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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-U04159-1
Contig ID Contig-U04159-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U04159-1 (Contig-U04159-1Q) /CSM_Contig/Contig-U04159-1Q.Seq.d
AAAAGCTCAATTAGAAACAGATTTAAAAAATATTTGCACTTTAGTACCAT
CAAATATTACAATGGAGTGTAAATTCTTTATGATATTAGCAGCTCCAATT
ATTGCTGGTGCTATTTCTAATGGTGAAAATCCACAAACACTTTGCTCTGA
CTATAAATTATGCACAACAACAACACAACAAACACCAACAACCAACAATT
ATAGTAATCAACCAAACATCAATATTATGAAAAACAAAATTAAAGATATT
TTTGTGGAATCAACTAACAATATTATTGAACCAAAAGAAAAAGTAACAAT
GAGAAGAAATTTTTAAACACTATTATTTAAAAAAAAATATAAATAAATAA
GCATTTTTGTAAAAAACAAAAA
Gap no gap
Contig length 372
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 1749803
End point 1749431
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 2
Link to clone list U04159
List of clone(s) 

est1=SLG865E,1,373
est2=SLH678E,1,373
Translated Amino Acid sequence 
KAQLETDLKNICTLVPSNITMECKFFMILAAPIIAGAISNGENPQTLCSDYKLCTTTTQQ
TPTTNNYSNQPNINIMKNKIKDIFVESTNNIIEPKEKVTMRRNF*tllfkkkyk*isifv
knk
Translated Amino Acid sequence (All Frames) 
Frame A:
kssirnrfkkylhfstikyyngv*ilydisssnycwcyf*w*kstntll*l*imhnnntt
ntnnqql**stkhqyyekqn*ryfcgin*qyy*tkrksnnekkflntii*kki*inkhfc
kkqk


Frame B:
KAQLETDLKNICTLVPSNITMECKFFMILAAPIIAGAISNGENPQTLCSDYKLCTTTTQQ
TPTTNNYSNQPNINIMKNKIKDIFVESTNNIIEPKEKVTMRRNF*tllfkkkyk*isifv
knk


Frame C:
kln*kqi*kifal*yhqilqwsvnsl*y*qlqlllvlflmvkihkhfaltinyaqqqhnk
hqqptiivinqtsil*ktklkiflwnqltillnqkkk*q*eeifkhyylkknink*afl*
ktk
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U04159-1 (Contig-U04159-1Q)
/CSM_Contig/Contig-U04159-1Q.Seq.d
         (372 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04159-1 (Contig-U04159-1Q) /CSM_Contig/Conti...   321  3e-88
Contig-U11426-1 (Contig-U11426-1Q) /CSM_Contig/Conti...    36  0.026
Contig-U09442-1 (Contig-U09442-1Q) /CSM_Contig/Conti...    36  0.026
Contig-U14102-1 (Contig-U14102-1Q) /CSM_Contig/Conti...    34  0.10
Contig-U12054-1 (Contig-U12054-1Q) /CSM_Contig/Conti...    34  0.10
Contig-U09658-1 (Contig-U09658-1Q) /CSM_Contig/Conti...    34  0.10
Contig-U01101-1 (Contig-U01101-1Q) /CSM_Contig/Conti...    34  0.10
Contig-U12643-1 (Contig-U12643-1Q) /CSM_Contig/Conti...    32  0.40
Contig-U12413-1 (Contig-U12413-1Q) /CSM_Contig/Conti...    32  0.40
Contig-U11436-1 (Contig-U11436-1Q) /CSM_Contig/Conti...    32  0.40

>Contig-U04159-1 (Contig-U04159-1Q) /CSM_Contig/Contig-U04159-1Q.Seq.d
          Length = 372

 Score =  321 bits (162), Expect = 3e-88
 Identities = 162/162 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aaaagctcaattagaaacagatttaaaaaatatttgcactttagtaccatcaaatattac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaaagctcaattagaaacagatttaaaaaatatttgcactttagtaccatcaaatattac 60

                                                                       
Query: 61  aatggagtgtaaattctttatgatattagcagctccaattattgctggtgctatttctaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aatggagtgtaaattctttatgatattagcagctccaattattgctggtgctatttctaa 120

                                                     
Query: 121 tggtgaaaatccacaaacactttgctctgactataaattatg 162
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tggtgaaaatccacaaacactttgctctgactataaattatg 162


 Score =  268 bits (135), Expect = 4e-72
 Identities = 153/162 (94%)
 Strand = Plus / Plus

                                                                       
Query: 199 ttatagtaatcaaccaaacatcaatattatgaaaaacaaaattaaagatatttttgtgga 258
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 199 ttatagtaatcaaccaaacatcaatattatgaaaaacaaaattaaagatatttttgtgga 258

                                                                       
Query: 259 atcaactaacaatattattgaaccaaaagaaaaagtaacaatgagaagaaatttttaaac 318
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 259 atcaactaacaatattattgaaccaaaagaaaaagtaacaatgagaagaaatttttaaac 318

                                                     
Query: 319 actattatttnnnnnnnnntataaataaataagcatttttgt 360
           ||||||||||         |||||||||||||||||||||||
Sbjct: 319 actattatttaaaaaaaaatataaataaataagcatttttgt 360


>Contig-U11426-1 (Contig-U11426-1Q) /CSM_Contig/Contig-U11426-1Q.Seq.d
          Length = 2889

 Score = 36.2 bits (18), Expect = 0.026
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 274  tattgaaccaaaagaaaa 291
            ||||||||||||||||||
Sbjct: 1291 tattgaaccaaaagaaaa 1308


>Contig-U09442-1 (Contig-U09442-1Q) /CSM_Contig/Contig-U09442-1Q.Seq.d
          Length = 663

 Score = 36.2 bits (18), Expect = 0.026
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 279 aaccaaaagaaaaagtaa 296
           ||||||||||||||||||
Sbjct: 542 aaccaaaagaaaaagtaa 559


  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: 9107
Number of Sequences: 6905
Number of extensions: 9107
Number of successful extensions: 746
Number of sequences better than 10.0: 191
length of query: 372
length of database: 5,674,871
effective HSP length: 16
effective length of query: 356
effective length of database: 5,564,391
effective search space: 1980923196
effective search space used: 1980923196
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. 6.14
Homology vs DNA 
Query= Contig-U04159-1 (Contig-U04159-1Q) /CSM_Contig/Contig-U04159-1Q.Seq.d
         (372 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

(AU039970) Dictyostelium discoideum slug cDNA, clone SLG865.      323   e-130  2
(AU039381) Dictyostelium discoideum slug cDNA, clone SLH678.      323   e-130  2
(AC217002) Solanum lycopersicum chromosome 11 clone C11HBa00...    44   0.045  2
(AC087744) Homo sapiens chromosome 18 clone RP11-673F9 map 1...    46   0.056  2
(AP001895) Homo sapiens genomic DNA, chromosome 18q12 clone:...    46   0.10   3
(EJ524390) 1092955172416 Global-Ocean-Sampling_GS-29-01-01-1...    38   0.35   2
(AC161952) Bos taurus clone CH240-109J2, WORKING DRAFT SEQUE...    40   0.78   2
(AC154904) Mus musculus BAC clone RP23-416C3 from chromosome...    46   0.93   1
(AC146608) Mus musculus BAC clone RP23-159D24 from chromosom...    46   0.93   1
(AC135377) Mus musculus BAC clone RP24-66B2 from chromosome ...    46   0.93   1
(AL133376) Human DNA sequence from clone RP1-76K20 on chromo...    46   0.93   1
(AC090358) Homo sapiens chromosome 18, clone RP11-775G23, co...    46   0.93   1
(AC090355) Homo sapiens chromosome 18, clone RP11-745C22, co...    46   0.93   1
(AC012569) Homo sapiens chromosome , clone RP11-8H2, complet...    46   0.93   1
(AC009659) Homo sapiens chromosome 11, clone RP11-362G8, com...    46   0.93   1
(AC079531) Mus musculus clone RP23-345C6, WORKING DRAFT SEQU...    46   0.93   1
(AP002479) Homo sapiens genomic DNA, chromosome 18q12 clone:...    46   0.93   1
(AP001563) Homo sapiens genomic DNA, chromosome 18q12 clone:...    46   0.93   1
(AP001532) Homo sapiens genomic DNA, chromosome 18q22 clone:...    46   0.93   1
(AP001400) Homo sapiens genomic DNA, chromosome 18q22 clone:...    46   0.93   1
(AC020785) Homo sapiens chromosome 4 clone RP11-114D20 map 4...    46   0.93   1
(AQ605668) HS_5386_A1_H01_MR RPCI-11 Human Male BAC Library ...    46   0.93   1
(AQ122635) HS_3086_A2_E02_MF CIT Approved Human Genomic Sper...    46   0.93   1
(BX476548) Homo sapiens mRNA; EST DKFZp686N08186_r1  (from c...    46   0.93   1
(EI810683) MUGQ_CH252P259C13T7_CN530_061 CHORI-252 Vervet Mo...    42   1.2    2
(EJ884014) 1093018408206 Global-Ocean-Sampling_GS-30-02-01-1...    40   1.3    2
(CT963112) Medicago truncatula chromosome 5 clone mth2-117d2...    42   2.5    3
(AL596172) Listeria innocua Clip11262 complete genome, segme...    36   2.5    4
(BH526281) BOGQZ40TR BOGQ Brassica oleracea genomic clone BO...    34   2.5    2
(AC137208) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    44   3.7    1
(AC131195) Rattus norvegicus clone CH230-68F17, *** SEQUENCI...    44   3.7    1
(AC231176) Bos taurus clone CH240-87P6, WORKING DRAFT SEQUEN...    44   3.7    1
(ET221683) MFSAA53TF Standard JTC phos vector with Fw & Rv p...    44   3.7    1
(EJ807452) 1093017468972 Global-Ocean-Sampling_GS-30-02-01-1...    44   3.7    1
(EJ748318) 1092963017953 Global-Ocean-Sampling_GS-30-02-01-1...    44   3.7    1
(EJ731950) 1092960184288 Global-Ocean-Sampling_GS-30-02-01-1...    44   3.7    1
(EJ399894) 1093012028870 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.7    1
(EJ375179) 1092963738834 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.7    1
(DU119307) KBrH102O10R Brassica rapa BAC library KBrH Brassi...    44   3.7    1
(DR756331) USDA-FP_116600-094 adult black-winged sharpshoote...    44   3.7    1
(DR586469) WS0342.B21_C11 WS-SE-N-A-19 Picea glauca cDNA clo...    44   3.7    1
(DN471730) USDA-FP_145720 Adult sharpshooter leafhopper Onco...    44   3.7    1
(CX576652) TTE00029448 Amplicon Express - Conjugative Form T...    44   3.7    1
(FF570813) TTEB884TVB Tetrahymena thermophila conjugation cD...    44   3.7    1
(EV849291) FTSAX07TF Tetrahymena thermophila SB210 cDNA libr...    44   3.7    1
(AE017194) Bacillus cereus ATCC 10987, complete genome.            44   3.7    1
(BX153656) Danio rerio genomic clone DKEY-120I17, genomic su...    34   4.1    2
(AC074246) Homo sapiens chromosome 18 clone RP11-430H7, WORK...    36   4.6    3
(AC141859) Canis lupus familiaris clone RP81-323H17, WORKING...    42   5.7    3
(AC147565) Mus musculus BAC clone RP23-116P18 from 9, comple...    42   6.2    3
(BX470164) Zebrafish DNA sequence from clone DKEY-24L11 in l...    32   6.6    2
(CT583674) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    32   6.6    2
(AC219228) Solanum lycopersicum chromosome 6 clone C06SLm013...    32   6.9    2
(EU016614) Uncultured Group I marine crenarchaea HF4000ANIW1...    32   7.5    2
(AL954251) Pan troglodytes chromosome 22 clone PTB-044H21 ma...    42   9.2    2

>(AU039970) Dictyostelium discoideum slug cDNA, clone SLG865.
          Length = 373

 Score =  323 bits (163), Expect(2) = e-130
 Identities = 163/163 (100%)
 Strand = Plus / Plus


Query: 1   aaaagctcaattagaaacagatttaaaaaatatttgcactttagtaccatcaaatattac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aaaagctcaattagaaacagatttaaaaaatatttgcactttagtaccatcaaatattac 60


Query: 61  aatggagtgtaaattctttatgatattagcagctccaattattgctggtgctatttctaa 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aatggagtgtaaattctttatgatattagcagctccaattattgctggtgctatttctaa 120


Query: 121 tggtgaaaatccacaaacactttgctctgactataaattatgc 163
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tggtgaaaatccacaaacactttgctctgactataaattatgc 163

 Score =  176 bits (89), Expect(2) = e-130
 Identities = 89/89 (100%)
 Strand = Plus / Plus


Query: 240 ttaaagatatttttgtggaatcaactaacaatattattgaaccaaaagaaaaagtaacaa 299
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240 ttaaagatatttttgtggaatcaactaacaatattattgaaccaaaagaaaaagtaacaa 299


Query: 300 tgagaagaaatttttaaacactattattt 328
           |||||||||||||||||||||||||||||
Sbjct: 300 tgagaagaaatttttaaacactattattt 328

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 420,171,897
Number of extensions: 28665684
Number of successful extensions: 2367038
Number of sequences better than 10.0: 55
Length of query: 372
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 349
Effective length of database: 99,442,330,388
Effective search space: 34705373305412
Effective search space used: 34705373305412
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.29
Homology vs Protein 
Query= Contig-U04159-1 (Contig-U04159-1Q) /CSM_Contig/Contig-U04159-1Q.Seq.d
         (372 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP001402_2576(CP001402|pid:none) Sulfolobus islandicus M.16.4, c...    36   0.37
CP001403_2732(CP001403|pid:none) Sulfolobus islandicus Y.G.57.14...    35   0.82
CP001401_2497(CP001401|pid:none) Sulfolobus islandicus M.16.27, ...    35   0.82
CR388420_1(CR388420|pid:none) Zebrafish DNA sequence from clone ...    35   1.1
AF162129_1(AF162129|pid:none) Drosophila melanogaster ecdysone d...    35   1.1
BC056717_1(BC056717|pid:none) Danio rerio prosaposin, mRNA (cDNA...    35   1.1
AF276996_1(AF276996|pid:none) Danio rerio lysosomal cofactor/neu...    35   1.1
DQ062781_1(DQ062781|pid:none) Drosophila simulans saposin-relate...    35   1.1
DQ363441_1(DQ363441|pid:none) Ictalurus punctatus clone C111BF07...    33   3.1
CP001357_639(CP001357|pid:none) Brachyspira hyodysenteriae WA1, ...    33   4.1
AE006641_2447(AE006641|pid:none) Sulfolobus solfataricus P2, com...    33   4.1
AB008449_1(AB008449|pid:none) Bombyx mori mRNA for BmP109, compl...    33   4.1
AC116956_84(AC116956|pid:none) Dictyostelium discoideum chromoso...    32   5.3
FN357292_36(FN357292|pid:none) Schistosoma mansoni genome sequen...    32   9.1

>CP001402_2576(CP001402|pid:none) Sulfolobus islandicus M.16.4,
           complete genome.
          Length = 658

 Score = 36.2 bits (82), Expect = 0.37
 Identities = 16/40 (40%), Positives = 25/40 (62%)
 Frame = -1

Query: 372 FLFFTKMLIYLYFFLNNSV*KFLLIVTFSFGSIILLVDST 253
           FL F   LI L FF N +V  FLL++   FG+I+ ++ ++
Sbjct: 328 FLIFPMFLIVLAFFTNGAVISFLLVIPILFGTILYIITTS 367

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: 465,116,893
Number of extensions: 6832692
Number of successful extensions: 15908
Number of sequences better than 10.0: 14
Number of HSP's gapped: 15905
Number of HSP's successfully gapped: 15
Length of query: 124
Length of database: 1,061,185,681
Length adjustment: 90
Effective length of query: 34
Effective length of database: 767,025,361
Effective search space: 26078862274
Effective search space used: 26078862274
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: 0.84  gvh: 0.60  alm: 0.31  top: 0.47  tms: 0.07  mit: 0.18  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: 1.00  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 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 28.0 %: endoplasmic reticulum
	 24.0 %: cytoplasmic
	 20.0 %: nuclear
	 12.0 %: mitochondrial
	  8.0 %: Golgi
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U04159-1 is end
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 2
SS (DIR, S) 0
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