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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-U05841-1
Contig ID Contig-U05841-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U05841-1 (Contig-U05841-1Q) /CSM_Contig/Contig-U05841-1Q.Seq.d
AAAAAATTAAAATAAAATGAAGCATCATACAAATTTATTACATTATTTTG
AAAAATTTGCAATTTATTACAATAGTAGACCAAAAAATTTAAAGGAAAAT
TCATTTGTTAAACAAAAGAAAGAAATGGTTCCAATTGAAATTAAATATCA
AACATTAATTCCATACTTTTAAGGAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 191
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 2676761
End point 2676570
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05841
List of clone(s) 

est1=SSM170F,1,192
Translated Amino Acid sequence 
kn*NKMKHHTNLLHYFEKFAIYYNSRPKNLKENSFVKQKKEMVPIEIKYQTLIPYF*gkk
kkk
Translated Amino Acid sequence (All Frames) 
Frame A:
kklk*neasykfitlf*kicnllq**tkkfkgkfic*tkerngsn*n*isninsillrkk
kkk


Frame B:
kn*NKMKHHTNLLHYFEKFAIYYNSRPKNLKENSFVKQKKEMVPIEIKYQTLIPYF*gkk
kkk


Frame C:
kikik*siiqiyyiilknlqfitivdqki*rkihllnkrkkwfqlklnikh*fhtfkekk
kkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05841-1 (Contig-U05841-1Q)
/CSM_Contig/Contig-U05841-1Q.Seq.d
         (191 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05841-1 (Contig-U05841-1Q) /CSM_Contig/Conti...   311  1e-85
Contig-U12512-1 (Contig-U12512-1Q) /CSM_Contig/Conti...    34  0.050
Contig-U02265-1 (Contig-U02265-1Q) /CSM_Contig/Conti...    34  0.050
Contig-U13979-1 (Contig-U13979-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U13828-1 (Contig-U13828-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U13648-1 (Contig-U13648-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U13406-1 (Contig-U13406-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U12787-1 (Contig-U12787-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U12229-1 (Contig-U12229-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U12006-1 (Contig-U12006-1Q) /CSM_Contig/Conti...    32  0.20

>Contig-U05841-1 (Contig-U05841-1Q) /CSM_Contig/Contig-U05841-1Q.Seq.d
          Length = 191

 Score =  311 bits (157), Expect = 1e-85
 Identities = 157/157 (100%)
 Strand = Plus / Plus

                                                                       
Query: 18  tgaagcatcatacaaatttattacattattttgaaaaatttgcaatttattacaatagta 77
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 18  tgaagcatcatacaaatttattacattattttgaaaaatttgcaatttattacaatagta 77

                                                                       
Query: 78  gaccaaaaaatttaaaggaaaattcatttgttaaacaaaagaaagaaatggttccaattg 137
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 78  gaccaaaaaatttaaaggaaaattcatttgttaaacaaaagaaagaaatggttccaattg 137

                                                
Query: 138 aaattaaatatcaaacattaattccatacttttaagg 174
           |||||||||||||||||||||||||||||||||||||
Sbjct: 138 aaattaaatatcaaacattaattccatacttttaagg 174


>Contig-U12512-1 (Contig-U12512-1Q) /CSM_Contig/Contig-U12512-1Q.Seq.d
          Length = 1972

 Score = 34.2 bits (17), Expect = 0.050
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 136  tgaaattaaatatcaaa 152
            |||||||||||||||||
Sbjct: 1108 tgaaattaaatatcaaa 1124


>Contig-U02265-1 (Contig-U02265-1Q) /CSM_Contig/Contig-U02265-1Q.Seq.d
          Length = 100

 Score = 34.2 bits (17), Expect = 0.050
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                               
Query: 29 acaaatttattacattatttt 49
          ||||||||||| |||||||||
Sbjct: 90 acaaatttattccattatttt 70


  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: 4494
Number of Sequences: 6905
Number of extensions: 4494
Number of successful extensions: 1604
Number of sequences better than 10.0: 164
length of query: 191
length of database: 5,674,871
effective HSP length: 15
effective length of query: 176
effective length of database: 5,571,296
effective search space: 980548096
effective search space used: 980548096
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. 6
Homology vs DNA 
Query= Contig-U05841-1 (Contig-U05841-1Q) /CSM_Contig/Contig-U05841-1Q.Seq.d
         (191 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

(AU074822) Dictyostelium discoideum slug cDNA, clone SSM170.      127   6e-36  2
(AC186774) Trichinella spiralis chromosome UNK clone TS195-1...    42   3e-04  2
(CR382385) Zebrafish DNA sequence from clone CH211-235I11 in...    46   0.42   1
(CR854987) Zebrafish DNA sequence from clone CH211-185J22 in...    44   1.7    1
(AC130803) Medicago truncatula clone mth2-10g3, complete seq...    44   1.7    1
(AC124972) Medicago truncatula clone mth2-24j4, complete seq...    44   1.7    1
(CR956635) Pig DNA sequence from clone CH242-184L20 on chrom...    44   1.7    1
(CR974453) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.7    1
(AC220770) Bos taurus clone CH240-347L7, WORKING DRAFT SEQUE...    44   1.7    1
(AC167498) Bos taurus clone CH240-107O8, WORKING DRAFT SEQUE...    44   1.7    1
(BU929082) AGENCOURT_10422457 NIH_MGC_57 Homo sapiens cDNA c...    44   1.7    1
(CP000721) Clostridium beijerinckii NCIMB 8052, complete gen...    44   1.7    1
(AJ562000) Cryptosporidium parvum GSS, PAC clone pica_0006_c...    40   3.0    2
(ED857828) OA_CBa0028G22.r OA_CBa Oryza australiensis genomi...    36   3.2    2
(EX188916) gmnbspic_0013p12.pDNRm13r Gadus morhua spleen lib...    32   3.5    2
(FG271628) gmnlla_0045m09.sp6 Gadus morhua larvae library Ga...    32   3.5    2
(AM442760) Vitis vinifera contig VV78X181460.10, whole genom...    32   3.5    2
(AP006270) Adoxophyes honmai nucleopolyhedrovirus DNA, compl...    40   3.6    3
(AZ183857) SP_1002_A1_D10_SP6 Strongylocentrotus purpuratus,...    32   4.3    2
(EJ265313) 1095351006679 Global-Ocean-Sampling_GS-27-01-01-1...    30   4.3    2
(AC225474) Medicago truncatula clone mth2-189l10, WORKING DR...    36   5.2    2
(BX927204) Zebrafish DNA sequence from clone CH211-103B12 in...    42   6.6    1
(BX537102) Zebrafish DNA sequence from clone DKEY-276L17 in ...    42   6.6    1
(BX005225) Zebrafish DNA sequence from clone DKEY-34L15 in l...    42   6.6    1
(AC102806) Mus musculus chromosome 3, clone RP23-341B15, com...    42   6.6    1
(AC201940) MACACA MULATTA BAC clone CH250-163A15 from chromo...    42   6.6    1
(AC190193) Rhesus macaque BAC clone CH250-90H12 from chromos...    42   6.6    1
(AM461297) Vitis vinifera, whole genome shotgun sequence, co...    42   6.6    1
(AM450441) Vitis vinifera contig VV78X137958.3, whole genome...    42   6.6    1
(AM445202) Vitis vinifera contig VV78X177874.6, whole genome...    42   6.6    1
(AM438855) Vitis vinifera contig VV78X154934.6, whole genome...    42   6.6    1
(DD230941) GENE PRODUCTS DIFFERENTIALLY EXPRESSED IN CANCERO...    42   6.6    1
(CS789425) Sequence 681 from Patent WO2005031001.                  42   6.6    1
(BD158302) Primer for synthesizing full-length cDNA and use ...    42   6.6    1
(AX880295) Sequence 15200 from Patent EP1074617.                   42   6.6    1
(AX408188) Sequence 835 from Patent WO0229103.                     42   6.6    1
(AR780272) Sequence 835 from patent US 6974667.                    42   6.6    1
(BC035167) Homo sapiens ELL associated factor 1, mRNA (cDNA ...    42   6.6    1
(AK023217) Homo sapiens cDNA FLJ13155 fis, clone NT2RP3003433.     42   6.6    1
(AC090883) Homo sapiens chromosome 3 clone RP11-117G9 map 3p...    42   6.6    1
(AC027125) Homo sapiens chromosome 3 clone RP11-584M7 map 3p...    42   6.6    1
(CU656008) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.6    1
(CU633215) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.6    1
(CU466532) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.6    1
(CU013537) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    42   6.6    1
(AC222709) Bos taurus clone CH240-441A2, WORKING DRAFT SEQUE...    42   6.6    1
(AC219340) Bos taurus clone CH240-337K11, WORKING DRAFT SEQU...    42   6.6    1
(AC184869) Zea mays chromosome 5 clone CH201-168D4; ZMMBBc01...    42   6.6    1
(AC179237) Strongylocentrotus purpuratus clone R3-42A21, WOR...    42   6.6    1
(AC170378) Bos taurus clone CH240-223K19, WORKING DRAFT SEQU...    42   6.6    1
(AC168988) Bos taurus clone CH240-198K6, WORKING DRAFT SEQUE...    42   6.6    1
(AC168126) Bos taurus clone CH240-222M3, WORKING DRAFT SEQUE...    42   6.6    1
(CR858987) Pongo abelii mRNA; cDNA DKFZp459A018 (from clone ...    42   6.6    1
(AZ772836) 1M0584I03F Mouse 10kb plasmid UUGC1M library Mus ...    42   6.6    1
(FH348821) CHO_OF4652xl09r1.ab1 CHO_OF4 Nicotiana tabacum ge...    42   6.6    1
(ER969789) AF__Bc0035A24r AF__Bc Aquilegia formosa genomic, ...    42   6.6    1
(EK547455) 1095516101229 Global-Ocean-Sampling_GS-32-01-01-1...    42   6.6    1
(EJ036430) 1095454070118 Global-Ocean-Sampling_GS-26-01-01-1...    42   6.6    1
(CZ515096) GMW2-87I16a.b1 GMW2 Glycine max genomic, genomic ...    42   6.6    1
(CU858032) A BAC library has been constructed from PN40024 g...    42   6.6    1
(CE575094) tigr-gss-dog-17000366182584 Dog Library Canis lup...    42   6.6    1
(BZ883056) CH240_218F19.TV CHORI-240 Bos taurus genomic clon...    42   6.6    1
(BZ627616) ih53g10.g1 WGS-SbicolorF (DH5a methyl filtered) S...    42   6.6    1
(BZ398173) EINCO08TF EI_10_12_KB Entamoeba invadens genomic ...    42   6.6    1
(BH762441) BMBAC329A08SP6_PSU Brugia malayi Genomic Bac Libr...    42   6.6    1
(DB556666) Homo sapiens hypothalamus cDNA, RIKEN full-length...    42   6.6    1
(DB513384) Homo sapiens testis cDNA, RIKEN full-length enric...    42   6.6    1
(DB318485) Homo sapiens cDNA clone HCHON2006576, 3' end, mRN...    42   6.6    1
(AU149385) Homo sapiens cDNA clone:NT2RM4002202, 3' end, exp...    42   6.6    1
(AI935241) wp17g03.x1 NCI_CGAP_Lu19 Homo sapiens cDNA clone ...    42   6.6    1
(CB985990) AGENCOURT_13650756 NIH_MGC_184 Homo sapiens cDNA ...    42   6.6    1
(CA429815) UI-H-FH1-bfn-h-23-0-UI.s1 NCI_CGAP_FH1 Homo sapie...    42   6.6    1
(CA427317) UI-H-FH1-bfi-g-19-0-UI.s1 NCI_CGAP_FH1 Homo sapie...    42   6.6    1
(CA427087) UI-H-DF0-bex-e-03-0-UI.s1 NCI_CGAP_DF0 Homo sapie...    42   6.6    1
(AI888088) wm29h01.x1 NCI_CGAP_Ut4 Homo sapiens cDNA clone I...    42   6.6    1
(BX106070) RZPD Homo sapiens cDNA clone IMAGp998P011821 = IM...    42   6.6    1
(BU753555) UI-1-BC1-ajl-c-12-0-UI.s1 NCI_CGAP_Pl2 Homo sapie...    42   6.6    1
(BU731892) UI-E-CI1-aft-i-16-0-UI.s1 UI-E-CI1 Homo sapiens c...    42   6.6    1
(BU684256) UI-CF-EN0-aco-e-20-0-UI.s1 UI-CF-EN0 Homo sapiens...    42   6.6    1
(BU677347) UI-CF-DU1-aaj-l-10-0-UI.s1 UI-CF-DU1 Homo sapiens...    42   6.6    1
(BQ775794) UI-H-FH0-bcn-l-15-0-UI.s1 NCI_CGAP_FH0 Homo sapie...    42   6.6    1
(BQ100711) ij22e10.x1 Melton Normalized Human Islet 4 N4-HIS...    42   6.6    1
(BM829418) K-EST0102411 S9SNU601 Homo sapiens cDNA clone S9S...    42   6.6    1
(BM708701) UI-E-CI1-aft-i-16-0-UI.r1 UI-E-CI1 Homo sapiens c...    42   6.6    1
(BM127262) ie96g11.x1 Melton Normalized Human Islet 4 N4-HIS...    42   6.6    1
(AA767729) ob49d08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone ...    42   6.6    1
(AA664156) ac04f05.s1 Stratagene lung (#937210) Homo sapiens...    42   6.6    1
(BE550916) 7b65h05.x1 NCI_CGAP_Lu24 Homo sapiens cDNA clone ...    42   6.6    1
(AW965161) EST377234 MAGE resequences, MAGI Homo sapiens cDN...    42   6.6    1
(AW772273) hn71a06.x1 NCI_CGAP_Kid11 Homo sapiens cDNA clone...    42   6.6    1
(AW770427) hl82a12.x1 NCI_CGAP_Kid13 Homo sapiens cDNA clone...    42   6.6    1
(AW363622) CM1-CT0339-301199-053-b02 CT0339 Homo sapiens cDN...    42   6.6    1
(AW362940) RC3-CT0297-071299-011-h05 CT0297 Homo sapiens cDN...    42   6.6    1
(FC171845) 1106908779534 BABEVPN-C-01-1-7KB Papio anubis cDN...    42   6.6    1
(FC152163) 1106908627902 BABEVPN-C-01-1-7KB Papio anubis cDN...    42   6.6    1
(FC145856) 1106908571556 BABEVPN-C-01-1-7KB Papio anubis cDN...    42   6.6    1
(FC135310) 1106908492029 BABEVPN-C-01-1-7KB Papio anubis cDN...    42   6.6    1
(AW074281) xb10d10.x1 NCI_CGAP_GU1 Homo sapiens cDNA clone I...    42   6.6    1
(AA402095) zu53g01.r1 Soares ovary tumor NbHOT Homo sapiens ...    42   6.6    1
(AA401940) zu53g01.s1 Soares ovary tumor NbHOT Homo sapiens ...    42   6.6    1

>(AU074822) Dictyostelium discoideum slug cDNA, clone SSM170.
          Length = 192

 Score =  127 bits (64), Expect(2) = 6e-36
 Identities = 64/64 (100%)
 Strand = Plus / Plus


Query: 18 tgaagcatcatacaaatttattacattattttgaaaaatttgcaatttattacaatagta 77
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 18 tgaagcatcatacaaatttattacattattttgaaaaatttgcaatttattacaatagta 77


Query: 78 gacc 81
          ||||
Sbjct: 78 gacc 81

 Score = 56.0 bits (28), Expect(2) = 6e-36
 Identities = 28/28 (100%)
 Strand = Plus / Plus


Query: 147 atcaaacattaattccatacttttaagg 174
           ||||||||||||||||||||||||||||
Sbjct: 147 atcaaacattaattccatacttttaagg 174

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 128,240,173
Number of extensions: 8697771
Number of successful extensions: 2627102
Number of sequences better than 10.0: 107
Length of query: 191
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 169
Effective length of database: 93,199,600,587
Effective search space: 15750732499203
Effective search space used: 15750732499203
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.20
Homology vs Protein 
Query= Contig-U05841-1 (Contig-U05841-1Q) /CSM_Contig/Contig-U05841-1Q.Seq.d
         (191 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54C19) RecName: Full=Uncharacterized protein DDB_G0293278;          110   2e-23

>(Q54C19) RecName: Full=Uncharacterized protein DDB_G0293278;
          Length = 51

 Score =  110 bits (275), Expect = 2e-23
 Identities = 51/51 (100%), Positives = 51/51 (100%)
 Frame = +2

Query: 17  MKHHTNLLHYFEKFAIYYNSRPKNLKENSFVKQKKEMVPIEIKYQTLIPYF 169
           MKHHTNLLHYFEKFAIYYNSRPKNLKENSFVKQKKEMVPIEIKYQTLIPYF
Sbjct: 1   MKHHTNLLHYFEKFAIYYNSRPKNLKENSFVKQKKEMVPIEIKYQTLIPYF 51

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: 3204285
Number of Hits to DB: 240,836,322
Number of extensions: 4109310
Number of successful extensions: 10471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 10471
Number of HSP's successfully gapped: 1
Length of query: 63
Length of database: 1,040,966,779
Length adjustment: 35
Effective length of query: 28
Effective length of database: 928,816,804
Effective search space: 26006870512
Effective search space used: 26006870512
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: 26 (14.6 bits)
PSORT 

 psg: 0.74  gvh: 0.21  alm: 0.59  top: 0.53  tms: 0.00  mit: 0.24  mip: 0.05
 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 

	 48.0 %: nuclear
	 24.0 %: cytoplasmic
	 16.0 %: mitochondrial
	  8.0 %: cytoskeletal
	  4.0 %: vacuolar

>> prediction for Contig-U05841-1 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) 1
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