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Dicty_cDB
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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-U05350-1
Contig ID Contig-U05350-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U05350-1 (Contig-U05350-1Q) /CSM_Contig/Contig-U05350-1Q.Seq.d
CAACAACTACTACTGGCACATCAACAACTACACCATCTTCTACTCCGATT
TTAATTAGAGATGGAATACCAATTAATGGTTGTCAAGTTAAATCTTTTAT
TGCTTGGGCTGGTGTAGATAGGTTGGGTAAACCTTGCCAATCAATTAATA
AAATACCTTCAAAATTTCAAGAATATTCTGCAACTTCAATAAAGAAAATT
GGTACTGGTTTATTAACTGATTTCTTATATCGTGTTAATGACCAAAATAA
TCCAAATACTCCATAAAAAAAAAAA
Gap no gap
Contig length 275
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 3137030
End point 3137305
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U05350
List of clone(s) 

est1=SSH402F,1,276
Translated Amino Acid sequence 
TTTTGTSTTTPSSTPILIRDGIPINGCQVKSFIAWAGVDRLGKPCQSINKIPSKFQEYSA
TSIKKIGTGLLTDFLYRVNDQNNPNTP*kkk
Translated Amino Acid sequence (All Frames) 
Frame A:
qqlllahqqlhhlllrf*lemeyqlmvvklnllllglv*igwvnlanqlikylqnfknil
qlq*rklvlvy*lisyivlmtkiiqilhkkk


Frame B:
nnyywhinnytifysdfn*rwntn*wlss*ifyclgwcr*vg*tlpin**ntfkisrifc
nfnkenwywfin*flisc**pk*skysikkk


Frame C:
TTTTGTSTTTPSSTPILIRDGIPINGCQVKSFIAWAGVDRLGKPCQSINKIPSKFQEYSA
TSIKKIGTGLLTDFLYRVNDQNNPNTP*kkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05350-1 (Contig-U05350-1Q)
/CSM_Contig/Contig-U05350-1Q.Seq.d
         (275 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05350-1 (Contig-U05350-1Q) /CSM_Contig/Conti...   523  e-149
Contig-U08908-1 (Contig-U08908-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U12548-1 (Contig-U12548-1Q) /CSM_Contig/Conti...    36  0.019
Contig-U13591-1 (Contig-U13591-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U13509-1 (Contig-U13509-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U12675-1 (Contig-U12675-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U11965-1 (Contig-U11965-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U11881-1 (Contig-U11881-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U11262-1 (Contig-U11262-1Q) /CSM_Contig/Conti...    34  0.074
Contig-U04906-1 (Contig-U04906-1Q) /CSM_Contig/Conti...    34  0.074

>Contig-U05350-1 (Contig-U05350-1Q) /CSM_Contig/Contig-U05350-1Q.Seq.d
          Length = 275

 Score =  523 bits (264), Expect = e-149
 Identities = 264/264 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   caacaactactactggcacatcaacaactacaccatcttctactccgattttaattagag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caacaactactactggcacatcaacaactacaccatcttctactccgattttaattagag 60

                                                                       
Query: 61  atggaataccaattaatggttgtcaagttaaatcttttattgcttgggctggtgtagata 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  atggaataccaattaatggttgtcaagttaaatcttttattgcttgggctggtgtagata 120

                                                                       
Query: 121 ggttgggtaaaccttgccaatcaattaataaaataccttcaaaatttcaagaatattctg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ggttgggtaaaccttgccaatcaattaataaaataccttcaaaatttcaagaatattctg 180

                                                                       
Query: 181 caacttcaataaagaaaattggtactggtttattaactgatttcttatatcgtgttaatg 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 caacttcaataaagaaaattggtactggtttattaactgatttcttatatcgtgttaatg 240

                                   
Query: 241 accaaaataatccaaatactccat 264
           ||||||||||||||||||||||||
Sbjct: 241 accaaaataatccaaatactccat 264


>Contig-U08908-1 (Contig-U08908-1Q) /CSM_Contig/Contig-U08908-1Q.Seq.d
          Length = 1042

 Score = 40.1 bits (20), Expect = 0.001
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 22  caacaactacaccatcttct 41
           ||||||||||||||||||||
Sbjct: 282 caacaactacaccatcttct 301


>Contig-U12548-1 (Contig-U12548-1Q) /CSM_Contig/Contig-U12548-1Q.Seq.d
          Length = 1214

 Score = 36.2 bits (18), Expect = 0.019
 Identities = 30/34 (88%)
 Strand = Plus / Plus

                                             
Query: 4   caactactactggcacatcaacaactacaccatc 37
           ||||||||||||  |||||| |||||||| ||||
Sbjct: 128 caactactactgaaacatcagcaactacaacatc 161


  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: 4526
Number of Sequences: 6905
Number of extensions: 4526
Number of successful extensions: 1464
Number of sequences better than 10.0: 186
length of query: 275
length of database: 5,674,871
effective HSP length: 15
effective length of query: 260
effective length of database: 5,571,296
effective search space: 1448536960
effective search space used: 1448536960
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. 7.19
Homology vs DNA 
Query= Contig-U05350-1 (Contig-U05350-1Q) /CSM_Contig/Contig-U05350-1Q.Seq.d
         (275 letters)

Database: ddbj_B
           105,743,758 sequences; 104,622,809,269 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(AY392439) Dictyostelium discoideum P-selectin gene, complet...   523   e-144  1
(AC115684) Dictyostelium discoideum chromosome 2 map 3108975...   523   e-144  1
(AU073506) Dictyostelium discoideum slug cDNA, clone SSH402.      476   e-130  1
(AC187530) Callithrix jacchus BAC clone CH259-76H12 from chr...    52   0.011  1
(AP001827) Homo sapiens genomic DNA, chromosome 11 clone:RP1...    50   0.044  1
(AP002877) Homo sapiens genomic DNA, chromosome 11q clone:RP...    50   0.044  1
(AY374498) Tetraodon nigroviridis class I helical cytokine r...    48   0.17   1
(FH989782) CHO_OF6846xl20r1.ab1 CHO_OF6 Nicotiana tabacum ge...    48   0.17   1
(FH254408) CHO_OF3221xm15r1.ab1 CHO_OF3 Nicotiana tabacum ge...    48   0.17   1
(AC178414) Strongylocentrotus purpuratus clone R3-3113A08, W...    36   0.65   4
(GO865549) CLS_CLiFpEfSpn_50a8_1_f18cLibkit3LD_C09 CLS_CLiFp...    34   0.74   2
(FN357481) Schistosoma mansoni genome sequence supercontig S...    44   2.7    1
(AL359637) Human DNA sequence from clone RP11-484M8 on chrom...    44   2.7    1
(AC034260) Homo sapiens clone RP11-10J15, WORKING DRAFT SEQU...    44   2.7    1
(CL909499) OA_ABa0009E04.r OA_ABa Oryza australiensis genomi...    44   2.7    1
(CX388295) JGI_XZT22119.fwd NIH_XGC_tropTad5 Xenopus (Silura...    44   2.7    1
(AM478819) Vitis vinifera contig VV78X211569.3, whole genome...    36   4.4    3
(AB130065) Homo sapiens DNA, STS on chromosome 2, D2S0012i, ...    38   4.8    2
(DJ449947) Method for analysing genome using microsatellite ...    38   4.8    2
(GP295246) Sequence 2288 from patent US 7510834.                   38   4.8    2
(AM230660) Monodelphis domestica partial rasl11c gene and pa...    30   5.2    2
(AL845257) Mouse DNA sequence from clone RP23-280K4 on chrom...    34   6.5    3
(AZ251406) RPCI-23-21F21.TV RPCI-23 Mus musculus genomic clo...    34   6.7    2
(CC218502) CH261-135G19_RM1.1 CH261 Gallus gallus genomic cl...    30   6.8    2
(BZ082007) lld80a11.b1 B.oleracea002 Brassica oleracea genom...    32   6.9    2
(CK577689) IST_WI5_17855 AD-wrmcDNA library Caenorhabditis e...    32   7.0    2
(BH511462) BOHKX08TR BOHK Brassica oleracea genomic clone BO...    32   7.1    2
(AC111136) Mus musculus chromosome 9 clone RP23-349C15 map 9...    30   7.7    5
(AC096104) Rattus norvegicus clone CH230-27J15, WORKING DRAF...    36   8.0    4
(FB571359) Sequence 226 from Patent EP1865317.                     42   8.5    3
(EJ407594) 1093012107625 Global-Ocean-Sampling_GS-28-01-01-1...    34   8.5    2
(EJ313308) 1095403247408 Global-Ocean-Sampling_GS-27-01-01-1...    34   8.7    2

>(AY392439) Dictyostelium discoideum P-selectin gene, complete cds.
          Length = 5251

 Score =  523 bits (264), Expect = e-144
 Identities = 264/264 (100%)
 Strand = Plus / Plus


Query: 1    caacaactactactggcacatcaacaactacaccatcttctactccgattttaattagag 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1194 caacaactactactggcacatcaacaactacaccatcttctactccgattttaattagag 1253


Query: 61   atggaataccaattaatggttgtcaagttaaatcttttattgcttgggctggtgtagata 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1254 atggaataccaattaatggttgtcaagttaaatcttttattgcttgggctggtgtagata 1313


Query: 121  ggttgggtaaaccttgccaatcaattaataaaataccttcaaaatttcaagaatattctg 180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1314 ggttgggtaaaccttgccaatcaattaataaaataccttcaaaatttcaagaatattctg 1373


Query: 181  caacttcaataaagaaaattggtactggtttattaactgatttcttatatcgtgttaatg 240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1374 caacttcaataaagaaaattggtactggtttattaactgatttcttatatcgtgttaatg 1433


Query: 241  accaaaataatccaaatactccat 264
            ||||||||||||||||||||||||
Sbjct: 1434 accaaaataatccaaatactccat 1457

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 355,529,082
Number of extensions: 20958883
Number of successful extensions: 1729478
Number of sequences better than 10.0: 32
Length of query: 275
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 252
Effective length of database: 102,190,702,835
Effective search space: 25752057114420
Effective search space used: 25752057114420
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 8. 1
Homology vs Protein 
Query= Contig-U05350-1 (Contig-U05350-1Q) /CSM_Contig/Contig-U05350-1Q.Seq.d
         (275 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC115684_25(AC115684|pid:none) Dictyostelium discoideum chromoso...   151   6e-36
AC116330_2(AC116330|pid:none) Dictyostelium discoideum chromosom...    97   2e-19
CP000384_1151(CP000384|pid:none) Mycobacterium sp. MCS, complete...    32   7.1
AP007167_269(AP007167|pid:none) Aspergillus oryzae RIB40 genomic...    32   7.1
(A8MCY4) RecName: Full=Shikimate dehydrogenase;          EC=1.1....    32   9.3

>AC115684_25(AC115684|pid:none) Dictyostelium discoideum chromosome
           2 map 3108975-3191114 strain AX4, complete sequence.
          Length = 354

 Score =  151 bits (382), Expect = 6e-36
 Identities = 72/72 (100%), Positives = 72/72 (100%)
 Frame = +3

Query: 48  ILIRDGIPINGCQVKSFIAWAGVDRLGKPCQSINKIPSKFQEYSATSIKKIGTGLLTDFL 227
           ILIRDGIPINGCQVKSFIAWAGVDRLGKPCQSINKIPSKFQEYSATSIKKIGTGLLTDFL
Sbjct: 283 ILIRDGIPINGCQVKSFIAWAGVDRLGKPCQSINKIPSKFQEYSATSIKKIGTGLLTDFL 342

Query: 228 YRVNDQNNPNTP 263
           YRVNDQNNPNTP
Sbjct: 343 YRVNDQNNPNTP 354

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: 435,236,239
Number of extensions: 9039199
Number of successful extensions: 21384
Number of sequences better than 10.0: 5
Number of HSP's gapped: 21383
Number of HSP's successfully gapped: 5
Length of query: 91
Length of database: 1,061,185,681
Length adjustment: 60
Effective length of query: 31
Effective length of database: 865,078,801
Effective search space: 26817442831
Effective search space used: 26817442831
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: 27 (15.0 bits)
PSORT 

 psg: 0.87  gvh: 0.35  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.39  mip: 0.08
 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 

	 40.0 %: mitochondrial
	 32.0 %: cytoplasmic
	 16.0 %: nuclear
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane
	  4.0 %: peroxisomal

>> prediction for Contig-U05350-1 is mit
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