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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-U08241-1
Contig ID Contig-U08241-1
Contig update 2002. 5. 9
Contig sequence 
>Contig-U08241-1 (Contig-U08241-1Q) /CSM_Contig/Contig-U08241-1Q.Seq.d
NNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNNATNTNNANNNATNNNNC
AATANNNNNNNNNGNNNAANNAAAGGNNNTANCNNNGNAANAAAAANTTA
NANAGNCAAATNATATNTTNGANTTCANCAGNNCAAACANTGATGCAATA
ANAAAAATAGAATTNCCACTTTCAATCCCTTCAAATCAATGGTTCTTCTC
CTNTCCAATAAAACATATCATGAGTTTCAGCCCAACNTATGGTACACCAT
CGAAAATTATCGATTCACCAAGTAAATTGTTAAACACACCAAAAAAGAAA
CAACAAGACAAAACAAACAAGACCAACAAAACACCAGTCAAACCAAAATT
GGGTGAATATGGACAAAAAAGCATAAAAACAAAA
Gap no gap
Contig length 384
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U08241
List of clone(s) 

est1=CFI277Z,1,375
Translated Amino Acid sequence 
XXXXXXXXXXXXXXXXXIXXXXXXKXXXXXXKXXXXNXXXXFXXXNXDAIXKIEXPLSIP
SNQWFFSXPIKHIMSFSPTYGTPSKIIDSPSKLLNTPKKKQQDKTNKTNKTPVKPKLGEY
GQKSIKTK
Translated Amino Acid sequence (All Frames) 
Frame A:
XXXXXXXXXXXXXXXXXIXXXXXXKXXXXXXKXXXXNXXXXFXXXNXDAIXKIEXPLSIP
SNQWFFSXPIKHIMSFSPTYGTPSKIIDSPSKLLNTPKKKQQDKTNKTNKTPVKPKLGEY
GQKSIKTK


Frame B:
xxxxxxxxxxxxxxxxqxxxxxxxrxxxxxkxlxxqxixxxsxxqtxmq*xk*nxhfqsl
qingsspxq*nis*vsaqxmvhhrklsihqvnc*thqkrnnktkqtrptkhqsnqnwvnm
dkka*kq


Frame C:
xxxxxxxxxxxxxxxxnxxxxxxkgxxxxxkxxxxkxyxxxxqxkx*cnxknrixtfnpf
ksmvlllsnktyhefqpnxwytienyrftk*ivkhtkkettrqnkqdqqntsqtkig*iw
tkkhknk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U08241-1 (Contig-U08241-1Q)
/CSM_Contig/Contig-U08241-1Q.Seq.d
         (384 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12544-1 (Contig-U12544-1Q) /CSM_Contig/Conti...   281  3e-76
Contig-U08241-1 (Contig-U08241-1Q) /CSM_Contig/Conti...   281  3e-76
Contig-U12482-1 (Contig-U12482-1Q) /CSM_Contig/Conti...    30  1.6
Contig-U01588-1 (Contig-U01588-1Q) /CSM_Contig/Conti...    30  1.6
Contig-U13984-1 (Contig-U13984-1Q) /CSM_Contig/Conti...    28  6.4
Contig-U13677-1 (Contig-U13677-1Q) /CSM_Contig/Conti...    28  6.4
Contig-U13513-1 (Contig-U13513-1Q) /CSM_Contig/Conti...    28  6.4
Contig-U12547-1 (Contig-U12547-1Q) /CSM_Contig/Conti...    28  6.4

>Contig-U12544-1 (Contig-U12544-1Q) /CSM_Contig/Contig-U12544-1Q.Seq.d
          Length = 2661

 Score =  281 bits (142), Expect = 3e-76
 Identities = 174/190 (91%)
 Strand = Plus / Plus

                                                                       
Query: 92  aaaaanttananagncaaatnatatnttnganttcancagnncaaacantgatgcaataa 151
           ||||| ||| | || ||||| |||| || || |||| |||  |||||| |||||||||||
Sbjct: 775 aaaaacttagagaggcaaatgatatcttcgacttcaccagcccaaacactgatgcaataa 834

                                                                       
Query: 152 naaaaatagaattnccactttcaatcccttcaaatcaatggttcttctcctntccaataa 211
            |||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 835 gaaaaatagaattcccactttcaatcccttcaaatcaatggttcttctcctctccaataa 894

                                                                       
Query: 212 aacatatcatgagtttcagcccaacntatggtacaccatcgaaaattatcgattcaccaa 271
           ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 895 aacatatcatgagtttcagcccaacctatggtacaccatcgaaaattatcgattcaccaa 954

                     
Query: 272 gtaaattgtt 281
           ||||||||||
Sbjct: 955 gtaaattgtt 964


>Contig-U08241-1 (Contig-U08241-1Q) /CSM_Contig/Contig-U08241-1Q.Seq.d
          Length = 384

 Score =  281 bits (142), Expect = 3e-76
 Identities = 190/190 (100%)
 Strand = Plus / Plus

                                                                       
Query: 92  aaaaanttananagncaaatnatatnttnganttcancagnncaaacantgatgcaataa 151
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 92  aaaaanttananagncaaatnatatnttnganttcancagnncaaacantgatgcaataa 151

                                                                       
Query: 152 naaaaatagaattnccactttcaatcccttcaaatcaatggttcttctcctntccaataa 211
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 152 naaaaatagaattnccactttcaatcccttcaaatcaatggttcttctcctntccaataa 211

                                                                       
Query: 212 aacatatcatgagtttcagcccaacntatggtacaccatcgaaaattatcgattcaccaa 271
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 212 aacatatcatgagtttcagcccaacntatggtacaccatcgaaaattatcgattcaccaa 271

                     
Query: 272 gtaaattgtt 281
           ||||||||||
Sbjct: 272 gtaaattgtt 281


>Contig-U12482-1 (Contig-U12482-1Q) /CSM_Contig/Contig-U12482-1Q.Seq.d
          Length = 1610

 Score = 30.2 bits (15), Expect = 1.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                           
Query: 264  ttcaccaagtaaatt 278
            |||||||||||||||
Sbjct: 1079 ttcaccaagtaaatt 1093


  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: 850
Number of Sequences: 6905
Number of extensions: 850
Number of successful extensions: 74
Number of sequences better than 10.0: 22
length of query: 384
length of database: 5,674,871
effective HSP length: 16
effective length of query: 368
effective length of database: 5,564,391
effective search space: 2047695888
effective search space used: 2047695888
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 2008.11.12
Homology vs DNA 
Query= Contig-U08241-1 (Contig-U08241-1Q) /CSM_Contig/Contig-U08241-1Q.Seq.d
         (384 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

(AY293825) Dictyostelium discoideum transposon cluster; tRNA...   281   9e-72  1
(AC117075) Dictyostelium discoideum chromosome 2 map 5201047...   281   9e-72  1
(AC116986) Dictyostelium discoideum chromosome 2 map 2234041...   281   9e-72  1
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720...   281   9e-72  1
(AC115680) Dictyostelium discoideum chromosome 2 map 4915084...   281   9e-72  1
(AU060775) Dictyostelium discoideum slug cDNA, clone SLB450.      281   9e-72  1
(AU052334) Dictyostelium discoideum slug cDNA, clone SLD158.      281   9e-72  1
(BJ398271) Dictyostelium discoideum cDNA clone:dds11a22, 3' ...   281   9e-72  1
(BJ375210) Dictyostelium discoideum cDNA clone:ddc17i20, 3' ...   281   9e-72  1
(BJ346399) Dictyostelium discoideum cDNA clone:dda30e22, 3' ...   276   5e-70  1
(X69171) D.discoideum mRNA of retrotransposable element DRE,...   274   2e-69  1
(X69170) D.discoideum mRNA of retrotransposable element DRE,...   274   2e-69  1
(X68231) D.discoideum genomic DNA of retrotransposable eleme...   274   2e-69  1
(X57034) D.discoideum retrotransposon DRE.                        274   2e-69  1
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470...   274   2e-69  1
(AC116977) Dictyostelium discoideum chromosome 2 map 5515173...   274   2e-69  1
(BJ343888) Dictyostelium discoideum cDNA clone:dda17c16, 3' ...   266   5e-67  1
(AC116032) Dictyostelium discoideum chromosome 2 map 4158743...   218   1e-52  1
(BJ341027) Dictyostelium discoideum cDNA clone:dda4k21, 3' e...   212   7e-51  1
(BJ343497) Dictyostelium discoideum cDNA clone:dda16c12, 3' ...   123   5e-24  1
(BJ345728) Dictyostelium discoideum cDNA clone:dda28j17, 3' ...   121   2e-23  1
(AC117082) Dictyostelium discoideum chromosome 2 map complem...   105   1e-18  1
(BJ342083) Dictyostelium discoideum cDNA clone:dda9o10, 3' e...   105   1e-18  1
(BJ340857) Dictyostelium discoideum cDNA clone:dda4m01, 3' e...    72   2e-08  1
(M24574) D.discoideum insertion element DRE2-I.                    68   2e-07  1
(M24571) Dictyostelium discoideum tRNA-Glu-GAA gene, clone y...    68   2e-07  1
(M24567) Dictyostelium discoideum tRNA-Glu-GAA gene, clone y...    68   2e-07  1
(M24565) Dictyostelium discoideum tRNA-Glu-GAA gene, clone y...    68   2e-07  1
(X59563) D. discoideum tRNA-Arg (UCU) 1 gene.                      60   6e-05  1
(M24578) Dictyostelium discoideum insertion elements DRE1a a...    60   6e-05  1
(M24577) D.discoideum insertion element DRE2-II.                   60   6e-05  1
(M24576) D.discoideum insertion element DRE2-II.                   60   6e-05  1
(M24064) D.discoideum Val-tRNA gene, clone lambda-ValGUU13.        60   6e-05  1
(M24058) D.discoideum Val-tRNA gene, clone lambda-ValGUU6.         60   6e-05  1

>(AY293825) Dictyostelium discoideum transposon cluster; tRNA-Leu
            gene, 5S ribosomal RNA pseudogene, and tRNA-Ser gene,
            complete sequence.
          Length = 22368

 Score =  281 bits (142), Expect = 9e-72
 Identities = 174/190 (91%)
 Strand = Plus / Plus


Query: 92   aaaaanttananagncaaatnatatnttnganttcancagnncaaacantgatgcaataa 151
            ||||| ||| | || ||||| |||| || || |||| |||  |||||| |||||||||||
Sbjct: 5196 aaaaacttagagaggcaaatgatatcttcgacttcaccagcccaaacactgatgcaataa 5255


Query: 152  naaaaatagaattnccactttcaatcccttcaaatcaatggttcttctcctntccaataa 211
             |||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 5256 gaaaaatagaattcccactttcaatcccttcaaatcaatggttcttctcctctccaataa 5315


Query: 212  aacatatcatgagtttcagcccaacntatggtacaccatcgaaaattatcgattcaccaa 271
            ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 5316 aacatatcatgagtttcagcccaacctatggtacaccatcgaaaattatcgattcaccaa 5375


Query: 272  gtaaattgtt 281
            ||||||||||
Sbjct: 5376 gtaaattgtt 5385

 Score =  276 bits (139), Expect = 5e-70
 Identities = 163/175 (93%)
 Strand = Plus / Plus


Query: 107   caaatnatatnttnganttcancagnncaaacantgatgcaataanaaaaatagaattnc 166
             ||||| |||| || || |||| |||  |||||| ||||||||||| |||||||||||| |
Sbjct: 12491 caaatgatatcttcgacttcaccagcccaaacactgatgcaataagaaaaatagaattcc 12550


Query: 167   cactttcaatcccttcaaatcaatggttcttctcctntccaataaaacatatcatgagtt 226
             |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 12551 cactttcaatcccttcaaatcaatggttcttctcctctccaataaaacatatcatgagtt 12610


Query: 227   tcagcccaacntatggtacaccatcgaaaattatcgattcaccaagtaaattgtt 281
             |||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 12611 tcagcccaacctatggtacaccatcgaaaattatcgattcaccaagtaaattgtt 12665

 Score =  274 bits (138), Expect = 2e-69
 Identities = 162/174 (93%)
 Strand = Plus / Plus


Query: 108   aaatnatatnttnganttcancagnncaaacantgatgcaataanaaaaatagaattncc 167
             |||| |||| || || |||| |||  |||||| ||||||||||| |||||||||||| ||
Sbjct: 14959 aaatgatatcttcgacttcaccagcccaaacactgatgcaataagaaaaatagaattccc 15018


Query: 168   actttcaatcccttcaaatcaatggttcttctcctntccaataaaacatatcatgagttt 227
             ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 15019 actttcaatcccttcaaatcaatggttcttctcctctccaataaaacatatcatgagttt 15078


Query: 228   cagcccaacntatggtacaccatcgaaaattatcgattcaccaagtaaattgtt 281
             ||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 15079 cagcccaacctatggtacaccatcgaaaattatcgattcaccaagtaaattgtt 15132

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 121,081,678
Number of extensions: 6625813
Number of successful extensions: 330803
Number of sequences better than 10.0: 34
Length of query: 384
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 361
Effective length of database: 93,106,754,628
Effective search space: 33611538420708
Effective search space used: 33611538420708
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.24
Homology vs Protein 
Query= Contig-U08241-1 (Contig-U08241-1Q) /CSM_Contig/Contig-U08241-1Q.Seq.d
         (384 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

X69170_1(X69170|pid:none) D.discoideum mRNA of retrotransposable...   111   7e-24
X69171_1(X69171|pid:none) D.discoideum mRNA of retrotransposable...   111   7e-24
S20105(S20105;S30206;S30208;S30210;S25645) hypothetical protein ...   111   7e-24
(Q4L6U5) RecName: Full=Probable nicotinate-nucleotide adenylyltr...    32   5.3

>X69170_1(X69170|pid:none) D.discoideum mRNA of retrotransposable
           element DRE, subtype b.
          Length = 446

 Score =  111 bits (278), Expect = 7e-24
 Identities = 60/97 (61%), Positives = 60/97 (61%)
 Frame = +1

Query: 94  KXXXXNXXXXFXXXNXDAIXKIEXPLSIPSNQWFFSXPIKHIMSFSPTYGTPSKIIDSPS 273
           K    N    F   N DAI KIE PLSIPSNQWFFS PIKHIMSFSPTYGTPSKIIDSPS
Sbjct: 292 KLREVNDIFDFTSPNTDAIRKIEFPLSIPSNQWFFSSPIKHIMSFSPTYGTPSKIIDSPS 351

Query: 274 KLLXXXXXXXXXXXXXXXXXXXXXXLGEYGQKSIKTK 384
           KLL                      LGEYGQKSIKTK
Sbjct: 352 KLLNTPKNKQQDKTNRTNKTPVKPKLGEYGQKSIKTK 388

Lambda     K      H
   0.315    0.134    0.396

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3204285
Number of Hits to DB: 406,511,190
Number of extensions: 18793455
Number of successful extensions: 9060
Number of sequences better than 10.0: 4
Number of HSP's gapped: 9055
Number of HSP's successfully gapped: 4
Length of query: 128
Length of database: 1,040,966,779
Length adjustment: 93
Effective length of query: 35
Effective length of database: 742,968,274
Effective search space: 26003889590
Effective search space used: 26003889590
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 (21.5 bits)
S2: 29 (15.8 bits)
PSORT 

 psg: 0.66  gvh: 0.40  alm: 0.57  top: 0.53  tms: 0.00  mit: 0.27  mip: 0.00
 nuc: 0.09  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 

	 44.0 %: nuclear
	 28.0 %: cytoplasmic
	 20.0 %: mitochondrial
	  8.0 %: cytoskeletal

>> prediction for Contig-U08241-1 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) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 1
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0