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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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-U13367-1
Contig ID Contig-U13367-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13367-1 (Contig-U13367-1Q) /CSM_Contig/Contig-U13367-1Q.Seq.d
ATCACTTACAACTTGAATTAGTATTAAGTGCTCTATCCAAAAGTACCATA
TCAATGTCCATTCATCTAGATGAGAATTGTCAATAATTCAATTCAACTAG
AAGACATTTATTCTTGCTTAGTATTGCCTTACCGCATTAACATATCCCCA
AGATGAATTTAGTACTTTAAATTTAGAACACTACCCCATCACCATCATCA
CCACCATCATCACCACCATCATCATCCACTTATTAATTCAAGGATTTCAA
GTTTATTTTTCCGATTAGAAAATTTTCTCTTTCAAACTATTTTAATAATT
CTTAGTGTTATTAAAATAGATTTGAAATGATCTTGTGTACAAGAAAAAAG
ATATTGACCCTAATAATTAGTCGAGTCGAATGGAAATCTATGCTTCCATT
GTAGTATTTTGCCATCTTTTATAAGAAAGATCCCAATCTAATTGCATCAA
ATAACCAAGCCCCAACACACGTAAACAAACTCTTACTGTGATCTATAACT
CGATATTATTCAATAAAAAAAAAAAAAAAAAAAAAAAAAATAATAATAAT
AATAAAAAGAGCTTTAATGTGCTCAATTAAAAAAAAAACTTATTGTTTAA
AC
Gap no gap
Contig length 602
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 649102
End point 648500
Strand (PLUS/MINUS) MINUS
Number of clones 3
Number of EST 3
Link to clone list U13367
List of clone(s) 

est1=SLD301E,1,519
est2=SLF216E,1,519
est3=SLJ139Z,346,603
Translated Amino Acid sequence 
itynln*y*vlypkvpyqcpfi*mrivnnsiqlediysclvlpyrinispr*i*YFKFRT
LPHHHHHHHHHHHHHPLINSRISSLFFRLENFLFQTILIILSVIKIDLK*scvqekry*p
**lvesngnlcfhcsilpsfirkipi*lhqitkpqht*tnsycdl*ldiiq*kkkkkkkk
*****kel*caqlkkkliv*
Translated Amino Acid sequence (All Frames) 
Frame A:
itynln*y*vlypkvpyqcpfi*mrivnnsiqlediysclvlpyrinispr*i*YFKFRT
LPHHHHHHHHHHHHHPLINSRISSLFFRLENFLFQTILIILSVIKIDLK*scvqekry*p
**lvesngnlcfhcsilpsfirkipi*lhqitkpqht*tnsycdl*ldiiq*kkkkkkkk
*****kel*caqlkkkliv*


Frame B:
sltt*isikcsiqkyhinvhssr*elsiiqfn*ktfila*ycltaltypqdefstlnleh
ypitiittiittiiihlliqgfqvyfsd*kifsfklf**flvllk*i*ndlvykkkdidp
nn*ssrmeiyasivvfchll*ersqsncik*pspntrkqtltviynsilfnkkkkkkkkn
nnnnkksfnvln*kknllfk


Frame C:
hlqlelvlsalskstismsihldencq*fnstrrhlfllsialph*hipkmnlvl*i*nt
tpspssppssppsssty*fkdfkfifpirkfslsnyfnns*cy*nrfemilctrkkiltl
iisrvewksmlpl*yfaifykkdpnliasnnqapthvnklll*sitryysikkkkkkkki
iiiikralmcsikkktycln
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13367-1 (Contig-U13367-1Q)
/CSM_Contig/Contig-U13367-1Q.Seq.d
         (602 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13367-1 (Contig-U13367-1Q) /CSM_Contig/Conti...   571  e-163
Contig-U13453-1 (Contig-U13453-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U12816-1 (Contig-U12816-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U12487-1 (Contig-U12487-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U01630-1 (Contig-U01630-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U14898-1 (Contig-U14898-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U14896-1 (Contig-U14896-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U14831-1 (Contig-U14831-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U14791-1 (Contig-U14791-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U03664-1 (Contig-U03664-1Q) /CSM_Contig/Conti...    32  0.66

>Contig-U13367-1 (Contig-U13367-1Q) /CSM_Contig/Contig-U13367-1Q.Seq.d
          Length = 602

 Score =  571 bits (288), Expect = e-163
 Identities = 288/288 (100%)
 Strand = Plus / Plus

                                                                       
Query: 227 cacttattaattcaaggatttcaagtttatttttccgattagaaaattttctctttcaaa 286
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 227 cacttattaattcaaggatttcaagtttatttttccgattagaaaattttctctttcaaa 286

                                                                       
Query: 287 ctattttaataattcttagtgttattaaaatagatttgaaatgatcttgtgtacaagaaa 346
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 287 ctattttaataattcttagtgttattaaaatagatttgaaatgatcttgtgtacaagaaa 346

                                                                       
Query: 347 aaagatattgaccctaataattagtcgagtcgaatggaaatctatgcttccattgtagta 406
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 347 aaagatattgaccctaataattagtcgagtcgaatggaaatctatgcttccattgtagta 406

                                                                       
Query: 407 ttttgccatcttttataagaaagatcccaatctaattgcatcaaataaccaagccccaac 466
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 407 ttttgccatcttttataagaaagatcccaatctaattgcatcaaataaccaagccccaac 466

                                                           
Query: 467 acacgtaaacaaactcttactgtgatctataactcgatattattcaat 514
           ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 467 acacgtaaacaaactcttactgtgatctataactcgatattattcaat 514


 Score =  367 bits (185), Expect = e-102
 Identities = 185/185 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   atcacttacaacttgaattagtattaagtgctctatccaaaagtaccatatcaatgtcca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   atcacttacaacttgaattagtattaagtgctctatccaaaagtaccatatcaatgtcca 60

                                                                       
Query: 61  ttcatctagatgagaattgtcaataattcaattcaactagaagacatttattcttgctta 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ttcatctagatgagaattgtcaataattcaattcaactagaagacatttattcttgctta 120

                                                                       
Query: 121 gtattgccttaccgcattaacatatccccaagatgaatttagtactttaaatttagaaca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 gtattgccttaccgcattaacatatccccaagatgaatttagtactttaaatttagaaca 180

                
Query: 181 ctacc 185
           |||||
Sbjct: 181 ctacc 185


 Score = 75.8 bits (38), Expect = 5e-14
 Identities = 38/38 (100%)
 Strand = Plus / Plus

                                                 
Query: 541 taataataataataaaaagagctttaatgtgctcaatt 578
           ||||||||||||||||||||||||||||||||||||||
Sbjct: 541 taataataataataaaaagagctttaatgtgctcaatt 578


>Contig-U13453-1 (Contig-U13453-1Q) /CSM_Contig/Contig-U13453-1Q.Seq.d
          Length = 1359

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 541 taataataataataaaaaga 560
           ||||||||||||||||||||
Sbjct: 20  taataataataataaaaaga 39


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 73  taataataataataa 87


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 70  taataataataataa 84


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 76  taataataataataa 90


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 14  taataataataataa 28


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 67  taataataataataa 81


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 64  taataataataataa 78


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 541 taataataataataa 555
           |||||||||||||||
Sbjct: 17  taataataataataa 31


>Contig-U12816-1 (Contig-U12816-1Q) /CSM_Contig/Contig-U12816-1Q.Seq.d
          Length = 479

 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 541 taataataataataaaaag 559
           |||||||||||||||||||
Sbjct: 301 taataataataataaaaag 319


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 542 aataataataataaa 556
           |||||||||||||||
Sbjct: 21  aataataataataaa 35


  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: 22,758
Number of Sequences: 6905
Number of extensions: 22758
Number of successful extensions: 10421
Number of sequences better than 10.0: 1529
length of query: 602
length of database: 5,674,871
effective HSP length: 16
effective length of query: 586
effective length of database: 5,564,391
effective search space: 3260733126
effective search space used: 3260733126
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.12. 8
Homology vs DNA 
Query= Contig-U13367-1 (Contig-U13367-1Q) /CSM_Contig/Contig-U13367-1Q.Seq.d
         (602 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

(AU052427) Dictyostelium discoideum slug cDNA, clone SLD301.      565   0.0    2
(AU052857) Dictyostelium discoideum slug cDNA, clone SLF216.      565   e-157  1
(AU061649) Dictyostelium discoideum slug cDNA, clone SLF216.      367   e-136  2
(AU053573) Dictyostelium discoideum slug cDNA, clone SLJ139.      295   8e-77  2
(AC164451) Bos taurus clone CH240-151K23, *** SEQUENCING IN ...    48   0.37   1
(AC139939) Mus musculus chromosome 1, clone RP23-458O23, com...    46   1.4    1
(BT036504) Zea mays full-length cDNA clone ZM_BFb0119F14 mRN...    46   1.4    1
(AC213009) Populus trichocarpa clone POP003-K05, complete se...    46   1.4    1
(AC214497) Zea mays chromosome 1 clone CH201-40O8; ZMMBBc004...    46   1.4    1
(CG348898) OGYAJ15TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(CG237318) OG2BI26TH ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(CG225285) OG1DU63TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(CG132924) PUIBT68TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    46   1.4    1
(CG050943) PUKCN30TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    46   1.4    1
(CC715537) OGMAH53TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(CC715527) OGMAH53TH ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(CC685153) OGWEI63TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    46   1.4    1
(DT948113) ZM_BFb0136L11.r ZM_BFb Zea mays cDNA 5', mRNA seq...    46   1.4    1
(DT652758) ZM_BFb0119F14.r ZM_BFb Zea mays cDNA 5', mRNA seq...    46   1.4    1
(DN882344) naf07b03.x1 Rabbit eye cornea. Unnormalized (naf)...    46   1.4    1
(DN881608) naf01g07.x1 Rabbit eye cornea. Unnormalized (naf)...    46   1.4    1
(AC177039) Strongylocentrotus purpuratus clone R3-1038D01, W...    34   2.6    5
(AC114969) Homo sapiens chromosome 5 clone RP11-356D23, comp...    36   4.5    3
(CT027613) Zebrafish DNA sequence from clone CH73-166M15 in ...    44   5.7    1
(AY312921) Takakia lepidozioides trnK-psbA intergenic spacer...    44   5.7    1
(CU469575) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   5.7    1
(CU469433) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.7    1
(CU468850) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.7    1
(ED162769) AUAC-aal17e10.b1 Ascaris suum whole genome shotgu...    44   5.7    1
(DE864349) Macropus eugenii DNA, BAC clone: MEB1-032A17_R, 3...    44   5.7    1
(CT457344) Sus scrofa genomic clone CH242-514C7, genomic sur...    44   5.7    1
(DY267532) IC0AAA21CH06RM1 CitNFL Citrus clementina cDNA 5',...    44   5.7    1
(BF198942) 248945 MARC 2PIG Sus scrofa cDNA 5', mRNA sequence.     44   5.7    1
(AP007934) Lotus japonicus genomic DNA, chromosome 5, clone:...    38   7.3    5
(AC108666) Rattus norvegicus clone CH230-236D9, *** SEQUENCI...    36   8.4    3
(DT140448) JGI_ANNO18767.rev ANNO Pimephales promelas Whole ...    34   8.9    2
(CU793701) A BAC library has been constructed from PN40024 g...    34   9.0    2

>(AU052427) Dictyostelium discoideum slug cDNA, clone SLD301.
          Length = 519

 Score =  565 bits (285), Expect(2) = 0.0
 Identities = 285/285 (100%)
 Strand = Plus / Plus


Query: 230 ttattaattcaaggatttcaagtttatttttccgattagaaaattttctctttcaaacta 289
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 230 ttattaattcaaggatttcaagtttatttttccgattagaaaattttctctttcaaacta 289


Query: 290 ttttaataattcttagtgttattaaaatagatttgaaatgatcttgtgtacaagaaaaaa 349
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 290 ttttaataattcttagtgttattaaaatagatttgaaatgatcttgtgtacaagaaaaaa 349


Query: 350 gatattgaccctaataattagtcgagtcgaatggaaatctatgcttccattgtagtattt 409
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 350 gatattgaccctaataattagtcgagtcgaatggaaatctatgcttccattgtagtattt 409


Query: 410 tgccatcttttataagaaagatcccaatctaattgcatcaaataaccaagccccaacaca 469
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 410 tgccatcttttataagaaagatcccaatctaattgcatcaaataaccaagccccaacaca 469


Query: 470 cgtaaacaaactcttactgtgatctataactcgatattattcaat 514
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 470 cgtaaacaaactcttactgtgatctataactcgatattattcaat 514

 Score =  367 bits (185), Expect(2) = 0.0
 Identities = 185/185 (100%)
 Strand = Plus / Plus


Query: 1   atcacttacaacttgaattagtattaagtgctctatccaaaagtaccatatcaatgtcca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   atcacttacaacttgaattagtattaagtgctctatccaaaagtaccatatcaatgtcca 60


Query: 61  ttcatctagatgagaattgtcaataattcaattcaactagaagacatttattcttgctta 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ttcatctagatgagaattgtcaataattcaattcaactagaagacatttattcttgctta 120


Query: 121 gtattgccttaccgcattaacatatccccaagatgaatttagtactttaaatttagaaca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 gtattgccttaccgcattaacatatccccaagatgaatttagtactttaaatttagaaca 180


Query: 181 ctacc 185
           |||||
Sbjct: 181 ctacc 185

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 582,634,022
Number of extensions: 34387158
Number of successful extensions: 2516898
Number of sequences better than 10.0: 37
Length of query: 602
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 579
Effective length of database: 93,106,754,628
Effective search space: 53908810929612
Effective search space used: 53908810929612
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13367-1 (Contig-U13367-1Q) /CSM_Contig/Contig-U13367-1Q.Seq.d
         (602 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: 761,391,761
Number of extensions: 12054236
Number of successful extensions: 18253
Number of sequences better than 10.0: 0
Number of HSP's gapped: 18252
Number of HSP's successfully gapped: 0
Length of query: 200
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 78
Effective length of database: 656,320,666
Effective search space: 51193011948
Effective search space used: 51193011948
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: 30 (16.2 bits)
PSORT 

 psg: 0.68  gvh: 0.34  alm: 0.28  top: 0.53  tms: 0.07  mit: 0.43  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.80  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  tyr: 0.13  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 

	 40.0 %: mitochondrial
	 24.0 %: nuclear
	 16.0 %: Golgi
	 12.0 %: cytoplasmic
	  8.0 %: endoplasmic reticulum

>> prediction for Contig-U13367-1 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) 3
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