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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U14616-1
Contig ID Contig-U14616-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14616-1 (Contig-U14616-1Q) /CSM_Contig/Contig-U14616-1Q.Seq.d
ACTTTAAATTCAACTAATCGAATCGAATTAATTTGATATTTATGTGGCCG
AAAAAAATTGATAACAATTTAAATTTATTAATTTTTAATATGAATTTAGT
ATAGATAAATAAAGCACACAAAATTATATAAAATAAATCATAGTTGGAAG
AAAAAAAAAANNNNNNNNN
Gap no gap
Contig length 169
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 527640
End point 527568
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U14616
List of clone(s) 

est1=SHH551F,1,160
Translated Amino Acid sequence 
fkfn*SNRINLIFMWPKKIDNNLNLLIFNMNLV*inkahkii*nks*leekkxxx
Translated Amino Acid sequence (All Frames) 
Frame A:
tlnstnrieli*ylcgrkkliti*iy*fli*i*yr*ikhtklykinhswkkkkxxx


Frame B:
l*iqliesn*fdiyvaekn**qfkfinf*yefsidk*stqnyik*iivgrkkkxxx


Frame C:
fkfn*SNRINLIFMWPKKIDNNLNLLIFNMNLV*inkahkii*nks*leekkxxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14616-1 (Contig-U14616-1Q)
/CSM_Contig/Contig-U14616-1Q.Seq.d
         (169 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14616-1 (Contig-U14616-1Q) /CSM_Contig/Conti...   256  6e-69
Contig-U06670-1 (Contig-U06670-1Q) /CSM_Contig/Conti...    52  2e-07
Contig-U14359-1 (Contig-U14359-1Q) /CSM_Contig/Conti...    44  5e-05
Contig-U06334-1 (Contig-U06334-1Q) /CSM_Contig/Conti...    42  2e-04
Contig-U11278-1 (Contig-U11278-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U12818-1 (Contig-U12818-1Q) /CSM_Contig/Conti...    38  0.003
Contig-U05408-1 (Contig-U05408-1Q) /CSM_Contig/Conti...    38  0.003
Contig-U11170-1 (Contig-U11170-1Q) /CSM_Contig/Conti...    36  0.011
Contig-U09225-1 (Contig-U09225-1Q) /CSM_Contig/Conti...    36  0.011
Contig-U04336-1 (Contig-U04336-1Q) /CSM_Contig/Conti...    30  0.68

>Contig-U14616-1 (Contig-U14616-1Q) /CSM_Contig/Contig-U14616-1Q.Seq.d
          Length = 169

 Score =  256 bits (129), Expect = 6e-69
 Identities = 143/150 (95%)
 Strand = Plus / Plus

                                                                       
Query: 1   actttaaattcaactaatcgaatcgaattaatttgatatttatgtggccgnnnnnnnttg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||       |||
Sbjct: 1   actttaaattcaactaatcgaatcgaattaatttgatatttatgtggccgaaaaaaattg 60

                                                                       
Query: 61  ataacaatttaaatttattaatttttaatatgaatttagtatagataaataaagcacaca 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ataacaatttaaatttattaatttttaatatgaatttagtatagataaataaagcacaca 120

                                         
Query: 121 aaattatataaaataaatcatagttggaag 150
           ||||||||||||||||||||||||||||||
Sbjct: 121 aaattatataaaataaatcatagttggaag 150


>Contig-U06670-1 (Contig-U06670-1Q) /CSM_Contig/Contig-U06670-1Q.Seq.d
          Length = 481

 Score = 52.0 bits (26), Expect = 2e-07
 Identities = 32/34 (94%)
 Strand = Plus / Minus

                                             
Query: 78  ttaatttttaatatgaatttagtatagataaata 111
           |||||||||||||| |||||||| ||||||||||
Sbjct: 56  ttaatttttaatatcaatttagtttagataaata 23


>Contig-U14359-1 (Contig-U14359-1Q) /CSM_Contig/Contig-U14359-1Q.Seq.d
          Length = 712

 Score = 44.1 bits (22), Expect = 5e-05
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                 
Query: 82  tttttaatatgaatttagtata 103
           ||||||||||||||||||||||
Sbjct: 88  tttttaatatgaatttagtata 109


  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: 5160
Number of Sequences: 6905
Number of extensions: 5160
Number of successful extensions: 2049
Number of sequences better than 10.0: 297
length of query: 169
length of database: 5,674,871
effective HSP length: 15
effective length of query: 154
effective length of database: 5,571,296
effective search space: 857979584
effective search space used: 857979584
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 2008.12.27
Homology vs DNA 
Query= Contig-U14616-1 (Contig-U14616-1Q) /CSM_Contig/Contig-U14616-1Q.Seq.d
         (169 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

(BJ395614) Dictyostelium discoideum cDNA clone:dds39e13, 5' ...   184   1e-66  2
(AF474338) Dictyostelium discoideum ABC transporter ABCC.6 (...   131   4e-31  2
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470...    84   5e-17  2
(AC117075) Dictyostelium discoideum chromosome 2 map 5201047...    78   1e-10  1
(AC116305) Dictyostelium discoideum chromosome 2 map 1005175...    76   4e-10  1
(AC116986) Dictyostelium discoideum chromosome 2 map 2234041...    74   2e-09  1
(AC115584) Dictyostelium discoideum chromosome 2 map complem...    62   6e-06  1
(AC116967) Dictyostelium discoideum chromosome 2 map 5481549...    58   1e-04  1
(AC115581) Dictyostelium discoideum chromosome 2 map complem...    58   1e-04  1
(AC116957) Dictyostelium discoideum chromosome 2 map 1685067...    46   3e-04  2
(AY254474) Dictyostelium discoideum RpkA (rpkA) gene, comple...    50   0.001  2
(AC116920) Dictyostelium discoideum chromosome 2 map 4415041...    50   0.001  2
(AC116982) Dictyostelium discoideum chromosome 2 map 3622643...    54   0.002  1
(AC116924) Dictyostelium discoideum chromosome 2 map 6357117...    54   0.002  1
(AY171066) Dictyostelium discoideum extrachromosomal palindr...    52   0.006  1
(AC116032) Dictyostelium discoideum chromosome 2 map 4158743...    52   0.006  1
(DT788680) 126445673 TL1 Tribolium castaneum cDNA clone 70O2...    52   0.006  1
(AU266752) Dictyostelium discoideum vegetative cDNA clone:VS...    52   0.006  1
(AU263418) Dictyostelium discoideum vegetative cDNA clone:VS...    52   0.006  1
(DX521427) GH_MBb0036C16r GH_MBb Gossypium hirsutum genomic ...    42   0.007  3
(AX652470) Sequence 2340 from Patent WO03000898.                   46   0.009  2
(BZ699876) PUBLM51TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    38   0.010  2
(CZ901154) gz31h09.x1.b.screen Soybean methylation filtered ...    48   0.012  2
(AM428082) Vitis vinifera contig VV78X097309.10, whole genom...    38   0.013  3
(EV414499) 210734578 NGP Nasonia giraulti cDNA clone 142A15 ...    36   0.015  2
(BH986983) oef80d12.b1 B.oleracea002 Brassica oleracea genom...    30   0.019  3
(BH589939) BOHOK91TF BOHO Brassica oleracea genomic clone BO...    40   0.019  3
(FH134708) CHO_OF3622xh07r1.ab1 CHO_OF3 Nicotiana tabacum ge...    36   0.019  2
(AF310892) Dictyostelium discoideum citrate synthase (gltA) ...    50   0.023  1
(AC116963) Dictyostelium discoideum chromosome 2 map 4657875...    50   0.023  1
(AC166783) Bos taurus clone CH240-125N11, WORKING DRAFT SEQU...    50   0.023  1
(AC166515) Bos taurus clone CH240-172D9, *** SEQUENCING IN P...    50   0.023  1
(ET922299) CHO_OF216xc23r1.ab1 CHO_OF Nicotiana tabacum geno...    50   0.023  1
(EK423821) 1095515650443 Global-Ocean-Sampling_GS-31-01-01-1...    50   0.023  1
(EJ716171) 1092959419565 Global-Ocean-Sampling_GS-30-02-01-1...    50   0.023  1
(EJ706309) 1092956054539 Global-Ocean-Sampling_GS-30-02-01-1...    50   0.023  1
(AC114261) Dictyostelium discoideum chromosome 2 map 126059-...    48   0.030  4
(U49822) Saccharomyces douglasii mitochondrial tRNA-Ser and ...    38   0.041  2
(AM431746) Vitis vinifera contig VV78X092673.12, whole genom...    42   0.053  3
(AL161533) Arabidopsis thaliana DNA chromosome 4, contig fra...    36   0.057  2
(AL049638) Arabidopsis thaliana DNA chromosome 4, BAC clone ...    36   0.059  2
(AM426703) Vitis vinifera contig VV78X009520.4, whole genome...    30   0.060  3
(AB370280) Drosophila fuyamai Obp57d, Obp57e genes for odora...    48   0.093  1
(AC153706) Bos taurus clone CH240-30N4, WORKING DRAFT SEQUEN...    48   0.093  1
(AC151139) Bos taurus clone CH240-488G16, WORKING DRAFT SEQU...    48   0.093  1
(AC112578) Rattus norvegicus clone CH230-38G5, *** SEQUENCIN...    48   0.093  1
(AC105778) Rattus norvegicus clone CH230-213M11, *** SEQUENC...    48   0.093  1
(AC167007) Bos taurus clone CH240-195N4, WORKING DRAFT SEQUE...    48   0.093  1
(BM166173) EST568696 PyBS Plasmodium yoelii yoelii cDNA clon...    48   0.093  1
(AC189491) Brassica rapa subsp. pekinensis clone KBrB084M06,...    44   0.098  4
(CL515413) SAIL_89_H12.v1 SAIL Collection Arabidopsis thalia...    38   0.12   2
(EU626444) Gossypium arboreum clone BAC 271C22, complete seq...    44   0.13   3
(AF466146) Melipona bicolor mitochondrial genome, partial se...    34   0.13   4
(AC007769) Drosophila melanogaster, chromosome 3R, region 88...    38   0.15   4
(BH543349) BOHBE33TR BOHB Brassica oleracea genomic clone BO...    44   0.16   2
(DE325348) Bombyx mori genomic DNA, BAC clone:BES_640_H07.         42   0.18   2
(AB088650) Graphium odin mitochondrial gene for NADH dehydro...    44   0.20   2
(AB059539) Graphium ridleyanus mitochondrial ND5 gene for NA...    44   0.20   2
(AB059535) Graphium incerta mitochondrial ND5 gene for NADH ...    44   0.20   2
(AC169085) Mus musculus chromosome 6 clone RP24-66N10, WORKI...    38   0.21   2
(AC126261) Mus musculus BAC clone RP23-340H19 from 6, comple...    38   0.21   2
(EV417320) 210764117 NGP Nasonia giraulti cDNA clone 145E11 ...    36   0.21   2
(AC096667) Homo sapiens BAC clone RP11-363K21 from 2, comple...    38   0.21   2
(EV416268) 210754993 NGP Nasonia giraulti cDNA clone 167G7 5...    36   0.21   2
(EV414490) 210734531 NGP Nasonia giraulti cDNA clone 142E1 5...    36   0.21   2
(AC202480) Medicago truncatula clone mth2-166i6, WORKING DRA...    34   0.22   2
(EV424092) 211375372 NGP Nasonia giraulti cDNA clone 240C21,...    36   0.22   2
(AM486556) Vitis vinifera contig VV78X015674.3, whole genome...    36   0.23   2
(BX158622) Danio rerio genomic clone DKEY-147I19, genomic su...    32   0.24   3
(DT784473) 127434134 TH1 Tribolium castaneum cDNA clone 113G...    34   0.25   3
(AM452895) Vitis vinifera contig VV78X105264.25, whole genom...    38   0.26   2
(CR239274) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(CR193747) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(CR225130) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(BX973131) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(CR250751) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(EK256675) 1095462013721 Global-Ocean-Sampling_GS-31-01-01-1...    38   0.27   2
(EV418432) 210771111 NGP Nasonia giraulti cDNA clone 135G1 5...    36   0.27   2
(CR270047) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(EH239139) JGI_ACAC20077.rev ACAC Phakopsora pachyrhizi TW72...    34   0.27   2
(CR144723) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(BH069803) RPCI-24-331A15.TVB RPCI-24 Mus musculus genomic c...    38   0.27   2
(CR223302) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(CR134169) Forward strand read from insert in 5'HPRT inserti...    38   0.27   2
(AC149298) Populus trichocarpa clone Pop1-021H24, complete s...    44   0.32   3
(DU912785) 329348 Tomato EcoRI BAC Library Solanum lycopersi...    34   0.32   3
(AC024907) Homo sapiens chromosome 3 clone RP11-911E23, WORK...    40   0.35   4
(DE433772) Bombyx mori genomic DNA, Fosmid clone:GBMFno19_j0...    34   0.36   3
(AC200518) Pongo abelii BAC clone CH276-405B23 from chromoso...    46   0.37   1
(AC200271) Pongo abelii BAC clone CH276-155A18 from chromoso...    46   0.37   1
(AC145777) Gorilla gorilla gorilla clone CH255-194M15, compl...    46   0.37   1
(AC138733) Pongo abelii clone CH253-482E4, complete sequence.      46   0.37   1
(AC006201) Arabidopsis thaliana chromosome 2 clone T27K22 ma...    46   0.37   1
(AX346024) Sequence 1095 from Patent WO0200928.                    46   0.37   1
(AY392444) Dictyostelium discoideum RNA-binding protein gene...    46   0.37   1
(AC117080) Dictyostelium discoideum chromosome 2 map complem...    46   0.37   1
(AC162124) Carollia perspicillata clone 483I20, WORKING DRAF...    46   0.37   1
(AC141841) Apis mellifera clone CH224-4A4, WORKING DRAFT SEQ...    46   0.37   1
(CU570711) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   0.37   1
(CU407284) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   0.37   1

>(BJ395614) Dictyostelium discoideum cDNA clone:dds39e13, 5' end,
           single read.
          Length = 160

 Score =  184 bits (93), Expect(2) = 1e-66
 Identities = 93/93 (100%)
 Strand = Plus / Plus


Query: 58  ttgataacaatttaaatttattaatttttaatatgaatttagtatagataaataaagcac 117
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 58  ttgataacaatttaaatttattaatttttaatatgaatttagtatagataaataaagcac 117


Query: 118 acaaaattatataaaataaatcatagttggaag 150
           |||||||||||||||||||||||||||||||||
Sbjct: 118 acaaaattatataaaataaatcatagttggaag 150

 Score = 99.6 bits (50), Expect(2) = 1e-66
 Identities = 50/50 (100%)
 Strand = Plus / Plus


Query: 1  actttaaattcaactaatcgaatcgaattaatttgatatttatgtggccg 50
          ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  actttaaattcaactaatcgaatcgaattaatttgatatttatgtggccg 50

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 248,171,597
Number of extensions: 19052100
Number of successful extensions: 6229548
Number of sequences better than 10.0: 1062
Length of query: 169
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 147
Effective length of database: 93,199,600,587
Effective search space: 13700341286289
Effective search space used: 13700341286289
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.12
Homology vs Protein 
Query= Contig-U14616-1 (Contig-U14616-1Q) /CSM_Contig/Contig-U14616-1Q.Seq.d
         (169 letters)

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

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

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

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: 173,350,239
Number of extensions: 2421965
Number of successful extensions: 1884
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1884
Number of HSP's successfully gapped: 0
Length of query: 56
Length of database: 1,051,180,864
Length adjustment: 29
Effective length of query: 27
Effective length of database: 957,320,653
Effective search space: 25847657631
Effective search space used: 25847657631
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: 26 (14.6 bits)
PSORT 

 psg: 0.89  gvh: 0.16  alm: 0.52  top: 0.47  tms: 0.00  mit: 0.31  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 

	 36.0 %: nuclear
	 32.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  8.0 %: vacuolar
	  8.0 %: mitochondrial
	  4.0 %: extracellular, including cell wall

>> prediction for Contig-U14616-1 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) 1
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0