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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-U14768-1
Contig ID Contig-U14768-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14768-1 (Contig-U14768-1Q) /CSM_Contig/Contig-U14768-1Q.Seq.d
ATTTCTTTTTATTGCGAACAAAAGGTTTATTAAATTTTTTTTGAATCTGA
TCAGTAGCAAACAATATACCATATTGTCAAATTGTTCAATATTTTGAAAT
ATAAAAGCAAAAATATTCTTCAATTTACAATTCAATTAGGAATCAAAAAA
AAACAAACGAAAACGAATAATAATAATTAATAGTAGTAATAATAATAACA
ATAATAACTAAATCATATAATCCAAAAAAAGAGAGTTAACAGTTCTCATT
TTTCTTTGTTCGATCACTTTATATTTTATAACATTATAGTTCAACTTTTA
TTTGTATAACAAAAAAAAGAACATCAAAAAAAAAA
Gap no gap
Contig length 335
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1751040
End point 1751374
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U14768
List of clone(s) 

est1=VHB866F,1,335
est2=VHB866Z,1,322
Translated Amino Acid sequence 
isfyceqkvy*iffesdq*QTIYHIVKLFNILKYKSKNILQFTIQLGIKKKQTKTNNNN*
******q**lnhiiqkkrvnsshfslfdhfifyniivqllfv*qkkehqkk
Translated Amino Acid sequence (All Frames) 
Frame A:
isfyceqkvy*iffesdq*QTIYHIVKLFNILKYKSKNILQFTIQLGIKKKQTKTNNNN*
******q**lnhiiqkkrvnsshfslfdhfifyniivqllfv*qkkehqkk


Frame B:
flfiankrfikfflnlisskqytilsncsif*nikakiffnlqfn*eskknkrkriiiin
ssnnnnnnn*ii*skkreltvliflcsitlyfitl*fnfylynkkknikkk


Frame C:
ffllrtkgllnff*i*svannipycqivqyfei*kqkyssiynsirnqkktnene***li
vviiitiitksynpkkes*qfsfffvrslyil*hysstficitkkrtskkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14768-1 (Contig-U14768-1Q)
/CSM_Contig/Contig-U14768-1Q.Seq.d
         (335 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14768-1 (Contig-U14768-1Q) /CSM_Contig/Conti...   238  3e-63
Contig-U02994-1 (Contig-U02994-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U09137-1 (Contig-U09137-1Q) /CSM_Contig/Conti...    36  0.023
Contig-U13782-1 (Contig-U13782-1Q) /CSM_Contig/Conti...    34  0.091
Contig-U12197-1 (Contig-U12197-1Q) /CSM_Contig/Conti...    34  0.091
Contig-U12918-1 (Contig-U12918-1Q) /CSM_Contig/Conti...    32  0.36
Contig-U03230-1 (Contig-U03230-1Q) /CSM_Contig/Conti...    32  0.36
Contig-U14694-1 (Contig-U14694-1Q) /CSM_Contig/Conti...    30  1.4
Contig-U13948-1 (Contig-U13948-1Q) /CSM_Contig/Conti...    30  1.4

>Contig-U14768-1 (Contig-U14768-1Q) /CSM_Contig/Contig-U14768-1Q.Seq.d
          Length = 335

 Score =  238 bits (120), Expect = 3e-63
 Identities = 136/144 (94%)
 Strand = Plus / Plus

                                                                       
Query: 1   atttctttttattgcgaacaaaaggtttattaaannnnnnnngaatctgatcagtagcaa 60
           ||||||||||||||||||||||||||||||||||        ||||||||||||||||||
Sbjct: 1   atttctttttattgcgaacaaaaggtttattaaattttttttgaatctgatcagtagcaa 60

                                                                       
Query: 61  acaatataccatattgtcaaattgttcaatattttgaaatataaaagcaaaaatattctt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  acaatataccatattgtcaaattgttcaatattttgaaatataaaagcaaaaatattctt 120

                                   
Query: 121 caatttacaattcaattaggaatc 144
           ||||||||||||||||||||||||
Sbjct: 121 caatttacaattcaattaggaatc 144


 Score =  163 bits (82), Expect = 1e-40
 Identities = 96/103 (93%)
 Strand = Plus / Plus

                                                                       
Query: 208 ctaaatcatataatccnnnnnnngagagttaacagttctcatttttctttgttcgatcac 267
           ||||||||||||||||       |||||||||||||||||||||||||||||||||||||
Sbjct: 208 ctaaatcatataatccaaaaaaagagagttaacagttctcatttttctttgttcgatcac 267

                                                      
Query: 268 tttatattttataacattatagttcaacttttatttgtataac 310
           |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 268 tttatattttataacattatagttcaacttttatttgtataac 310


>Contig-U02994-1 (Contig-U02994-1Q) /CSM_Contig/Contig-U02994-1Q.Seq.d
          Length = 616

 Score = 38.2 bits (19), Expect = 0.006
 Identities = 25/27 (92%)
 Strand = Plus / Minus

                                      
Query: 85  ttcaatattttgaaatataaaagcaaa 111
           |||||| |||| |||||||||||||||
Sbjct: 602 ttcaatgttttaaaatataaaagcaaa 576


 Score = 28.2 bits (14), Expect = 5.6
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                             
Query: 268 tttatattttataacatt 285
           ||||||||||| ||||||
Sbjct: 582 tttatattttaaaacatt 599


>Contig-U09137-1 (Contig-U09137-1Q) /CSM_Contig/Contig-U09137-1Q.Seq.d
          Length = 542

 Score = 36.2 bits (18), Expect = 0.023
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 108 caaaaatattcttcaatt 125
           ||||||||||||||||||
Sbjct: 334 caaaaatattcttcaatt 351


  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: 3785
Number of Sequences: 6905
Number of extensions: 3785
Number of successful extensions: 402
Number of sequences better than 10.0: 115
length of query: 335
length of database: 5,674,871
effective HSP length: 15
effective length of query: 320
effective length of database: 5,571,296
effective search space: 1782814720
effective search space used: 1782814720
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 2008.12.31
Homology vs DNA 
Query= Contig-U14768-1 (Contig-U14768-1Q) /CSM_Contig/Contig-U14768-1Q.Seq.d
         (335 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

(BJ437523) Dictyostelium discoideum cDNA clone:ddv34d18, 3' ...   202   e-102  3
(BJ418940) Dictyostelium discoideum cDNA clone:ddv34d18, 5' ...   202   e-102  3
(CZ190924) OA_BBa0110K21.f OA_BBa Oryza alta genomic clone O...    34   0.15   2
(DR093052) STRR1_5_E11.g1_A033 Stem Response Resistant Pinus...    48   0.20   1
(DR092969) STRR1_5_E11.b1_A033 Stem Response Resistant Pinus...    48   0.20   1
(DR068786) RTDK1_2_H06.g1_A029 Roots, dark Pinus taeda cDNA ...    48   0.20   1
(DR068702) RTDK1_2_H06.b1_A029 Roots, dark Pinus taeda cDNA ...    48   0.20   1
(DR057588) RTNIT1_6_E02.g1_A029 Roots minus nitrogen Pinus t...    48   0.20   1
(DR048260) RTBOR1_7_C10.g2_A029 Roots plus added boron Pinus...    48   0.20   1
(CV031944) RTNACL1_4_F01.g1_A029 Roots plus added NaCl Pinus...    48   0.20   1
(CO157914) FLD1_3_B11.b1_A029 Root flooded Pinus taeda cDNA ...    48   0.20   1
(BM158976) NXLV_042_B08_F NXLV (Nsf Xylem Late wood Vertical...    48   0.20   1
(BG040764) NXSI_114_G06_F NXSI (Nsf Xylem Side wood Inclined...    48   0.20   1
(CR381619) Zebrafish DNA sequence from clone DKEY-1O2 in lin...    36   0.42   2
(AC021180) Homo sapiens BAC clone RP11-727M10 from 4, comple...    44   0.68   4
(AC126310) Rattus norvegicus clone CH230-306O15, *** SEQUENC...    42   0.72   2
(BH543242) BOGBI94TR BOGB Brassica oleracea genomic clone BO...    46   0.78   1
(AC200585) Macaca mulatta clone CH250-277O16, WORKING DRAFT ...    38   1.4    3
(BH624653) 1007079E03.1EL_y2 1007 - RescueMu Grid H Zea mays...    34   2.2    2
(BH628128) 1007080E03.1EL_y1 1007 - RescueMu Grid H Zea mays...    34   2.2    2
(AM452592) Vitis vinifera contig VV78X111271.2, whole genome...    44   3.1    1
(AM424203) Vitis vinifera contig VV78X247388.5, whole genome...    44   3.1    1
(AC161392) Bos taurus clone CH240-93M22, WORKING DRAFT SEQUE...    44   3.1    1
(AC144370) Bos taurus clone RP42-511G24, WORKING DRAFT SEQUE...    44   3.1    1
(EK552702) 1095516124404 Global-Ocean-Sampling_GS-32-01-01-1...    44   3.1    1
(CT543405) A BAC library has been constructed from cultivar ...    44   3.1    1
(CT494022) A BAC library has been constructed from cultivar ...    44   3.1    1
(CT426748) Sus scrofa genomic clone CH242-504M20, genomic su...    44   3.1    1
(AC074245) Homo sapiens chromosome 2 clone RP11-341F8, WORKI...    34   3.2    5
(CK472148) AGENCOURT_17617303 NIH_MGC_236 Rattus norvegicus ...    40   3.2    2
(AC125245) Homo sapiens BAC clone RP11-236P13 from 4, comple...    34   3.9    4
(AM442217) Vitis vinifera contig VV78X025827.4, whole genome...    42   4.3    2
(AC112227) Homo sapiens BAC clone RP13-552G12 from 4, comple...    34   5.0    4
(AM446587) Vitis vinifera, whole genome shotgun sequence, co...    30   5.1    5
(AL096868) Human DNA sequence from clone RP3-493D19 on chrom...    32   5.8    2
(CR956644) Zebrafish DNA sequence from clone DKEY-5F20 in li...    32   5.8    2
(AC009797) Homo sapiens chromosome 11 clone 216_I_08 map 11,...    32   6.0    2
(AC073571) Homo sapiens 12 BAC RP11-136F16 (Roswell Park Can...    38   6.8    2
(AC221621) Bos taurus clone CH240-391B19, WORKING DRAFT SEQU...    32   7.0    6
(AP001692) Homo sapiens genomic DNA, chromosome 21q, section...    38   7.5    5
(CU138538) Zebrafish DNA sequence from clone DKEY-190O8 in l...    42   7.7    3
(AG050694) Pan troglodytes DNA, clone: PTB-031D05.R.               32   7.8    2
(AM649458) Entamoeba moshkovskii FIC GSS, clone mosh067h10.p1k.    32   7.9    2
(CT827853) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   8.1    2
(CU407246) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   8.4    2
(AC109518) Homo sapiens BAC clone RP11-492P11 from 4, comple...    32   8.7    5
(CU656006) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   8.8    4
(AM482964) Vitis vinifera, whole genome shotgun sequence, co...    38   8.9    3

>(BJ437523) Dictyostelium discoideum cDNA clone:ddv34d18, 3' end,
           single read.
          Length = 322

 Score =  202 bits (102), Expect(3) = e-102
 Identities = 102/102 (100%)
 Strand = Plus / Minus


Query: 43  gaatctgatcagtagcaaacaatataccatattgtcaaattgttcaatattttgaaatat 102
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 280 gaatctgatcagtagcaaacaatataccatattgtcaaattgttcaatattttgaaatat 221


Query: 103 aaaagcaaaaatattcttcaatttacaattcaattaggaatc 144
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 220 aaaagcaaaaatattcttcaatttacaattcaattaggaatc 179

 Score =  159 bits (80), Expect(3) = e-102
 Identities = 80/80 (100%)
 Strand = Plus / Minus


Query: 231 gagagttaacagttctcatttttctttgttcgatcactttatattttataacattatagt 290
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 92  gagagttaacagttctcatttttctttgttcgatcactttatattttataacattatagt 33


Query: 291 tcaacttttatttgtataac 310
           ||||||||||||||||||||
Sbjct: 32  tcaacttttatttgtataac 13

 Score = 67.9 bits (34), Expect(3) = e-102
 Identities = 34/34 (100%)
 Strand = Plus / Minus


Query: 1   atttctttttattgcgaacaaaaggtttattaaa 34
           ||||||||||||||||||||||||||||||||||
Sbjct: 322 atttctttttattgcgaacaaaaggtttattaaa 289

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 345,298,252
Number of extensions: 23012760
Number of successful extensions: 2156703
Number of sequences better than 10.0: 48
Length of query: 335
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 312
Effective length of database: 93,106,754,628
Effective search space: 29049307443936
Effective search space used: 29049307443936
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.12
Homology vs Protein 
Query= Contig-U14768-1 (Contig-U14768-1Q) /CSM_Contig/Contig-U14768-1Q.Seq.d
         (335 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: 384,079,412
Number of extensions: 5747962
Number of successful extensions: 8735
Number of sequences better than 10.0: 0
Number of HSP's gapped: 8734
Number of HSP's successfully gapped: 0
Length of query: 111
Length of database: 1,051,180,864
Length adjustment: 78
Effective length of query: 33
Effective length of database: 798,729,262
Effective search space: 26358065646
Effective search space used: 26358065646
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: 28 (15.4 bits)
PSORT 

 psg: 0.64  gvh: 0.14  alm: 0.55  top: 0.53  tms: 0.00  mit: 0.42  mip: 0.00
 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 

	 44.0 %: nuclear
	 28.0 %: mitochondrial
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U14768-1 is nuc
VS (DIR, S) 0
VH (FL, L) 1
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) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0