.2    1
(AC223348) Bos taurus clone CH240-421E22, WORKING DRAFT SEQU...    44   3.2    1
(AC180472) Strongylocentrotus purpuratus clone R3-3100E03, W...    44   3.2    1
(AC178794) Strongylocentrotus purpuratus clone R3-29N24, WOR...    44   3.2    1
(AC178210) Strongylocentrotus purpuratus clone R3-3085F07, W...    44   3.2    1
(AC177622) Strongylocentrotus purpuratus clone R3-1020M15, W...    44   3.2    1
(AC170427) Bos taurus clone CH240-252G10, WORKING DRAFT SEQU...    44   3.2    1
(FI252358) CccaBb013-L2JF CccABb Cajanus cajan genomic clone...    44   3.2    1
(ES393488) MUS13-G14.y1d-s SHGC-MUS Mytilus californianus cD...    44   3.2    1
(ES393277) MUS13-K08.y1d-s SHGC-MUS Mytilus californianus cD...    44   3.2    1
(BW802980) Branchiostoma floridae cDNA, larva clone:bflv026b...    44   3.2    1
(FD645558) MF1_27_A09.b2_F001 Limnanthes alba EST Library MF...    44   3.2    1
(DU932468) 356958 Tomato EcoRI BAC Library Solanum lycopersi...    40   3.9    2
(AL157883) Human DNA sequence from clone RP11-360J12 on chro...    42   8.1    2
(AC176736) Strongylocentrotus purpuratus clone R3-3096P11, W...    40   8.2    3
(EF594316) Astatotilapia burtoni clone BAC 19E16 Hoxdb gene ...    42   8.5    2
(AC133808) Rattus norvegicus clone CH230-397I1, WORKING DRAF...    42   9.3    2

>(AC114261) Dictyostelium discoideum chromosome 2 map 126059-159710
             strain AX4, complete sequence.
          Length = 33651

 Score =  644 bits (325), Expect = 0.0
 Identities = 325/325 (100%)
 Strand = Plus / Plus


Query: 1     ccaatgtttgataatggatcatgtaattatataccaaaacaaattttaccaccacaaact 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16368 ccaatgtttgataatggatcatgtaattatataccaaaacaaattttaccaccacaaact 16427


Query: 61    gcagactcattaattcaaatttgtgttggtaaaattgtacaaaacattcattctttaaca 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16428 gcagactcattaattcaaatttgtgttggtaaaattgtacaaaacattcattctttaaca 16487


Query: 121   tcagtaaaaggtacaacaataccagaggaaatcttacaaaagattattacattattaatt 180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16488 tcagtaaaaggtacaacaataccagaggaaatcttacaaaagattattacattattaatt 16547


Query: 181   agtcaagataaaattaagggtggtagtaatgatccaataaccaatcaattggatgatagt 240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16548 agtcaagataaaattaagggtggtagtaatgatccaataaccaatcaattggatgatagt 16607


Query: 241   ttattagcaagattattaagtccattcatgcaatcattagatttagagggtgcaaaattc 300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 16608 ttattagcaagattattaagtccattcatgcaatcattagatttagagggtgcaaaattc 16667


Query: 301   ttatcgacaatatcattgaaaacca 325
             |||||||||||||||||||||||||
Sbjct: 16668 ttatcgacaatatcattgaaaacca 16692

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 419,280,107
Number of extensions: 23972404
Number of successful extensions: 1934694
Number of sequences better than 10.0: 34
Length of query: 325
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 302
Effective length of database: 99,442,330,388
Effective search space: 30031583777176
Effective search space used: 30031583777176
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01815-1 (Contig-U01815-1Q) /CSM_Contig/Contig-U01815-1Q.Seq.d
         (325 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC114261_3(AC114261|pid:none) Dictyostelium discoideum chromosom...   213   2e-54
CP000721_1433(CP000721|pid:none) Clostridium beijerinckii NCIMB ...    34   1.8
CP001393_2639(CP001393|pid:none) Anaerocellum thermophilum DSM 6...    32   6.9
FM209186_3836(FM209186|pid:none) Pseudomonas aeruginosa LESB58 c...    32   9.0
CP000438_3745(CP000438|pid:none) Pseudomonas aeruginosa UCBPP-PA...    32   9.0

>AC114261_3(AC114261|pid:none) Dictyostelium discoideum chromosome 2
            map 126059-159710 strain AX4, complete sequence.
          Length = 2159

 Score =  213 bits (542), Expect = 2e-54
 Identities = 108/108 (100%), Positives = 108/108 (100%)
 Frame = +1

Query: 1    PMFDNGSCNYIPKQILPPQTADSLIQICVGKIVQNIHSLTSVKGTTIPEEILQKIITLLI 180
            PMFDNGSCNYIPKQILPPQTADSLIQICVGKIVQNIHSLTSVKGTTIPEEILQKIITLLI
Sbjct: 1473 PMFDNGSCNYIPKQILPPQTADSLIQICVGKIVQNIHSLTSVKGTTIPEEILQKIITLLI 1532

Query: 181  SQDKIKGGSNDPITNQLDDSLLARLLSPFMQSLDLEGAKFLSTISLKT 324
            SQDKIKGGSNDPITNQLDDSLLARLLSPFMQSLDLEGAKFLSTISLKT
Sbjct: 1533 SQDKIKGGSNDPITNQLDDSLLARLLSPFMQSLDLEGAKFLSTISLKT 1580

Lambda     K      H
   0.317    0.136    0.378

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: 479,997,466
Number of extensions: 8126584
Number of successful extensions: 15605
Number of sequences better than 10.0: 5
Number of HSP's gapped: 15602
Number of HSP's successfully gapped: 5
Length of query: 108
Length of database: 1,051,180,864
Length adjustment: 76
Effective length of query: 32
Effective length of database: 805,202,380
Effective search space: 25766476160
Effective search space used: 25766476160
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 (21.6 bits)
S2: 28 (15.4 bits)
PSORT 

 psg: 0.75  gvh: 0.38  alm: 0.45  top: 0.53  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 

	 40.0 %: nuclear
	 32.0 %: cytoplasmic
	 24.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U01815-1 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) 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