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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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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-U01006-1
Contig ID Contig-U01006-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01006-1 (Contig-U01006-1Q) /CSM_Contig/Contig-U01006-1Q.Seq.d
CACGTTNCAATAATAGACCCGAATTCTTTGAGCGTGCAAAAGAAAATCAA
ATTCAAGTTATCAATAATAATAATGTTCAATTAGCTATTGATCTTCAAAA
TATTTATACTTCAATGAAAAAAGATATTGATGAAGAAAATAATGAATTAA
AAAATTTATTAACAATAAGNAATTNTTAGAACCATATGATTTAAGAAAGA
TTAGAGAATGTTTAGAAGGATTAAAATCACATCTTAGAATTGTTGATGTA
TTATATAATGAATTAAAATATGTTTTGAATAGAAAGAAACCAGAATGTTG
TGCAGCATTGATTATAACACAACAACCCTATTCTCAAGTTATTTTTAGAG
GAGGAAAAGGTATGGGAGAAATANTTAAGGTTCAAATGATATTTGGTGTA
CTTCAACCCGACAATATCTCACCAGTTTATGCAACCATAAACAA
Gap no gap
Contig length 444
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 5075846
End point 5076232
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U01006
List of clone(s) 

est1=SFJ451Z,1,445
Translated Amino Acid sequence 
txq**tril*ackrksnssyq***csisy*sskylyfnekry**rk**IKKFINNKXXLE
PYDLRKIRECLEGLKSHLRIVDVLYNELKYVLNRKKPECCAALIITQQPYSQVIFRGGKG
MGEIXKVQMIFGVLQPDNISPVYATIN
Translated Amino Acid sequence (All Frames) 
Frame A:
hvxiidpnslsvqkkikfklsiiimfn*llifkifilq*kkilmkkimn*kiy*q*xixr
ti*fkkd*rmfrrikits*nc*cii**ikicfe*ketrmlcsidyntttlfssyf*rrkr
ygrnx*gsndiwctstrqyltslcnhkq


Frame B:
txq**tril*ackrksnssyq***csisy*sskylyfnekry**rk**IKKFINNKXXLE
PYDLRKIRECLEGLKSHLRIVDVLYNELKYVLNRKKPECCAALIITQQPYSQVIFRGGKG
MGEIXKVQMIFGVLQPDNISPVYATIN


Frame C:
rxnnrpefferakenqiqvinnnnvqlaidlqniytsmkkdideennelknlltixnx*n
hmi*erlenv*kd*nhilellmyyimn*nmf*iernqnvvqh*l*hnnpilklfleeekv
wekxlrfk*ylvyfnptishqfmqp*t
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01006-1 (Contig-U01006-1Q)
/CSM_Contig/Contig-U01006-1Q.Seq.d
         (444 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01006-1 (Contig-U01006-1Q) /CSM_Contig/Conti...   856  0.0
Contig-U10977-1 (Contig-U10977-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U12278-1 (Contig-U12278-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U11975-1 (Contig-U11975-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U12132-1 (Contig-U12132-1Q) /CSM_Contig/Conti...    36  0.043
Contig-U12113-1 (Contig-U12113-1Q) /CSM_Contig/Conti...    36  0.043
Contig-U11869-1 (Contig-U11869-1Q) /CSM_Contig/Conti...    36  0.043
Contig-U11790-1 (Contig-U11790-1Q) /CSM_Contig/Conti...    36  0.043
Contig-U11677-1 (Contig-U11677-1Q) /CSM_Contig/Conti...    36  0.043
Contig-U11672-1 (Contig-U11672-1Q) /CSM_Contig/Conti...    36  0.043

>Contig-U01006-1 (Contig-U01006-1Q) /CSM_Contig/Contig-U01006-1Q.Seq.d
          Length = 444

 Score =  856 bits (432), Expect = 0.0
 Identities = 444/444 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   cacgttncaataatagacccgaattctttgagcgtgcaaaagaaaatcaaattcaagtta 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cacgttncaataatagacccgaattctttgagcgtgcaaaagaaaatcaaattcaagtta 60

                                                                       
Query: 61  tcaataataataatgttcaattagctattgatcttcaaaatatttatacttcaatgaaaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tcaataataataatgttcaattagctattgatcttcaaaatatttatacttcaatgaaaa 120

                                                                       
Query: 121 aagatattgatgaagaaaataatgaattaaaaaatttattaacaataagnaattnttaga 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 aagatattgatgaagaaaataatgaattaaaaaatttattaacaataagnaattnttaga 180

                                                                       
Query: 181 accatatgatttaagaaagattagagaatgtttagaaggattaaaatcacatcttagaat 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 accatatgatttaagaaagattagagaatgtttagaaggattaaaatcacatcttagaat 240

                                                                       
Query: 241 tgttgatgtattatataatgaattaaaatatgttttgaatagaaagaaaccagaatgttg 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tgttgatgtattatataatgaattaaaatatgttttgaatagaaagaaaccagaatgttg 300

                                                                       
Query: 301 tgcagcattgattataacacaacaaccctattctcaagttatttttagaggaggaaaagg 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 tgcagcattgattataacacaacaaccctattctcaagttatttttagaggaggaaaagg 360

                                                                       
Query: 361 tatgggagaaatanttaaggttcaaatgatatttggtgtacttcaacccgacaatatctc 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 tatgggagaaatanttaaggttcaaatgatatttggtgtacttcaacccgacaatatctc 420

                                   
Query: 421 accagtttatgcaaccataaacaa 444
           ||||||||||||||||||||||||
Sbjct: 421 accagtttatgcaaccataaacaa 444


>Contig-U10977-1 (Contig-U10977-1Q) /CSM_Contig/Contig-U10977-1Q.Seq.d
          Length = 2336

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                 
Query: 114  atgaaaaaagatattgatgaa 134
            |||||||||||||||||||||
Sbjct: 1269 atgaaaaaagatattgatgaa 1289


>Contig-U12278-1 (Contig-U12278-1Q) /CSM_Contig/Contig-U12278-1Q.Seq.d
          Length = 1658

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                               
Query: 141 aatgaattaaaaaatttatt 160
           ||||||||||||||||||||
Sbjct: 248 aatgaattaaaaaatttatt 229


  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: 26,330
Number of Sequences: 8361
Number of extensions: 26330
Number of successful extensions: 2423
Number of sequences better than 10.0: 235
length of query: 444
length of database: 7,895,291
effective HSP length: 16
effective length of query: 428
effective length of database: 7,761,515
effective search space: 3321928420
effective search space used: 3321928420
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. 4.20
Homology vs DNA 
Query= Contig-U01006-1 (Contig-U01006-1Q) /CSM_Contig/Contig-U01006-1Q.Seq.d
         (444 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

(BJ401839) Dictyostelium discoideum cDNA clone:dds19f14, 3' ...   545   0.0    2
(AC116305) Dictyostelium discoideum chromosome 2 map 1005175...   527   0.0    2
(EL847077) CBXT6574.b1 NICHD_XGC_trop_25 Xenopus (Silurana) ...   149   1e-31  1
(EL847078) CBXT6574.g1 NICHD_XGC_trop_25 Xenopus (Silurana) ...   113   4e-24  2
(ER475690) 1093015232391 Global-Ocean-Sampling_GS-35-01-01-1...    44   0.14   2
(EJ542925) 1092955411961 Global-Ocean-Sampling_GS-29-01-01-1...    48   0.28   1
(AE001438) Clostridium acetobutylicum ATCC 824 megaplasmid p...    48   0.28   1
(BI150294) 602915315F1 NCI_CGAP_Lu29 Mus musculus cDNA clone...    36   0.43   2
(AL929114) Zebrafish DNA sequence from clone CH211-133L11 in...    46   1.1    1
(EU966099) Zea mays clone 291725 hypothetical protein mRNA, ...    46   1.1    1
(AC006438) Arabidopsis thaliana chromosome 2 clone F19G14 ma...    46   1.1    1
(AC092126) Homo sapiens chromosome 16 clone RP11-1114G22, co...    46   1.1    1
(AC009085) Homo sapiens chromosome 16 clone RP11-368L12, com...    46   1.1    1
(AC120097) Rattus norvegicus clone CH230-220A12, *** SEQUENC...    46   1.1    1
(AC103502) Rattus norvegicus clone CH230-95B23, *** SEQUENCI...    46   1.1    1
(AC200669) Zea mays chromosome 6 clone CH201-131N16; ZMMBBc0...    46   1.1    1
(AC176847) Strongylocentrotus purpuratus clone R3-3120I11, W...    46   1.1    1
(BZ680318) PUBCC44TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    46   1.1    1
(FL217820) 1053699 CERES-196 Zea mays cDNA clone 223300 5', ...    46   1.1    1
(FL217819) 1374002 CERES-196 Zea mays cDNA clone 291725 5', ...    46   1.1    1
(CR381633) Zebrafish DNA sequence from clone CH211-230M9 in ...    40   2.1    3
(AC097487) Homo sapiens BAC clone RP11-217C7 from 4, complet...    34   2.2    2
(AC232437) Brassica rapa subsp. pekinensis clone KBrB002B23,...    34   2.3    2
(AC189351) Brassica rapa subsp. pekinensis clone KBrB043F18,...    34   2.3    2
(AL591418) Zebrafish DNA sequence from clone BUSM1-139E19 in...    38   2.8    2
(AC186392) Pan troglodytes BAC clone CH251-425I12 from chrom...    42   3.9    2
(BX897715) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    38   4.2    2
(CU467068) Zebrafish DNA sequence from clone CH73-194K14 in ...    44   4.4    1
(CR749749) Zebrafish DNA sequence from clone CH211-153P17 in...    44   4.4    1
(AC187710) Callithrix jacchus BAC clone CH259-11H12 from chr...    44   4.4    1
(AM433916) Vitis vinifera contig VV78X101351.7, whole genome...    44   4.4    1
(DJ060411) Method and nucleic acids for the improved treatme...    44   4.4    1
(DJ060289) Method and nucleic acids for the improved treatme...    44   4.4    1
(DD392063) Method and nucleic acids for the improved treatme...    44   4.4    1
(DD391789) Method and nucleic acids for the improved treatme...    44   4.4    1
(CS124758) Sequence 444 from Patent WO2005059172.                  44   4.4    1
(CS124636) Sequence 322 from Patent WO2005059172.                  44   4.4    1
(CQ807319) Sequence 769 from Patent WO2004035803.                  44   4.4    1
(CQ807045) Sequence 495 from Patent WO2004035803.                  44   4.4    1
(CU469434) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.4    1
(AC186942) Callicebus moloch clone LB5-393P6, WORKING DRAFT ...    44   4.4    1
(ER424928) 1092963742655 Global-Ocean-Sampling_GS-35-01-01-1...    44   4.4    1
(EK338859) 1095467052915 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.4    1
(EI353185) GM_WBc0102N05.r GM_WBc Glycine max genomic clone ...    44   4.4    1
(DE889769) Macropus eugenii DNA, BAC clone: MEB1-065N18_R, 3...    44   4.4    1
(CU810800) A BAC library has been constructed from PN40024 g...    44   4.4    1
(FE665295) UAHYP_23A_R_G06 UaHyphae_ARS Uromyces appendicula...    44   4.4    1
(FE665233) UAHYP_23A_F_G06 UaHyphae_ARS Uromyces appendicula...    44   4.4    1
(BF297751) 055PbG02 Pb cDNA #17, Tommaso Pace, Marta Ponzi, ...    40   4.7    2
(CU041381) Platypus DNA sequence from clone CLM1-572A11.           42   6.7    4
(CT573056) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    36   7.0    5
(AC186824) Gallus gallus BAC clone CH261-143N19 from chromos...    34   7.2    5
(AX345916) Sequence 987 from Patent WO0200928.                     42   7.4    2
(AC069132) Homo sapiens chromosome 5 clone RP11-556L8, *** S...    38   9.6    2
(AC206110) Saccoglossus kowalevskii  BAC CUGI_SK_BA 001B1 (C...    38   9.8    2

>(BJ401839) Dictyostelium discoideum cDNA clone:dds19f14, 3' end,
           single read.
          Length = 445

 Score =  545 bits (275), Expect(2) = 0.0
 Identities = 284/284 (100%)
 Strand = Plus / Minus


Query: 161 aacaataagnaattnttagaaccatatgatttaagaaagattagagaatgtttagaagga 220
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 285 aacaataagnaattnttagaaccatatgatttaagaaagattagagaatgtttagaagga 226


Query: 221 ttaaaatcacatcttagaattgttgatgtattatataatgaattaaaatatgttttgaat 280
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 225 ttaaaatcacatcttagaattgttgatgtattatataatgaattaaaatatgttttgaat 166


Query: 281 agaaagaaaccagaatgttgtgcagcattgattataacacaacaaccctattctcaagtt 340
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 165 agaaagaaaccagaatgttgtgcagcattgattataacacaacaaccctattctcaagtt 106


Query: 341 atttttagaggaggaaaaggtatgggagaaatanttaaggttcaaatgatatttggtgta 400
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 105 atttttagaggaggaaaaggtatgggagaaatanttaaggttcaaatgatatttggtgta 46


Query: 401 cttcaacccgacaatatctcaccagtttatgcaaccataaacaa 444
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45  cttcaacccgacaatatctcaccagtttatgcaaccataaacaa 2

 Score =  184 bits (93), Expect(2) = 0.0
 Identities = 96/96 (100%)
 Strand = Plus / Minus


Query: 1   cacgttncaataatagacccgaattctttgagcgtgcaaaagaaaatcaaattcaagtta 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 445 cacgttncaataatagacccgaattctttgagcgtgcaaaagaaaatcaaattcaagtta 386


Query: 61  tcaataataataatgttcaattagctattgatcttc 96
           ||||||||||||||||||||||||||||||||||||
Sbjct: 385 tcaataataataatgttcaattagctattgatcttc 350

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 496,340,538
Number of extensions: 33863690
Number of successful extensions: 2717029
Number of sequences better than 10.0: 57
Length of query: 444
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 421
Effective length of database: 99,442,330,388
Effective search space: 41865221093348
Effective search space used: 41865221093348
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.14
Homology vs Protein 
Query= Contig-U01006-1 (Contig-U01006-1Q) /CSM_Contig/Contig-U01006-1Q.Seq.d
         (444 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116305_84(AC116305|pid:none) Dictyostelium discoideum chromoso...   180   1e-62
(O00910) RecName: Full=Signal transducer and activator of transc...    39   0.043
CP001217_529(CP001217|pid:none) Helicobacter pylori P12, complet...    32   5.2
FM992692_257(FM992692|pid:none) Candida dubliniensis CD36 chromo...    32   6.9
AY639938_5(AY639938|pid:none) Onychiurus orientalis mitochondrio...    32   9.2

>AC116305_84(AC116305|pid:none) Dictyostelium discoideum chromosome
           2 map 1005175-1418323 strain AX4, complete sequence.
          Length = 811

 Score =  180 bits (457), Expect(2) = 1e-62
 Identities = 88/89 (98%), Positives = 88/89 (98%)
 Frame = +2

Query: 176 LEPYDLRKIRECLEGLKSHLRIVDVLYNELKYVLNRKKPECCAALIITQQPYSQVIFRGG 355
           LEPYDLRKIRECLEGLKSHLRIVDVLYNELKYVLNRKKPECCAALIITQQPYSQVIFRGG
Sbjct: 421 LEPYDLRKIRECLEGLKSHLRIVDVLYNELKYVLNRKKPECCAALIITQQPYSQVIFRGG 480

Query: 356 KGMGEIXKVQMIFGVLQPDNISPVYATIN 442
           KGMGEI KVQMIFGVLQPDNISPVYATIN
Sbjct: 481 KGMGEIFKVQMIFGVLQPDNISPVYATIN 509

 Score = 81.6 bits (200), Expect(2) = 1e-62
 Identities = 42/55 (76%), Positives = 42/55 (76%)
 Frame = +3

Query: 3   RXNNRPEFFERAKEXXXXXXXXXXXXLAIDLQNIYTSMKKDIDEENNELKNLLTI 167
           R NNRPEFFERAKE            LAIDLQNIYTSMKKDIDEENNELKNLLTI
Sbjct: 364 RYNNRPEFFERAKENQIQVINNNNVQLAIDLQNIYTSMKKDIDEENNELKNLLTI 418

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: 585,551,336
Number of extensions: 10372329
Number of successful extensions: 20142
Number of sequences better than 10.0: 5
Number of HSP's gapped: 20141
Number of HSP's successfully gapped: 6
Length of query: 148
Length of database: 1,051,180,864
Length adjustment: 110
Effective length of query: 38
Effective length of database: 695,159,374
Effective search space: 26416056212
Effective search space used: 26416056212
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: 0.20  alm: 0.44  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.00
 nuc: 0.03  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 

	 52.0 %: nuclear
	 24.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: mitochondrial
	  4.0 %: vacuolar

>> prediction for Contig-U01006-1 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) 1
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0