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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-U12715-1
Contig ID Contig-U12715-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12715-1 (Contig-U12715-1Q) /CSM_Contig/Contig-U12715-1Q.Seq.d
ATTCAATTTCTTTATTTTATTTTATTTTATTTTTTTTTATTAATATCCAT
TTTATTTATTTTTTAAATATAATAATAATAATAATAATAATTGATGATGG
CATCACCATCATCTAGGTTATTAAAATTTATTACAAATGGAAGTAAATTA
CATTCAGCAAAAAATAATAATATGATTAAAAATAAGAATATAATATCACC
AACAATAACAAAATTATTTTCAACATCAAAAATTTCAAATGAAATTGGTA
ATATTAGAAATTTTAATAATAAAATATCAACAAATTTAATCAATTCAAAT
ATAAATACAAAACCATTTTTTGAAATACCAAAATTATTTGAAAAGAAATA
TTATTCATATATACCACCAACATGGGAAGAAAAAGATAAGGAAAAACAAT
TCAATTCCATAACATCCACTAG
Gap no gap
Contig length 422
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 481597
End point 482018
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 2
Link to clone list U12715
List of clone(s) 

est1=AHH449F,1,422
est2=AHL534F,12,418
Translated Amino Acid sequence 
iqflyfilfyffllisilfif*i*******LMMASPSSRLLKFITNGSKLHSAKNNNMIK
NKNIISPTITKLFSTSKISNEIGNIRNFNNKISTNLINSNINTKPFFEIPKLFEKKYYSY
IPPTWEEKDKEKQFNSITST
Translated Amino Acid sequence (All Frames) 
Frame A:
iqflyfilfyffllisilfif*i*******LMMASPSSRLLKFITNGSKLHSAKNNNMIK
NKNIISPTITKLFSTSKISNEIGNIRNFNNKISTNLINSNINTKPFFEIPKLFEKKYYSY
IPPTWEEKDKEKQFNSITST


Frame B:
fnffilfyfiffy*ypfylffkynnnnnnn**whhhhlgy*nllqmevnyiqqkiii*lk
iri*yhqq*qnyfqhqkfqmklvileiliikyqqi*siqi*iqnhflkyqnylkrniihi
yhqhgkkkirknnsip*hpl


Frame C:
sislfyfilfffinihfiyflniiiiiiiiddgitii*vikiyykwk*itfskk**yd*k
*eynitnnnkiifniknfk*nw*y*kf***ninkfnqfkykyktif*ntkii*keilfiy
ttnmgrkr*gktiqfhnih*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12715-1 (Contig-U12715-1Q)
/CSM_Contig/Contig-U12715-1Q.Seq.d
         (422 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12715-1 (Contig-U12715-1Q) /CSM_Contig/Conti...   218  4e-57
Contig-U14190-1 (Contig-U14190-1Q) /CSM_Contig/Conti...    42  5e-04
Contig-U11191-1 (Contig-U11191-1Q) /CSM_Contig/Conti...    38  0.007
Contig-U01343-1 (Contig-U01343-1Q) /CSM_Contig/Conti...    38  0.007
Contig-U12520-1 (Contig-U12520-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U11270-1 (Contig-U11270-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U11206-1 (Contig-U11206-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U12133-1 (Contig-U12133-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U11777-1 (Contig-U11777-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U11411-1 (Contig-U11411-1Q) /CSM_Contig/Conti...    34  0.12

>Contig-U12715-1 (Contig-U12715-1Q) /CSM_Contig/Contig-U12715-1Q.Seq.d
          Length = 422

 Score =  218 bits (110), Expect = 4e-57
 Identities = 110/110 (100%)
 Strand = Plus / Plus

                                                                       
Query: 313 ccattttttgaaataccaaaattatttgaaaagaaatattattcatatataccaccaaca 372
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 313 ccattttttgaaataccaaaattatttgaaaagaaatattattcatatataccaccaaca 372

                                                             
Query: 373 tgggaagaaaaagataaggaaaaacaattcaattccataacatccactag 422
           ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 373 tgggaagaaaaagataaggaaaaacaattcaattccataacatccactag 422


 Score =  127 bits (64), Expect = 1e-29
 Identities = 64/64 (100%)
 Strand = Plus / Plus

                                                                       
Query: 92  tgatgatggcatcaccatcatctaggttattaaaatttattacaaatggaagtaaattac 151
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 92  tgatgatggcatcaccatcatctaggttattaaaatttattacaaatggaagtaaattac 151

               
Query: 152 attc 155
           ||||
Sbjct: 152 attc 155


 Score = 71.9 bits (36), Expect = 5e-13
 Identities = 36/36 (100%)
 Strand = Plus / Plus

                                               
Query: 215 tattttcaacatcaaaaatttcaaatgaaattggta 250
           ||||||||||||||||||||||||||||||||||||
Sbjct: 215 tattttcaacatcaaaaatttcaaatgaaattggta 250


>Contig-U14190-1 (Contig-U14190-1Q) /CSM_Contig/Contig-U14190-1Q.Seq.d
          Length = 1316

 Score = 42.1 bits (21), Expect = 5e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                
Query: 329 caaaattatttgaaaagaaat 349
           |||||||||||||||||||||
Sbjct: 310 caaaattatttgaaaagaaat 290


>Contig-U11191-1 (Contig-U11191-1Q) /CSM_Contig/Contig-U11191-1Q.Seq.d
          Length = 1417

 Score = 38.2 bits (19), Expect = 0.007
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                   
Query: 377  aagaaaaagataaggaaaaacaa 399
            |||||||||| ||||||||||||
Sbjct: 979  aagaaaaagaaaaggaaaaacaa 1001


  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: 5866
Number of Sequences: 6905
Number of extensions: 5866
Number of successful extensions: 797
Number of sequences better than 10.0: 248
length of query: 422
length of database: 5,674,871
effective HSP length: 16
effective length of query: 406
effective length of database: 5,564,391
effective search space: 2259142746
effective search space used: 2259142746
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. 2
Homology vs DNA 
Query= Contig-U12715-1 (Contig-U12715-1Q) /CSM_Contig/Contig-U12715-1Q.Seq.d
         (422 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

(BJ334202) Dictyostelium discoideum cDNA clone:dda45b14, 5' ...   188   4e-75  2
(BJ336534) Dictyostelium discoideum cDNA clone:dda54c09, 5' ...   180   9e-73  2
(CU013542) M.truncatula DNA sequence from clone MTH2-64I10 o...    50   0.064  1
(AC135796) Medicago truncatula chromosome 8 clone mth2-28b18...    50   0.064  1
(AC112186) Homo sapiens chromosome 5 clone RP11-235B3, compl...    48   0.25   1
(AC099487) Homo sapiens chromosome 5 clone CTD-2340E1, compl...    48   0.25   1
(AC117533) Homo sapiens chromosome 5 clone RP11-777F13, WORK...    48   0.25   1
(AC026927) Homo sapiens clone RP11-777F13, WORKING DRAFT SEQ...    48   0.25   1
(AC022169) Homo sapiens chromosome 17 clone RP11-104I20, WOR...    44   0.28   2
(DQ471386) Paracantha genitilis 16S ribosomal RNA gene, part...    36   0.57   2
(DQ268751) Citrullus lanatus var. citroides seed accession T...    46   0.99   1
(DQ268750) Citrullus lanatus var. citroides seed accession T...    46   0.99   1
(DQ268749) Citrullus lanatus var. citroides seed accession N...    46   0.99   1
(DQ268748) Citrullus lanatus var. citroides seed accession N...    46   0.99   1
(DQ268747) Citrullus lanatus var. citroides seed accession N...    46   0.99   1
(DQ268746) Citrullus lanatus var. citroides seed accession N...    46   0.99   1
(DQ268745) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268744) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268743) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268742) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268741) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268740) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268739) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(DQ268738) Citrullus lanatus var. citroides seed accession P...    46   0.99   1
(EI314071) GM_WBc0046I02.r GM_WBc Glycine max genomic clone ...    46   0.99   1
(DX042572) KBrB042P23F KBrB, Brassica rapa BamHI BAC library...    32   3.2    3
(DQ268761) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268760) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268759) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268757) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268756) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268755) Citrullus lanatus var. lanatus Sweet Siberian trn...    44   3.9    1
(DQ268754) Citrullus lanatus var. lanatus AU-Producer trnE-t...    44   3.9    1
(DQ268753) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(DQ268752) Citrullus lanatus var. lanatus seed accession PI ...    44   3.9    1
(AY695900) Citrullus colocynthis cultivar TCN 767 tRNA-Glu g...    44   3.9    1
(AY695899) Citrullus colocynthis cultivar PI 549161 tRNA-Glu...    44   3.9    1
(AY695898) Citrullus colocynthis cultivar TCN 955 tRNA-Glu g...    44   3.9    1
(AY695897) Citrullus colocynthis cultivar PI 525081 tRNA-Glu...    44   3.9    1
(AY695896) Citrullus colocynthis cultivar PI 432337 tRNA-Glu...    44   3.9    1
(AY695895) Citrullus colocynthis cultivar accession 34256 fr...    44   3.9    1
(AY695894) Citrullus colocynthis cultivar PI 386016 tRNA-Glu...    44   3.9    1
(AY695893) Citrullus colocynthis cultivar PI 269365 tRNA-Glu...    44   3.9    1
(AY695892) Citrullus colocynthis cultivar PI 537277 tRNA-Glu...    44   3.9    1
(AY695891) Citrullus colocynthis cultivar PI 14202 tRNA-Glu ...    44   3.9    1
(AM463557) Vitis vinifera contig VV78X042504.8, whole genome...    44   3.9    1
(AM455330) Vitis vinifera, whole genome shotgun sequence, co...    44   3.9    1
(AC087510) Homo sapiens chromosome 17, clone RP11-104I20, co...    44   3.9    1
(AC023389) Homo sapiens chromosome 17, clone RP11-82O19, com...    44   3.9    1
(ER604002) 1093016263356 Global-Ocean-Sampling_GS-36-01-01-2...    44   3.9    1
(ER578878) 1093015825749 Global-Ocean-Sampling_GS-36-01-01-2...    44   3.9    1
(EK555358) 1095516160114 Global-Ocean-Sampling_GS-32-01-01-1...    44   3.9    1
(EK482793) 1095469529700 Global-Ocean-Sampling_GS-32-01-01-1...    44   3.9    1
(EK219804) 1095460137174 Global-Ocean-Sampling_GS-31-01-01-1...    44   3.9    1
(EJ505443) 1095403699472 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.9    1
(EJ399501) 1093012026536 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.9    1
(EJ044593) 1095454112975 Global-Ocean-Sampling_GS-26-01-01-1...    44   3.9    1
(ED805547) MG__Bb0012H06r MG__Bb Mimulus guttatus genomic, g...    44   3.9    1
(DH282741) Oryzias latipes Fosmid clone:GOLWFno622_k10, reve...    44   3.9    1
(CU842813) A BAC library has been constructed from PN40024 g...    44   3.9    1
(AG497109) Mus musculus molossinus DNA, clone:MSMg01-396I23....    44   3.9    1
(CL048182) CH216-67I1_RM1.1 CH216 Xenopus (Silurana) tropica...    44   3.9    1
(AE008384) Methanosarcina mazei strain Goe1, complete genome.      44   3.9    1
(AC005506) Plasmodium falciparum chromosome 12 clone 3D7, **...    32   5.3    6
(AC199970) Populus trichocarpa clone Pop1-114B01, complete s...    38   5.3    3
(AC211043) Solanum lycopersicum chromosome 6 clone C06HBa010...    38   6.9    3
(AC161496) Mus musculus chromosome 3, clone RP23-119A9, comp...    42   8.1    3
(AC172861) Brassica rapa subsp. pekinensis clone KBrB044C04,...    36   9.0    5

>(BJ334202) Dictyostelium discoideum cDNA clone:dda45b14, 5' end,
           single read.
          Length = 422

 Score =  188 bits (95), Expect(2) = 4e-75
 Identities = 95/95 (100%)
 Strand = Plus / Plus


Query: 328 ccaaaattatttgaaaagaaatattattcatatataccaccaacatgggaagaaaaagat 387
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 328 ccaaaattatttgaaaagaaatattattcatatataccaccaacatgggaagaaaaagat 387


Query: 388 aaggaaaaacaattcaattccataacatccactag 422
           |||||||||||||||||||||||||||||||||||
Sbjct: 388 aaggaaaaacaattcaattccataacatccactag 422

 Score =  129 bits (65), Expect(2) = 4e-75
 Identities = 65/65 (100%)
 Strand = Plus / Plus


Query: 93  gatgatggcatcaccatcatctaggttattaaaatttattacaaatggaagtaaattaca 152
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 93  gatgatggcatcaccatcatctaggttattaaaatttattacaaatggaagtaaattaca 152


Query: 153 ttcag 157
           |||||
Sbjct: 153 ttcag 157

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 273,649,174
Number of extensions: 19112855
Number of successful extensions: 1850452
Number of sequences better than 10.0: 68
Length of query: 422
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 399
Effective length of database: 93,106,754,628
Effective search space: 37149595096572
Effective search space used: 37149595096572
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 4
Homology vs Protein 
Query= Contig-U12715-1 (Contig-U12715-1Q) /CSM_Contig/Contig-U12715-1Q.Seq.d
         (422 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54K38) RecName: Full=Mitochondrial escape protein 2 homolog;        153   2e-36
(A4FZ86) RecName: Full=Putative O-sialoglycoprotein endopeptidas...    35   1.1
CP000939_1069(CP000939|pid:none) Clostridium botulinum B1 str. O...    32   5.2
AM412317_1061(AM412317|pid:none) Clostridium botulinum A str. AT...    32   5.2
CP000962_1120(CP000962|pid:none) Clostridium botulinum A3 str. L...    32   5.2

>(Q54K38) RecName: Full=Mitochondrial escape protein 2 homolog;
          Length = 878

 Score =  153 bits (387), Expect = 2e-36
 Identities = 80/108 (74%), Positives = 80/108 (74%)
 Frame = +1

Query: 97  MASPSSRLLKFITNGSKLHSAXXXXXXXXXXXXSPTITKLFSTSKISNEIGNIRNFXXXX 276
           MASPSSRLLKFITNGSKLHSA            SPTITKLFSTSKISNEIGNIRNF
Sbjct: 1   MASPSSRLLKFITNGSKLHSAKNNNMIKNKNIISPTITKLFSTSKISNEIGNIRNFNNKI 60

Query: 277 XXXXXXXXXXXXPFFEIPKLFEKKYYSYIPPTWEEKDKEKQFNSITST 420
                       PFFEIPKLFEKKYYSYIPPTWEEKDKEKQFNSITST
Sbjct: 61  STNLINSNINTKPFFEIPKLFEKKYYSYIPPTWEEKDKEKQFNSITST 108

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: 389,045,530
Number of extensions: 5477182
Number of successful extensions: 13630
Number of sequences better than 10.0: 5
Number of HSP's gapped: 13625
Number of HSP's successfully gapped: 5
Length of query: 140
Length of database: 1,051,180,864
Length adjustment: 104
Effective length of query: 36
Effective length of database: 714,578,728
Effective search space: 25724834208
Effective search space used: 25724834208
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: 0.76  gvh: 0.42  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.41  mip: 0.10
 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 

	 60.0 %: mitochondrial
	 20.0 %: nuclear
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U12715-1 is mit
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 2
AF (FL, S) 0
SL (DIR, L) 0
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