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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-U08578-1
Contig ID Contig-U08578-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U08578-1 (Contig-U08578-1Q) /CSM_Contig/Contig-U08578-1Q.Seq.d
GGAAAAGATCAACAAAAATCAAAAGAAAATAGTATAGTATCATTAAATAA
TTTAGTTATACATTTTGGTTCAAATAATTCACCAAGATTAAAGATATCTT
CTAAATCATTGATTATATTTCAATTATTTGATTCTGGTGATGATGAAGTA
TTACAATTTCAAATGTATCAAAC
Gap no gap
Contig length 173
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 5337655
End point 5337828
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U08578
List of clone(s) 

est1=SLI784F,1,174
Translated Amino Acid sequence 
GKDQQKSKENSIVSLNNLVIHFGSNNSPRLKISSKSLIIFQLFDSGDDEVLQFQMYQ
Translated Amino Acid sequence (All Frames) 
Frame A:
GKDQQKSKENSIVSLNNLVIHFGSNNSPRLKISSKSLIIFQLFDSGDDEVLQFQMYQ


Frame B:
ekinknqkkiv*yh*ii*lyilvqiihqd*ryllnh*lyfnylilvmmkyynfkcik


Frame C:
krstkikrk*ysiik*fsytfwfk*ftkikdif*iidyisii*fw***sitisnvsn
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U08578-1 (Contig-U08578-1Q)
/CSM_Contig/Contig-U08578-1Q.Seq.d
         (173 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U08578-1 (Contig-U08578-1Q) /CSM_Contig/Conti...   343  4e-95
Contig-U10654-1 (Contig-U10654-1Q) /CSM_Contig/Conti...    42  2e-04
Contig-U11064-1 (Contig-U11064-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U09613-1 (Contig-U09613-1Q) /CSM_Contig/Conti...    38  0.003
Contig-U13905-1 (Contig-U13905-1Q) /CSM_Contig/Conti...    36  0.011
Contig-U11807-1 (Contig-U11807-1Q) /CSM_Contig/Conti...    36  0.011
Contig-U14417-1 (Contig-U14417-1Q) /CSM_Contig/Conti...    34  0.045
Contig-U11348-1 (Contig-U11348-1Q) /CSM_Contig/Conti...    34  0.045
Contig-U12459-1 (Contig-U12459-1Q) /CSM_Contig/Conti...    28  2.8
Contig-U12426-1 (Contig-U12426-1Q) /CSM_Contig/Conti...    28  2.8

>Contig-U08578-1 (Contig-U08578-1Q) /CSM_Contig/Contig-U08578-1Q.Seq.d
          Length = 173

 Score =  343 bits (173), Expect = 4e-95
 Identities = 173/173 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ggaaaagatcaacaaaaatcaaaagaaaatagtatagtatcattaaataatttagttata 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ggaaaagatcaacaaaaatcaaaagaaaatagtatagtatcattaaataatttagttata 60

                                                                       
Query: 61  cattttggttcaaataattcaccaagattaaagatatcttctaaatcattgattatattt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cattttggttcaaataattcaccaagattaaagatatcttctaaatcattgattatattt 120

                                                                
Query: 121 caattatttgattctggtgatgatgaagtattacaatttcaaatgtatcaaac 173
           |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 caattatttgattctggtgatgatgaagtattacaatttcaaatgtatcaaac 173


>Contig-U10654-1 (Contig-U10654-1Q) /CSM_Contig/Contig-U10654-1Q.Seq.d
          Length = 976

 Score = 42.1 bits (21), Expect = 2e-04
 Identities = 24/25 (96%)
 Strand = Plus / Plus

                                    
Query: 7   gatcaacaaaaatcaaaagaaaata 31
           ||||||||||||||||| |||||||
Sbjct: 826 gatcaacaaaaatcaaatgaaaata 850


>Contig-U11064-1 (Contig-U11064-1Q) /CSM_Contig/Contig-U11064-1Q.Seq.d
          Length = 2103

 Score = 40.1 bits (20), Expect = 7e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 11   aacaaaaatcaaaagaaaat 30
            ||||||||||||||||||||
Sbjct: 1866 aacaaaaatcaaaagaaaat 1885


  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: 5631
Number of Sequences: 6905
Number of extensions: 5631
Number of successful extensions: 1955
Number of sequences better than 10.0: 238
length of query: 173
length of database: 5,674,871
effective HSP length: 15
effective length of query: 158
effective length of database: 5,571,296
effective search space: 880264768
effective search space used: 880264768
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 2008.11.13
Homology vs DNA 
Query= Contig-U08578-1 (Contig-U08578-1Q) /CSM_Contig/Contig-U08578-1Q.Seq.d
         (173 letters)

Database: ddbj_A
           92,845,959 sequences; 95,242,211,685 total letters

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

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

(AU062262) Dictyostelium discoideum slug cDNA, clone SLI784.      343   1e-90  1
(FH436399) CHO_OF4993xe13f1.ab1 CHO_OF4 Nicotiana tabacum ge...    38   0.014  2
(FH436484) CHO_OF4993xe13r1.ab1 CHO_OF4 Nicotiana tabacum ge...    38   0.016  2
(AC155564) Zea mays strain B73 clone ZMMBBc0171N08, *** SEQU...    36   0.025  4
(AC117070) Dictyostelium discoideum chromosome 2 map 2097701...    36   0.063  5
(AC161878) Mus musculus BAC clone RP23-303B4 from chromosome...    34   0.13   5
(FI080042) CHO_OF7392xd23f1.ab1 CHO_OF7 Nicotiana tabacum ge...    36   0.25   3
(FH151019) CHO_OF3059xn22f1.ab1 CHO_OF3 Nicotiana tabacum ge...    36   0.25   3
(AC116956) Dictyostelium discoideum chromosome 2 map 1418423...    40   0.27   8
(AC080096) Homo sapiens 3 BAC RP11-443O18 (Roswell Park Canc...    46   0.38   1
(AC175209) Cavia porcellus clone CH234-491B10, WORKING DRAFT...    46   0.38   1
(FG841662) UCRVU05_CCNN4718_b1 Cowpea IT84S-2049 Mixed Tissu...    46   0.38   1
(AC198936) Zea mays chromosome 7 clone CH201-340K18; ZMMBBc0...    36   0.38   3
(AC117080) Dictyostelium discoideum chromosome 2 map complem...    32   0.47   5
(AC193460) Zea mays chromosome 10 clone CH201-383L19; ZMMBBc...    40   0.47   3
(AC214625) Populus trichocarpa clone POP008-A22, complete se...    34   0.52   7
(AE014852) Plasmodium falciparum 3D7 chromosome 12, section ...    34   0.69   9
(AC191474) Aotus nancymaae clone CH258-486N23, WORKING DRAFT...    32   0.75   5
(CU657919) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    32   0.76   7
(AC187543) Medicago truncatula chromosome 2 BAC clone mth2-7...    32   0.80   2
(BH135388) ENTMY19TR Entamoeba histolytica Sheared DNA Entam...    32   1.0    2
(AZ531532) ENTCX66TF Entamoeba histolytica Sheared DNA Entam...    32   1.0    2
(EJ063198) 1095458011898 Global-Ocean-Sampling_GS-26-01-01-1...    34   1.0    2
(AF250284) Amsacta moorei entomopoxvirus, complete genome.         32   1.2    4
(CU694916) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   1.3    7
(AC180495) Strongylocentrotus purpuratus clone R3-3016B07, W...    34   1.4    6
(BV665473) S216P61369RC12.T0 Masuku Pan troglodytes troglody...    44   1.5    1
(BV278557) S232P6537FA4.T0 Beagle Canis familiaris STS genom...    44   1.5    1
(DQ927303) Tetrahymena malaccensis strain MP75 mitochondrion...    44   1.5    1
(AC148249) Otolemur garnettii clone CH256-196E5, WORKING DRA...    44   1.5    1
(AC148127) Otolemur garnettii clone CH256-473N15, WORKING DR...    44   1.5    1
(AC120608) Rattus norvegicus clone CH230-68O20, *** SEQUENCI...    44   1.5    1
(AC098016) Rattus norvegicus clone CH230-107P8, WORKING DRAF...    44   1.5    1
(AC208896) Zea mays chromosome 4 clone CH201-139L11; ZMMBBc0...    44   1.5    1
(AC206841) Zea mays chromosome 7 clone CH201-486P12; ZMMBBc0...    44   1.5    1
(AC205486) Zea mays chromosome 4 clone CH201-353L12; ZMMBBc0...    44   1.5    1
(AC189477) Brassica rapa subsp. pekinensis clone KBrB080O07,...    44   1.5    1
(AC188274) Callicebus moloch clone LB5-307A16, WORKING DRAFT...    44   1.5    1
(BH317676) CH230-63G23.TJ CHORI-230 Segment 1 Rattus norvegi...    44   1.5    1
(BH272753) CH230-107P8.TV CHORI-230 Segment 1 Rattus norvegi...    44   1.5    1
(FI081925) CHO_OF7399xm14r1.ab1 CHO_OF7 Nicotiana tabacum ge...    44   1.5    1
(FI081842) CHO_OF7399xm14f1.ab1 CHO_OF7 Nicotiana tabacum ge...    44   1.5    1
(EK002094) 1093025613070 Global-Ocean-Sampling_GS-30-02-01-1...    44   1.5    1
(EJ842425) 1093017839441 Global-Ocean-Sampling_GS-30-02-01-1...    44   1.5    1
(DX334905) OR_ABa0259J18.f OR_ABa Oryza ridleyi genomic clon...    44   1.5    1
(DX295469) OR_ABa0201D09.f OR_ABa Oryza ridleyi genomic clon...    44   1.5    1
(ES481990) BGBV-aac84d03.g1 Snail_EST_pSMART Biomphalaria gl...    44   1.5    1
(CO843287) LM_GM5_000877 Locusta migratoria gregarious phase...    44   1.5    1
(CP000724) Alkaliphilus metalliredigens QYMF, complete genome.     44   1.5    1
(AP008981) Orientia tsutsugamushi str. Ikeda DNA, complete g...    44   1.5    1
(AM180355) Clostridium difficile 630 complete genome.              44   1.5    1
(CU571130) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    36   1.5    3
(ES450814) 25784 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   1.6    2
(ES450083) 25052 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   1.7    2
(ES450976) 25946 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   1.8    2
(ES450395) 25365 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   1.9    2
(AC112913) Homo sapiens chromosome 3 clone RP11-608P9, *** S...    36   1.9    3
(AC026138) Homo sapiens chromosome 1 clone RP11-269I13 map 1...    38   1.9    4
(ES451772) 26742 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   2.0    2
(EC389600) H02_H02h1p4_pDNRf_462571 Myzus persicae, tobacco ...    34   2.1    2
(AC150012) Callithrix jacchus clone CH259-460O10, WORKING DR...    32   2.1    6
(AF143579) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.1    2
(AL161510) Arabidopsis thaliana DNA chromosome 4, contig fra...    32   2.1    5
(AP002332) Homo sapiens genomic DNA, chromosome 4q22-q24, cl...    36   2.1    4
(AF143578) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.2    2
(EC389923) G10_G10h2h19_pDNRf_473376 Myzus persicae, tobacco...    34   2.2    2
(DW012762) w17o13_M13F Myzus persicae, tobacco lineage, whol...    34   2.2    2
(AM908402) Solanum tuberosum EST, clone 4I5.                       34   2.2    2
(BX005075) Zebrafish DNA sequence from clone CH211-112P11 in...    32   2.2    7
(DW013090) w18n8_M13F Myzus persicae, tobacco lineage, whole...    34   2.2    2
(DW011323) w13g10_M13F Myzus persicae, tobacco lineage, whol...    34   2.3    2
(ES451551) 26521 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   2.3    2
(ES450148) 25117 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   2.4    2
(ES450052) 25021 Myzus persicae 2001-12 (red), Fenton Myzus ...    34   2.4    2
(AC153201) Bos taurus clone CH240-33I1, WORKING DRAFT SEQUEN...    40   2.4    4
(DW011566) w14c12_M13F Myzus persicae, tobacco lineage, whol...    34   2.4    2
(EU196565) Brachycaudus tragopogonis isolate 1378 cytochrome...    34   2.5    2
(AF143580) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(DW010607) w11c5_M13F Myzus persicae, tobacco lineage, whole...    34   2.5    2
(EC389610) H05_H05h1l10_pDNRf_462499 Myzus persicae, tobacco...    34   2.5    2
(DW014856) w9i20_M13F Myzus persicae, tobacco lineage, whole...    34   2.5    2
(AF143575) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(DW014961) w9n18_M13F Myzus persicae, tobacco lineage, whole...    34   2.5    2
(AF143588) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143592) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143591) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143590) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143589) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143587) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143586) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143585) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143584) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143583) Myzus persicae cytochrome oxidase subunit II (COI...    34   2.5    2
(AF143581) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(AF143577) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(AF143576) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(AF143574) Myzus nicotianae cytochrome oxidase subunit II (C...    34   2.5    2
(DW011876) w15e4_M13F Myzus persicae, tobacco lineage, whole...    34   2.6    2
(DW011039) w12i9_M13F Myzus persicae, tobacco lineage, whole...    34   2.6    2
(DW010942) w12d17_M13F Myzus persicae, tobacco lineage, whol...    34   2.6    2

>(AU062262) Dictyostelium discoideum slug cDNA, clone SLI784.
          Length = 174

 Score =  343 bits (173), Expect = 1e-90
 Identities = 173/173 (100%)
 Strand = Plus / Plus


Query: 1   ggaaaagatcaacaaaaatcaaaagaaaatagtatagtatcattaaataatttagttata 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ggaaaagatcaacaaaaatcaaaagaaaatagtatagtatcattaaataatttagttata 60


Query: 61  cattttggttcaaataattcaccaagattaaagatatcttctaaatcattgattatattt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cattttggttcaaataattcaccaagattaaagatatcttctaaatcattgattatattt 120


Query: 121 caattatttgattctggtgatgatgaagtattacaatttcaaatgtatcaaac 173
           |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 caattatttgattctggtgatgatgaagtattacaatttcaaatgtatcaaac 173

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 280,976,195
Number of extensions: 19357547
Number of successful extensions: 5851574
Number of sequences better than 10.0: 302
Length of query: 173
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 151
Effective length of database: 93,199,600,587
Effective search space: 14073139688637
Effective search space used: 14073139688637
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.24
Homology vs Protein 
Query= Contig-U08578-1 (Contig-U08578-1Q) /CSM_Contig/Contig-U08578-1Q.Seq.d
         (173 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

 ***** No hits found ******

Lambda     K      H
   0.314    0.132    0.352

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3204285
Number of Hits to DB: 143,075,632
Number of extensions: 1941074
Number of successful extensions: 3547
Number of sequences better than 10.0: 0
Number of HSP's gapped: 3547
Number of HSP's successfully gapped: 0
Length of query: 57
Length of database: 1,040,966,779
Length adjustment: 30
Effective length of query: 27
Effective length of database: 944,838,229
Effective search space: 25510632183
Effective search space used: 25510632183
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 (21.5 bits)
S2: 26 (14.6 bits)
PSORT 

 psg: 0.82  gvh: 0.35  alm: 0.49  top: 0.53  tms: 0.00  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: 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
	 16.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U08578-1 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) 1
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