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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-U13237-1
Contig ID Contig-U13237-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13237-1 (Contig-U13237-1Q) /CSM_Contig/Contig-U13237-1Q.Seq.d
ATGCAAAGTTATATATAGCACATTGACCATTCCCTCAGGTTGTAAATTTA
TTTTTATTTTCAAAATTAATTTTTTTTTTTATACACACACTAAAGAAATC
AAACCCACTTAAATCACATACACAAAACAAACCAATCCCACTTGAATCAA
TTACACTAAACAAATCAATCCCACTTCACAAAAAATTAAATTATTTCTTC
CTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANCCCCCCCNTNAAAA
AAAAA
Gap no gap
Contig length 255
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 2166955
End point 2167209
Strand (PLUS/MINUS) PLUS
Number of clones 2
Number of EST 2
Link to clone list U13237
List of clone(s) 

est1=SHC771F,1,255
est2=SHJ485F,92,255
Translated Amino Acid sequence 
aklyiah*PFPQVVNLFLFSKLIFFFIHTLKKSNPLKSHTQNKPIPLESITLNKSIPLHK
KLNYFFLKKKKKKKKKKXPPXXKK
Translated Amino Acid sequence (All Frames) 
Frame A:
mqsyi*hidhslrl*iyfyfqn*ffflyth*rnqthlnhihktnqshlnqlh*tnqshft
kn*iiss*kkkkkkkkkkxppxkkk


Frame B:
ckviystltipsgckfififkinfffythtkeikpt*itytkqtnpt*inytkqinptsq
kiklflpkkkkkkkkkkkxppxkk


Frame C:
aklyiah*PFPQVVNLFLFSKLIFFFIHTLKKSNPLKSHTQNKPIPLESITLNKSIPLHK
KLNYFFLKKKKKKKKKKXPPXXKK
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13237-1 (Contig-U13237-1Q)
/CSM_Contig/Contig-U13237-1Q.Seq.d
         (255 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13237-1 (Contig-U13237-1Q) /CSM_Contig/Conti...   335  1e-92
Contig-U11408-1 (Contig-U11408-1Q) /CSM_Contig/Conti...    46  2e-05
Contig-U04448-1 (Contig-U04448-1Q) /CSM_Contig/Conti...    46  2e-05
Contig-U14772-1 (Contig-U14772-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U12218-1 (Contig-U12218-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U12255-1 (Contig-U12255-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U10050-1 (Contig-U10050-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U04510-1 (Contig-U04510-1Q) /CSM_Contig/Conti...    38  0.004
Contig-U14276-1 (Contig-U14276-1Q) /CSM_Contig/Conti...    36  0.017
Contig-U13926-1 (Contig-U13926-1Q) /CSM_Contig/Conti...    36  0.017

>Contig-U13237-1 (Contig-U13237-1Q) /CSM_Contig/Contig-U13237-1Q.Seq.d
          Length = 255

 Score =  335 bits (169), Expect = 1e-92
 Identities = 191/202 (94%)
 Strand = Plus / Plus

                                                                       
Query: 1   atgcaaagttatatatagcacattgaccattccctcaggttgtaaatttatttttatttt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   atgcaaagttatatatagcacattgaccattccctcaggttgtaaatttatttttatttt 60

                                                                       
Query: 61  caaaattaannnnnnnnnnnatacacacactaaagaaatcaaacccacttaaatcacata 120
           |||||||||           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  caaaattaatttttttttttatacacacactaaagaaatcaaacccacttaaatcacata 120

                                                                       
Query: 121 cacaaaacaaaccaatcccacttgaatcaattacactaaacaaatcaatcccacttcaca 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 cacaaaacaaaccaatcccacttgaatcaattacactaaacaaatcaatcccacttcaca 180

                                 
Query: 181 aaaaattaaattatttcttcct 202
           ||||||||||||||||||||||
Sbjct: 181 aaaaattaaattatttcttcct 202


>Contig-U11408-1 (Contig-U11408-1Q) /CSM_Contig/Contig-U11408-1Q.Seq.d
          Length = 2056

 Score = 46.1 bits (23), Expect = 2e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                  
Query: 47  tttatttttattttcaaaattaa 69
           |||||||||||||||||||||||
Sbjct: 204 tttatttttattttcaaaattaa 226


>Contig-U04448-1 (Contig-U04448-1Q) /CSM_Contig/Contig-U04448-1Q.Seq.d
          Length = 983

 Score = 46.1 bits (23), Expect = 2e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                 
Query: 43 taaatttatttttattttcaaaa 65
          |||||||||||||||||||||||
Sbjct: 50 taaatttatttttattttcaaaa 72


 Score = 28.2 bits (14), Expect = 4.2
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                        
Query: 47 tttatttttatttt 60
          ||||||||||||||
Sbjct: 90 tttatttttatttt 77


  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: 8140
Number of Sequences: 6905
Number of extensions: 8140
Number of successful extensions: 3560
Number of sequences better than 10.0: 788
length of query: 255
length of database: 5,674,871
effective HSP length: 15
effective length of query: 240
effective length of database: 5,571,296
effective search space: 1337111040
effective search space used: 1337111040
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-U13237-1 (Contig-U13237-1Q) /CSM_Contig/Contig-U13237-1Q.Seq.d
         (255 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

(BJ392988) Dictyostelium discoideum cDNA clone:dds29n17, 5' ...   242   6e-95  2
(BJ396420) Dictyostelium discoideum cDNA clone:dds42j22, 5' ...   172   7e-47  2
(AC230192) Bos taurus clone CH240-518L15, WORKING DRAFT SEQU...    50   0.037  1
(BX716866) Xenopus tropicalis EST, clone TTpA029m06 3'.            50   0.037  1
(AP000624) Homo sapiens genomic DNA, chromosome 11q22 clone:...    42   0.067  3
(CS374584) Sequence 687 from Patent WO2006034879.                  32   0.077  4
(AX344561) Sequence 12 from Patent WO0200932.                      40   0.078  5
(AC010826) Homo sapiens clone RP11-5N5, WORKING DRAFT SEQUEN...    42   0.12   3
(EK063722) 1092960103069 Global-Ocean-Sampling_GS-31-01-01-1...    38   0.13   2
(BX664712) Oryza sativa chromosome 12, . BAC B1373G08 of chr...    48   0.15   1
(BX000345) Oryza sativa chromosome 12, . BAC OSJNBb0111J10 o...    48   0.15   1
(AP008218) Oryza sativa (japonica cultivar-group) genomic DN...    48   0.15   1
(AM453008) Vitis vinifera contig VV78X063326.16, whole genom...    48   0.15   1
(AL831805) Oryza sativa chromosome 12, . BAC OSJNBa0085J02 o...    48   0.15   1
(EA724823) Sequence 103702 from patent US 7365185.                 48   0.15   1
(CT025677) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    48   0.15   1
(EI249566) OR__Ba0051M09.f OR__Ba Oryza rufipogon genomic cl...    48   0.15   1
(EI246829) OR__Ba0048A22.r OR__Ba Oryza rufipogon genomic cl...    48   0.15   1
(EI213071) OR__Ba0002F09.r OR__Ba Oryza rufipogon genomic cl...    48   0.15   1
(CL794161) OR_CBa0003I13.f OR_CBa Oryza rufipogon genomic cl...    48   0.15   1
(EJ406778) 1093012100134 Global-Ocean-Sampling_GS-28-01-01-1...    36   0.15   2
(AP001023) Homo sapiens genomic DNA, chromosome 11 clone:RP1...    42   0.16   3
(BD460217) Diagnosis of Diseases Associated with Cell Cycle.       40   0.16   2
(BD452139) Diagnosis of Diseases Associated with Cell Cycle.       40   0.16   2
(AX348558) Sequence 16 from Patent WO0202807.                      40   0.16   2
(AX344167) Sequence 14 from Patent WO0200926.                      40   0.16   2
(AX251753) Sequence 14 from Patent WO0168911.                      40   0.16   2
(AC109690) Rattus norvegicus clone CH230-268H4, *** SEQUENCI...    38   0.20   5
(EF206804) Glycine max clone GM_WBb0040F22, *** SEQUENCING I...    44   0.28   3
(BJ419387) Dictyostelium discoideum cDNA clone:ddv35o23, 5' ...    40   0.40   2
(CC957109) BOICP33TR BO_1.4_1.6_KB_nuc Brassica oleracea gen...    42   0.41   2
(DD118571) ISOLATED HUMAN TRANSPORTER PROTEINS, NUCLEIC ACID...    42   0.44   3
(BZ446396) BONRI67TR BO_1.6_2_KB_tot Brassica oleracea genom...    42   0.46   2
(BH164948) ENTTB40TR Entamoeba histolytica Sheared DNA Entam...    36   0.55   2
(AF133300) Mus musculus MOR 3'Beta1, MOR 3'Beta2, MOR 3'Beta...    46   0.58   1
(AL732639) Oryza sativa chromosome 12, . BAC OSJNBa0038H18 o...    46   0.58   1
(AL713941) Oryza sativa chromosome 12, . BAC OSJNBa0006M08 o...    46   0.58   1
(AC210344) Populus trichocarpa clone POP100-P10, complete se...    46   0.58   1
(EA680783) Sequence 59662 from patent US 7365185.                  46   0.58   1
(EA635015) Sequence 13894 from patent US 7365185.                  46   0.58   1
(AC096471) Rattus norvegicus clone CH230-83A1, WORKING DRAFT...    46   0.58   1
(FH519639) CHO_OF4716xn02f1.ab1 CHO_OF4 Nicotiana tabacum ge...    46   0.58   1
(ER620033) 1093017390656 Global-Ocean-Sampling_GS-36-01-01-2...    46   0.58   1
(ER415144) 1095390160473 Global-Ocean-Sampling_GS-34-01-01-1...    46   0.58   1
(EK433463) 1095516170984 Global-Ocean-Sampling_GS-31-01-01-1...    46   0.58   1
(EK347995) 1095467584595 Global-Ocean-Sampling_GS-31-01-01-1...    46   0.58   1
(EJ415499) 1093012178318 Global-Ocean-Sampling_GS-28-01-01-1...    46   0.58   1
(EJ059261) 1095456054115 Global-Ocean-Sampling_GS-26-01-01-1...    46   0.58   1
(AU074749) Dictyostelium discoideum slug cDNA, clone SSL749.       46   0.58   1
(BJ365526) Dictyostelium discoideum cDNA clone:ddc35m14, 5' ...    46   0.58   1
(FG773829) G1147P356RG20.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG709308) G1144P348RM4.T0 Anolis carolinensis pooled normal...    46   0.58   1
(FG703736) G1144P329RM15.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG701690) G1144P323RG23.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG700300) G1144P337RK20.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG699488) G1144P343RL21.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG663556) G1142P328RA14.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG663508) G1142P328FA14.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG662677) G1142P328RG9.T0 Anolis carolinensis pooled normal...    46   0.58   1
(FG662629) G1142P328FG9.T0 Anolis carolinensis pooled normal...    46   0.58   1
(FG662312) G1142P313RN18.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG659735) G1142P324RA23.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG659639) G1142P324FA23.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG656655) G1142P311RE17.T0 Anolis carolinensis pooled norma...    46   0.58   1
(FG656486) G1142P323RP8.T0 Anolis carolinensis pooled normal...    46   0.58   1
(FG655188) G1142P323RK1.T0 Anolis carolinensis pooled normal...    46   0.58   1
(AC178320) Strongylocentrotus purpuratus clone R3-1114J15, W...    36   0.68   3
(CR749766) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    34   0.70   5
(CR927050) Zebrafish DNA sequence from clone DKEY-217G21.          40   0.74   3
(AM486716) Vitis vinifera contig VV78X105441.6, whole genome...    40   0.74   2
(CR847825) Zebrafish DNA sequence from clone DKEY-98D20 in l...    44   0.86   2
(AC100734) Mus musculus chromosome 15, clone RP24-316L11, co...    36   0.89   4
(Z99942) Caenorhabditis elegans Fosmid H13N06.                     38   0.95   2
(AC158420) Callithrix jacchus clone CH259-40F15, WORKING DRA...    36   0.95   4
(AX344556) Sequence 7 from Patent WO0200932.                       32   0.99   6
(AC161347) Mus musculus chromosome 15, clone RP23-273M5, com...    36   1.0    4
(BX914214) Zebrafish DNA sequence from clone DKEY-9I5 in lin...    40   1.0    2
(AC093739) Homo sapiens chromosome 2 clone RP11-22A4, WORKIN...    40   1.1    2
(AX346954) Sequence 2025 from Patent WO0200928.                    30   1.2    4
(BX897734) Zebrafish DNA sequence from clone CH211-194J14.         42   1.2    3
(AC189195) Brassica rapa subsp. pekinensis clone KBrB004B12,...    34   1.3    4
(AC140822) Homo sapiens chromosome 5 clone RP11-771C20, WORK...    42   1.3    3
(AC005059) Homo sapiens clone RG074A24, *** SEQUENCING IN PR...    44   1.4    3
(CT456752) Sus scrofa genomic clone CH242-503I7, genomic sur...    38   1.5    2
(AC195099) Rhesus Macaque  BAC CH250-197I3 () complete seque...    36   1.5    3
(DT745101) EST1178950 Aquilegia cDNA library Aquilegia formo...    32   1.6    2
(DR937304) EST1128843 Aquilegia cDNA library Aquilegia formo...    32   1.6    2
(DT766474) EST1200323 Aquilegia cDNA library Aquilegia formo...    32   1.6    2
(DT762071) EST1195920 Aquilegia cDNA library Aquilegia formo...    32   1.6    2
(BH995213) oef81b08.b1 B.oleracea002 Brassica oleracea genom...    36   1.6    2
(AB107101) Homo sapiens genomic DNA, chromosome 3q25-q26, cl...    42   1.7    3
(DV946449) SB03005A2D12.f1 Normalized subtracted Keck-Tagu L...    34   1.7    2
(EK305652) 1095462380512 Global-Ocean-Sampling_GS-31-01-01-1...    34   1.7    2
(CR163734) Reverse strand read from insert in 3'HPRT inserti...    36   1.7    2
(DX558757) GH_MBb0016H17f GH_MBb Gossypium hirsutum genomic ...    34   1.8    2
(AC225328) Solanum lycopersicum chromosome 9 clone C09HBa019...    34   1.9    4
(AP006713) Lotus japonicus genomic DNA, chromosome 1, clone:...    40   1.9    4
(EK283999) 1095462305980 Global-Ocean-Sampling_GS-31-01-01-1...    36   1.9    2
(EJ014705) 1095433013557 Global-Ocean-Sampling_GS-26-01-01-1...    38   2.0    2
(AC215354) Solanum lycopersicum chromosome 2 clone C02HBa001...    44   2.1    4

>(BJ392988) Dictyostelium discoideum cDNA clone:dds29n17, 5' end,
           single read.
          Length = 255

 Score =  242 bits (122), Expect(2) = 6e-95
 Identities = 122/122 (100%)
 Strand = Plus / Plus


Query: 81  atacacacactaaagaaatcaaacccacttaaatcacatacacaaaacaaaccaatccca 140
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 81  atacacacactaaagaaatcaaacccacttaaatcacatacacaaaacaaaccaatccca 140


Query: 141 cttgaatcaattacactaaacaaatcaatcccacttcacaaaaaattaaattatttcttc 200
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 141 cttgaatcaattacactaaacaaatcaatcccacttcacaaaaaattaaattatttcttc 200


Query: 201 ct 202
           ||
Sbjct: 201 ct 202

 Score =  137 bits (69), Expect(2) = 6e-95
 Identities = 69/69 (100%)
 Strand = Plus / Plus


Query: 1  atgcaaagttatatatagcacattgaccattccctcaggttgtaaatttatttttatttt 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atgcaaagttatatatagcacattgaccattccctcaggttgtaaatttatttttatttt 60


Query: 61 caaaattaa 69
          |||||||||
Sbjct: 61 caaaattaa 69

 Score = 42.1 bits (21), Expect = 9.0
 Identities = 48/57 (84%)
 Strand = Plus / Plus


Query: 120 acacaaaacaaaccaatcccacttgaatcaattacactaaacaaatcaatcccactt 176
           |||| ||| ||| ||| ||||||| |||||  ||||| ||||||| |||||||||||
Sbjct: 87  acactaaagaaatcaaacccacttaaatcacatacacaaaacaaaccaatcccactt 143

 Score = 42.1 bits (21), Expect = 9.0
 Identities = 48/57 (84%)
 Strand = Plus / Plus


Query: 87  acactaaagaaatcaaacccacttaaatcacatacacaaaacaaaccaatcccactt 143
           |||| ||| ||| ||| ||||||| |||||  ||||| ||||||| |||||||||||
Sbjct: 120 acacaaaacaaaccaatcccacttgaatcaattacactaaacaaatcaatcccactt 176

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 355,962,715
Number of extensions: 27760077
Number of successful extensions: 3312078
Number of sequences better than 10.0: 501
Length of query: 255
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 232
Effective length of database: 93,106,754,628
Effective search space: 21600767073696
Effective search space used: 21600767073696
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13237-1 (Contig-U13237-1Q) /CSM_Contig/Contig-U13237-1Q.Seq.d
         (255 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: 299,121,733
Number of extensions: 4282509
Number of successful extensions: 6354
Number of sequences better than 10.0: 0
Number of HSP's gapped: 6351
Number of HSP's successfully gapped: 0
Length of query: 85
Length of database: 1,051,180,864
Length adjustment: 55
Effective length of query: 30
Effective length of database: 873,170,119
Effective search space: 26195103570
Effective search space used: 26195103570
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: 0.90  gvh: 0.48  alm: 0.32  top: 0.63  tms: 0.07  mit: 0.32  mip: 0.00
 nuc: 0.51  erl: 0.00  erm: 0.60  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  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: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 28.0 %: nuclear
	 24.0 %: cytoplasmic
	 20.0 %: mitochondrial
	  8.0 %: plasma membrane
	  8.0 %: vesicles of secretory system
	  8.0 %: endoplasmic reticulum
	  4.0 %: peroxisomal

>> prediction for Contig-U13237-1 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) 2
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0