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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U13312-1
Contig ID Contig-U13312-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13312-1 (Contig-U13312-1Q) /CSM_Contig/Contig-U13312-1Q.Seq.d
AAATTATAAATAATAATAATAATAAAATAAAAAAATAAAATAAAATAAAA
AATTTTATTTCTGTAAATAATAACAACCCCTTCTTTTTGGTCTTCATTTA
TTATTAAATAATTTCCAAATAAAAAAAATAATAGAAGTTTAGAACTTAAA
TAGTTTTATTACGACTCTTTAAATTTTAACATTCAATAAATATTATAATA
AATCAAATAAAATTATTTTTTTTTTAATAAAAGAAAAAAANGGAAAAAAA
AAANNNNNNNNN
Gap no gap
Contig length 262
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 2459153
End point 2459406
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13312
List of clone(s) 

est1=SHL836F,1,253
Translated Amino Acid sequence 
nyk*****nkkik*nkkfyfck**qpllfglhlllnnfqikkiiev*nlnsfittl*ILT
FNKYYNKSNKIIFFLIKEKXGKKKXXX
Translated Amino Acid sequence (All Frames) 
Frame A:
kl*iiiiik*knkik*kilfl*iittpsfwssfiik*fpnkknnrslelk*fyydslnfn
iq*il**ik*nyfffnkrkkxkkkxxx


Frame B:
nyk*****nkkik*nkkfyfck**qpllfglhlllnnfqikkiiev*nlnsfittl*ILT
FNKYYNKSNKIIFFLIKEKXGKKKXXX


Frame C:
iinnnnnkikk*nkiknfisvnnnnpfflvfiyy*iisk*kk**kfrt*ivllrlfkf*h
siniiinqiklfff**kkkxekkxxx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13312-1 (Contig-U13312-1Q)
/CSM_Contig/Contig-U13312-1Q.Seq.d
         (262 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13312-1 (Contig-U13312-1Q) /CSM_Contig/Conti...   276  1e-74
Contig-U12384-1 (Contig-U12384-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U07084-1 (Contig-U07084-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U10447-1 (Contig-U10447-1Q) /CSM_Contig/Conti...    36  0.018
Contig-U09440-1 (Contig-U09440-1Q) /CSM_Contig/Conti...    36  0.018
Contig-U06998-1 (Contig-U06998-1Q) /CSM_Contig/Conti...    36  0.018
Contig-U03848-1 (Contig-U03848-1Q) /CSM_Contig/Conti...    36  0.018
Contig-U12615-1 (Contig-U12615-1Q) /CSM_Contig/Conti...    34  0.070
Contig-U11482-1 (Contig-U11482-1Q) /CSM_Contig/Conti...    34  0.070
Contig-U11235-1 (Contig-U11235-1Q) /CSM_Contig/Conti...    34  0.070

>Contig-U13312-1 (Contig-U13312-1Q) /CSM_Contig/Contig-U13312-1Q.Seq.d
          Length = 262

 Score =  276 bits (139), Expect = 1e-74
 Identities = 155/163 (95%)
 Strand = Plus / Plus

                                                                       
Query: 53  ttttatttctgtaaataataacaaccccttctttttggtcttcatttattattaaataat 112
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 53  ttttatttctgtaaataataacaaccccttctttttggtcttcatttattattaaataat 112

                                                                       
Query: 113 ttccaaatnnnnnnnntaatagaagtttagaacttaaatagttttattacgactctttaa 172
           ||||||||        ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 113 ttccaaataaaaaaaataatagaagtttagaacttaaatagttttattacgactctttaa 172

                                                      
Query: 173 attttaacattcaataaatattataataaatcaaataaaatta 215
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 173 attttaacattcaataaatattataataaatcaaataaaatta 215


>Contig-U12384-1 (Contig-U12384-1Q) /CSM_Contig/Contig-U12384-1Q.Seq.d
          Length = 1671

 Score = 38.2 bits (19), Expect = 0.004
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                               
Query: 96   atttattattaaataattt 114
            |||||||||||||||||||
Sbjct: 1583 atttattattaaataattt 1601


>Contig-U07084-1 (Contig-U07084-1Q) /CSM_Contig/Contig-U07084-1Q.Seq.d
          Length = 1017

 Score = 38.2 bits (19), Expect = 0.004
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 96  atttattattaaataattt 114
           |||||||||||||||||||
Sbjct: 566 atttattattaaataattt 584


  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: 6548
Number of Sequences: 6905
Number of extensions: 6548
Number of successful extensions: 2301
Number of sequences better than 10.0: 293
length of query: 262
length of database: 5,674,871
effective HSP length: 15
effective length of query: 247
effective length of database: 5,571,296
effective search space: 1376110112
effective search space used: 1376110112
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. 7
Homology vs DNA 
Query= Contig-U13312-1 (Contig-U13312-1Q) /CSM_Contig/Contig-U13312-1Q.Seq.d
         (262 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

(BJ397724) Dictyostelium discoideum cDNA clone:dds47h10, 5' ...   172   5e-73  2
(AC117075) Dictyostelium discoideum chromosome 2 map 5201047...    38   0.064  4
(DX479195) Cpl21487 Papaya Genomic DNA BAC Library Carica pa...    36   0.11   2
(DX471404) Cpl13463 Papaya Genomic DNA BAC Library Carica pa...    36   0.13   2
(AL935145) Zebrafish DNA sequence from clone CH211-173B9 in ...    36   0.39   3
(DQ927304) Tetrahymena paravorax strain RP mitochondrion, co...    32   0.48   5
(DD000782) PLANT ARTIFICIAL CHROMOSOME COMPOSITIONS AND METH...    42   0.49   2
(AX059467) Sequence 200 from Patent WO0055325.                     42   0.49   2
(CR354391) Zebrafish DNA sequence from clone CH211-256L9 in ...    40   0.54   3
(AL954387) Zebrafish DNA sequence from clone CH211-288B20 in...    46   0.60   1
(AM423587) Vitis vinifera contig VV78X018426.5, whole genome...    46   0.60   1
(AC149290) Solanum demissum chromosome 5 clone PGEC093P17, c...    46   0.60   1
(AC184828) Canis Familiaris chromosome 14, clone XX-10P18, c...    46   0.60   1
(DQ023055) Protomognathus americanus isolate pamericanus 16S...    46   0.60   1
(AC099486) Homo sapiens chromosome 5 clone CTD-2011G10, comp...    46   0.60   1
(AC157062) Bos taurus clone CH240-64J5, WORKING DRAFT SEQUEN...    46   0.60   1
(AC128823) Rattus norvegicus clone CH230-492P4, *** SEQUENCI...    46   0.60   1
(AC114890) Canis familiaris clone RP81-411G22, WORKING DRAFT...    46   0.60   1
(AC113573) Canis familiaris clone RP81-92J9, WORKING DRAFT S...    46   0.60   1
(AC095659) Rattus norvegicus clone CH230-7K13, *** SEQUENCIN...    46   0.60   1
(CU695208) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   0.60   1
(AC020725) Homo sapiens chromosome 5 clone RP11-495N17, WORK...    46   0.60   1
(DE543018) Bombyx mori genomic DNA, Fosmid clone:GBMFno173_m...    46   0.60   1
(EY387718) CAXA6911.fwd CAXA Helobdella robusta Subtracted L...    46   0.60   1
(AX346176) Sequence 1247 from Patent WO0200928.                    38   0.78   3
(AC131773) Mus musculus BAC clone RP24-308A19 from chromosom...    36   0.81   4
(BX000487) Zebrafish DNA sequence from clone BUSM1-162F22 in...    40   0.85   2
(BX323030) Zebrafish DNA sequence from clone DKEYP-77D7 in l...    38   0.97   4
(CT826389) Zebrafish DNA sequence from clone CH73-159H15 in ...    40   0.99   2
(CU633800) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.3    2
(CU138507) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    40   1.3    3
(AC099704) Mus musculus chromosome 15, clone RP23-256A2, com...    36   1.3    4
(Z81035) Caenorhabditis elegans Cosmid C15H11.                     44   1.4    2
(AF538053) Monosiga brevicollis mitochondrion, complete genome.    36   1.4    3
(CR774194) Zebrafish DNA sequence from clone DKEYP-11A2 in l...    36   1.4    3
(AC222716) Bos taurus clone CH240-441E22, WORKING DRAFT SEQU...    38   1.4    2
(DD000790) PLANT ARTIFICIAL CHROMOSOME COMPOSITIONS AND METH...    42   1.5    2
(AX059475) Sequence 208 from Patent WO0055325.                     42   1.5    2
(CU812708) A BAC library has been constructed from PN40024 g...    40   1.5    2
(BX510660) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    38   1.6    3
(EU004203) Saccharomyces cerevisiae YJM789 mitochondrion, co...    38   1.7    3
(BX927066) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    36   1.7    3
(BH585321) BOHAG20TF BOHA Brassica oleracea genomic clone BO...    38   1.9    2
(AJ294725) Astasia longa complete chloroplast genome.              32   1.9    5
(AC008046) Arabidopsis thaliana chromosome I BAC F5A13 genom...    42   1.9    3
(AR777036) Sequence 191 from patent US 6972197.                    42   1.9    3
(AC004688) Plasmodium falciparum chromosome 12 clone 3D7, **...    32   2.0    6
(AC154678) Mus musculus BAC clone RP24-302G10 from chromosom...    38   2.0    3
(CK873028) AGENCOURT_19404357 NIH_ZGC_16 Danio rerio cDNA cl...    40   2.0    2
(AC079101) Homo sapiens chromosome 4 clone RP11-110N1 map 4,...    42   2.1    2
(BH134838) ENTNQ95TR Entamoeba histolytica Sheared DNA Entam...    38   2.1    2
(AL772198) Zebrafish DNA sequence from clone CH211-194D6 in ...    40   2.2    3
(DQ314875) Homo sapiens mitogen-activated protein kinase kin...    38   2.3    2
(CZ968758) 168814 Tomato MboI BAC Library Solanum lycopersic...    40   2.3    2
(CR735102) Zebrafish DNA sequence from clone DKEYP-8H9 in li...    44   2.4    1
(BX936451) Zebrafish DNA sequence from clone CH211-201F1 in ...    44   2.4    1
(BX000485) Zebrafish DNA sequence from clone CH211-142G3 in ...    44   2.4    1
(AL732631) Mouse DNA sequence from clone RP23-345P19 on chro...    44   2.4    1
(AC156645) Mus musculus BAC clone RP23-59I22 from chromosome...    44   2.4    1
(AC132221) Mus musculus BAC clone RP24-545C12 from chromosom...    44   2.4    1
(AC129333) Mus musculus BAC clone RP23-104F23 from 6, comple...    44   2.4    1
(AC122394) Mus musculus BAC clone RP24-85N8 from 6, complete...    44   2.4    1
(AC108775) Mus musculus chromosome 1, clone RP23-331M15, com...    44   2.4    1
(AC206064) Pongo abelii BAC clone CH276-502K14 from chromoso...    44   2.4    1
(AY186738) Lycopersicon esculentum SP9D (SP9D) gene, complet...    44   2.4    1
(AY275311) Metylophorus novaescotiae 12S ribosomal RNA gene,...    44   2.4    1
(AF266098) Ladona fulva large subunit ribosomal RNA gene, pa...    44   2.4    1
(AC084734) Homo sapiens chromosome 8, clone RP11-317J10, com...    44   2.4    1
(AC044891) Homo sapiens chromosome 8, clone RP11-624C23, com...    44   2.4    1
(AC023202) Homo sapiens chromosome 8, clone RP11-203E8, comp...    44   2.4    1
(AC008862) Homo sapiens chromosome 5 clone CTD-2187G18, comp...    44   2.4    1
(AC157331) Bos taurus clone CH240-53J2, WORKING DRAFT SEQUEN...    44   2.4    1
(AC130017) Rattus norvegicus clone CH230-170G23, *** SEQUENC...    44   2.4    1
(AC128506) Rattus norvegicus clone CH230-33B7, *** SEQUENCIN...    44   2.4    1
(AC123434) Rattus norvegicus clone CH230-449B17, *** SEQUENC...    44   2.4    1
(CU407258) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   2.4    1
(CR388203) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    44   2.4    1
(AP009888) Lotus japonicus genomic DNA, clone: LjT35F15, TM1...    44   2.4    1
(AP008173) Lotus japonicus genomic DNA, chromosome 1, clone:...    44   2.4    1
(AL844506) Plasmodium falciparum chromosome  7.                    44   2.4    1
(AC224142) Bos taurus clone CH240-449F20, WORKING DRAFT SEQU...    44   2.4    1
(AC206923) Pongo abelii chromosome UNKNOWN clone CH276-449D5...    44   2.4    1
(AC190918) Zea mays chromosome 3 clone CH201-530N5; ZMMBBc05...    44   2.4    1
(AC182051) Bos taurus clone CH240-341M2, WORKING DRAFT SEQUE...    44   2.4    1
(AC025131) Homo sapiens clone RP11-178A2, WORKING DRAFT SEQU...    44   2.4    1
(AZ546504) ENTDB22TR Entamoeba histolytica Sheared DNA Entam...    44   2.4    1
(AZ206424) SP_0108_A1_H06_T7A Strongylocentrotus purpuratus,...    44   2.4    1
(DX405141) GR_Sa0004K06.b1 Gossypium raimondii WGS library G...    44   2.4    1
(CZ499668) GMW2-27D5a.g1 GMW2 Glycine max genomic, genomic s...    44   2.4    1
(EB172005) EST006904 injuried spinal cord cDNA library in Ge...    44   2.4    1
(DY305163) KN0AAH2CH04RM1 PhII-III-Vesicles1 Citrus clementi...    44   2.4    1
(DN304507) PL05006A1B05 cDNA from sexually mature hermaphodi...    44   2.4    1
(CT603880) Danio rerio EST, clone ZF_mu_17l20 5'.                  44   2.4    1
(AM055498) Polyplastron multivesiculatum EST, clone Pm05_H04.      44   2.4    1
(CK583647) IST_WI5_49992 AD-wrmcDNA library Caenorhabditis e...    44   2.4    1
(BP062298) Lotus japonicus cDNA, clone:GENf096g08, 3' end.         44   2.4    1
(BP055341) Lotus japonicus cDNA, clone:SPDL053d03_f, 3' end.       44   2.4    1
(BJ152080) Caenorhabditis elegans cDNA clone:yk1303a12 : 3' ...    44   2.4    1
(BJ151895) Caenorhabditis elegans cDNA clone:yk1300h02 : 3' ...    44   2.4    1
(BJ129655) Caenorhabditis elegans cDNA clone:yk1033c07 : 3' ...    44   2.4    1

>(BJ397724) Dictyostelium discoideum cDNA clone:dds47h10, 5' end,
           single read.
          Length = 253

 Score =  172 bits (87), Expect(2) = 5e-73
 Identities = 87/87 (100%)
 Strand = Plus / Plus


Query: 129 taatagaagtttagaacttaaatagttttattacgactctttaaattttaacattcaata 188
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 129 taatagaagtttagaacttaaatagttttattacgactctttaaattttaacattcaata 188


Query: 189 aatattataataaatcaaataaaatta 215
           |||||||||||||||||||||||||||
Sbjct: 189 aatattataataaatcaaataaaatta 215

 Score =  133 bits (67), Expect(2) = 5e-73
 Identities = 67/67 (100%)
 Strand = Plus / Plus


Query: 54  tttatttctgtaaataataacaaccccttctttttggtcttcatttattattaaataatt 113
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 54  tttatttctgtaaataataacaaccccttctttttggtcttcatttattattaaataatt 113


Query: 114 tccaaat 120
           |||||||
Sbjct: 114 tccaaat 120

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 285,332,993
Number of extensions: 20762560
Number of successful extensions: 1934733
Number of sequences better than 10.0: 309
Length of query: 262
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 239
Effective length of database: 93,106,754,628
Effective search space: 22252514356092
Effective search space used: 22252514356092
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13312-1 (Contig-U13312-1Q) /CSM_Contig/Contig-U13312-1Q.Seq.d
         (262 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: 181,545,906
Number of extensions: 2121682
Number of successful extensions: 1459
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1459
Number of HSP's successfully gapped: 0
Length of query: 87
Length of database: 1,051,180,864
Length adjustment: 57
Effective length of query: 30
Effective length of database: 866,697,001
Effective search space: 26000910030
Effective search space used: 26000910030
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: 27 (15.0 bits)
PSORT 

 psg: 0.79  gvh: 0.11  alm: 0.61  top: 0.53  tms: 0.00  mit: 0.30  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.40  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 

	 68.0 %: nuclear
	 24.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U13312-1 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