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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-U12677-1
Contig ID Contig-U12677-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12677-1 (Contig-U12677-1Q) /CSM_Contig/Contig-U12677-1Q.Seq.d
CAATTTCTTTTTATATTTTCGTTAGTAGAAAAGTAAAATAAGAGAAAGTA
TTTATAAATTTTTAGTAATGTTTGTTGGTACATTGGTCATTATTATATGC
ACGACATTGATCATTATTATTAAAAAAATTTTAAAAAGGAAAAAAGAAAA
ATTAAATCTTAAAGAAAGCAAAAAAAAAAACCAA
Gap no gap
Contig length 184
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 1273824
End point 1273641
Strand (PLUS/MINUS) MINUS
Number of clones 5
Number of EST 5
Link to clone list U12677
List of clone(s) 

est1=AHK787F,1,179
est2=AHE374F,13,184
est3=AHH133F,25,180
est4=AHK677F,35,181
est5=AHH771F,76,179
Translated Amino Acid sequence 
nfflyfr**KSKIRESIYKFLVMFVGTLVIIICTTLIIIIKKILKRKKEKLNLKESKKKN
Q
Translated Amino Acid sequence (All Frames) 
Frame A:
qflfifslvek*nkrkyl*ifsnvcwyighyymhdidhyy*knfkkekrkiks*rkqkkk
p


Frame B:
nfflyfr**KSKIRESIYKFLVMFVGTLVIIICTTLIIIIKKILKRKKEKLNLKESKKKN
Q


Frame C:
isfyifvsrkvk*ekvfinf**cllvhwsllyarh*slllkkf*kgkkkn*ilkkakkkt
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12677-1 (Contig-U12677-1Q)
/CSM_Contig/Contig-U12677-1Q.Seq.d
         (184 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12677-1 (Contig-U12677-1Q) /CSM_Contig/Conti...   240  4e-64
Contig-U10929-1 (Contig-U10929-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U12375-1 (Contig-U12375-1Q) /CSM_Contig/Conti...    34  0.048
Contig-U00762-1 (Contig-U00762-1Q) /CSM_Contig/Conti...    34  0.048
Contig-U13384-1 (Contig-U13384-1Q) /CSM_Contig/Conti...    32  0.19
Contig-U11916-1 (Contig-U11916-1Q) /CSM_Contig/Conti...    32  0.19
Contig-U10024-1 (Contig-U10024-1Q) /CSM_Contig/Conti...    32  0.19
Contig-U09887-1 (Contig-U09887-1Q) /CSM_Contig/Conti...    32  0.19
Contig-U04683-1 (Contig-U04683-1Q) /CSM_Contig/Conti...    32  0.19
Contig-U04327-1 (Contig-U04327-1Q) /CSM_Contig/Conti...    32  0.19

>Contig-U12677-1 (Contig-U12677-1Q) /CSM_Contig/Contig-U12677-1Q.Seq.d
          Length = 184

 Score =  240 bits (121), Expect = 4e-64
 Identities = 121/121 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   caatttctttttatattttcgttagtagaaaagtaaaataagagaaagtatttataaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caatttctttttatattttcgttagtagaaaagtaaaataagagaaagtatttataaatt 60

                                                                       
Query: 61  tttagtaatgtttgttggtacattggtcattattatatgcacgacattgatcattattat 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tttagtaatgtttgttggtacattggtcattattatatgcacgacattgatcattattat 120

            
Query: 121 t 121
           |
Sbjct: 121 t 121


>Contig-U10929-1 (Contig-U10929-1Q) /CSM_Contig/Contig-U10929-1Q.Seq.d
          Length = 1727

 Score = 36.2 bits (18), Expect = 0.012
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                 
Query: 66  taatgtttgttggtacattggt 87
           ||||||| ||||||||||||||
Sbjct: 812 taatgttggttggtacattggt 833


>Contig-U12375-1 (Contig-U12375-1Q) /CSM_Contig/Contig-U12375-1Q.Seq.d
          Length = 1431

 Score = 34.2 bits (17), Expect = 0.048
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 2   aatttctttttatattt 18
           |||||||||||||||||
Sbjct: 100 aatttctttttatattt 84


  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: 3430
Number of Sequences: 6905
Number of extensions: 3430
Number of successful extensions: 1336
Number of sequences better than 10.0: 99
length of query: 184
length of database: 5,674,871
effective HSP length: 15
effective length of query: 169
effective length of database: 5,571,296
effective search space: 941549024
effective search space used: 941549024
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. 2
Homology vs DNA 
Query= Contig-U12677-1 (Contig-U12677-1Q) /CSM_Contig/Contig-U12677-1Q.Seq.d
         (184 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

(BJ336157) Dictyostelium discoideum cDNA clone:dda52n21, 5' ...   240   1e-59  1
(BJ332626) Dictyostelium discoideum cDNA clone:dda39d19, 5' ...   216   2e-52  1
(BJ334127) Dictyostelium discoideum cDNA clone:dda45a09, 5' ...   192   3e-45  1
(BJ336133) Dictyostelium discoideum cDNA clone:dda52i20, 5' ...   172   3e-39  1
(BJ334509) Dictyostelium discoideum cDNA clone:dda46n17, 5' ...    92   8e-15  1
(AC152081) Bos taurus clone CH240-2J4, WORKING DRAFT SEQUENC...    40   0.017  2
(AC175227) Atelerix albiventris clone LB4-484H11, WORKING DR...    34   0.064  2
(AC170058) Atelerix albiventris clone LB4-290K10, WORKING DR...    34   0.064  2
(AL355775) Arabidopsis thaliana DNA chromosome 3, BAC clone ...    46   0.40   1
(AP000427) Homo sapiens genomic DNA, chromosome 8q23, clone:...    46   0.40   1
(AC021001) Homo sapiens chromosome 8, clone RP11-419L20, com...    46   0.40   1
(AQ964085) LERGU53TR LERG Arabidopsis thaliana genomic clone...    46   0.40   1
(AQ964084) LERGU53TF LERG Arabidopsis thaliana genomic clone...    46   0.40   1
(FH440574) CHO_OF4617xa01r1.ab1 CHO_OF4 Nicotiana tabacum ge...    46   0.40   1
(FH088140) CHO_OF3877xi03f1.ab1 CHO_OF3 Nicotiana tabacum ge...    46   0.40   1
(AJ526347) Arabidopsis thaliana T-DNA flanking sequence, lef...    46   0.40   1
(DQ227736) Bacillus subtilis isolate DV3-A-1 quorum-sensing ...    46   0.40   1
(EA333237) Sequence 5729 from patent US 7306913.                   36   0.81   2
(AC158400) Pan troglodytes BAC clone CH251-530D15 from chrom...    36   0.84   2
(AC010354) Homo sapiens chromosome 5 clone CTD-2027D14, WORK...    36   0.85   2
(AC098585) Homo sapiens chromosome 4 clone RP11-25N23, WORKI...    36   0.85   2
(AC097492) Homo sapiens BAC clone RP11-264A4 from 4, complet...    36   0.86   2
(AP006656) Lotus japonicus genomic DNA, chromosome 1, clone:...    40   1.0    3
(BH763879) BMBAC314E09T7_PSU Brugia malayi Genomic Bac Libra...    36   1.1    2
(BH763308) BMBAC336D05SP6_PSU Brugia malayi Genomic Bac Libr...    36   1.1    2
(EA350422) Sequence 22914 from patent US 7306913.                  36   1.2    2
(AC185990) Pan troglodytes BAC clone CH251-344N16 from chrom...    44   1.6    1
(AC183985) Pan troglodytes BAC clone CH251-305G20 from chrom...    44   1.6    1
(AC182490) Pan troglodytes BAC clone CH251-430P12 from chrom...    44   1.6    1
(AC120782) Pan troglodytes clone rp43-45g12, complete sequence.    44   1.6    1
(AC120781) Pan troglodytes clone rp43-28m17, complete sequence.    44   1.6    1
(AL354682) Human DNA sequence from clone RP11-282L14 on chro...    44   1.6    1
(AC145214) Homo sapiens fosmid clone XXFOS-82587F5 from 2, c...    44   1.6    1
(AC073869) Homo sapiens BAC clone RP11-109E12 from 2, comple...    44   1.6    1
(AC129277) Rattus norvegicus clone CH230-9B13, *** SEQUENCIN...    44   1.6    1
(AC120839) Pan troglodytes clone rp43-5n22, WORKING DRAFT SE...    44   1.6    1
(AC108977) Rattus norvegicus clone CH230-287G14, WORKING DRA...    44   1.6    1
(AC097692) Rattus norvegicus clone CH230-62N8, *** SEQUENCIN...    44   1.6    1
(AC095553) Rattus norvegicus clone CH230-8B22, *** SEQUENCIN...    44   1.6    1
(AC225371) Pongo abelii chromosome UNKNOWN clone CH276-233M1...    44   1.6    1
(AC211708) Pongo abelii chromosome UNKNOWN clone CH276-364F1...    44   1.6    1
(AC210856) Pongo abelii chromosome UNKNOWN clone CH276-103D2...    44   1.6    1
(AC022629) Homo sapiens clone RP11-24O13, WORKING DRAFT SEQU...    44   1.6    1
(AQ485648) RPCI-11-257H21.TJ RPCI-11 Homo sapiens genomic cl...    44   1.6    1
(EI965803) SB_BBc236-A19.R SB_BBc Sorghum bicolor genomic 3'...    44   1.6    1
(BH954069) odi39f07.g1 B.oleracea002 Brassica oleracea genom...    44   1.6    1
(BH577973) BOHEM32TR BOHE Brassica oleracea genomic clone BO...    44   1.6    1
(CP000673) Clostridium kluyveri DSM 555, complete genome.          44   1.6    1
(BH709730) BOMLE73TR BO_2_3_KB Brassica oleracea genomic clo...    28   2.0    3
(AC177496) Strongylocentrotus purpuratus clone R3-61P11, WOR...    34   2.0    4
(DL016928) Diagnosis of existing illnesses or that praedispo...    34   2.2    2
(DL016927) Diagnosis of existing illnesses or that praedispo...    34   2.2    2
(AC200995) Strongylocentrotus purpuratus clone R3-12C5, WORK...    38   2.5    2
(AC008249) Homo sapiens 3 BAC RP11-211P13 (Roswell Park Canc...    32   3.1    2
(AC170059) Atelerix albiventris clone LB4-528L17, WORKING DR...    34   3.1    2
(AC175796) Atelerix albiventris clone LB4-349O14, WORKING DR...    34   3.1    2
(CG447840) OGTAS87TV ZM_0.7_1.5_KB Zea mays genomic clone ZM...    34   3.7    2
(AL445565) Mycoplasma pulmonis (strain UAB CTIP) complete ge...    34   3.8    5
(CG754213) P049-3-C11.ya Ppa EcoRI BAC Library Pristionchus ...    34   4.0    2
(AJ856747) Brassica rapa subsp. pekinensis GSS, clone KBrH05...    32   4.1    2
(EI487868) PV_GBa0102O16.r PV_GBa Phaseolus vulgaris genomic...    34   4.1    2
(CF150733) AGENCOURT_14927688 NICHD_XGC_Emb8 Xenopus (Silura...    32   4.1    2
(EL913315) INIT2_59_D06.g2_A006 G5 trophont cDNA (INIT2) Ich...    32   4.2    2
(EJ250832) 1095344031366 Global-Ocean-Sampling_GS-27-01-01-1...    32   4.9    3
(AM452457) Vitis vinifera contig VV78X022673.4, whole genome...    34   5.5    3
(BX663612) Zebrafish DNA sequence from clone DKEY-24M14 in l...    42   6.3    1
(AX346124) Sequence 1195 from Patent WO0200928.                    42   6.3    1
(AL355798) Human DNA sequence from clone RP11-417A17 on chro...    42   6.3    1
(AC108103) Homo sapiens chromosome 5 clone RP11-197O8, compl...    42   6.3    1
(AC097679) Rattus norvegicus clone CH230-90C4, WORKING DRAFT...    42   6.3    1
(CU928495) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   6.3    1
(AL591717) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    42   6.3    1
(AC230368) Bos taurus clone CH240-511A13, WORKING DRAFT SEQU...    42   6.3    1
(AC220374) Bos taurus clone CH240-360B6, WORKING DRAFT SEQUE...    42   6.3    1
(AC215498) Zea mays chromosome 8 clone CH201-478G23; ZMMBBc0...    42   6.3    1
(AC204072) Macaca mulatta clone CH250-454C19, WORKING DRAFT ...    42   6.3    1
(AC179010) Strongylocentrotus purpuratus clone R3-32H16, WOR...    42   6.3    1
(EJ198953) 1092344281028 Global-Ocean-Sampling_GS-27-01-01-1...    42   6.3    1
(DU910496) 332224 Tomato EcoRI BAC Library Solanum lycopersi...    42   6.3    1
(CZ421402) 1017105 RP42 Bos taurus genomic clone RP42-43G22,...    42   6.3    1
(CU077942) Equus caballus GSS, BAC clone CH241-170J3, T7 end...    42   6.3    1
(CT431949) Sus scrofa genomic clone CH242-502M21, genomic su...    42   6.3    1
(CE824018) tigr-gss-dog-17000318981789 Dog Library Canis lup...    42   6.3    1
(CE182599) tigr-gss-dog-17000326793863 Dog Library Canis lup...    42   6.3    1
(CC429378) PUHJN41TB ZM_0.6_1.0_KB Zea mays genomic clone ZM...    42   6.3    1
(CC267304) CH261-30A10_RM1.1 CH261 Gallus gallus genomic clo...    42   6.3    1
(BH740229) gf27e09.b1 TO1000 Brassica oleracea genomic clone...    42   6.3    1
(DN574816) 91973769 Sea Urchin primary mesenchyme cell cDNA ...    42   6.3    1
(EY702389) CS00-C3-701-006-D11-CT.F Sweet orange fruit, deve...    42   6.3    1
(AJ235271) Rickettsia prowazekii strain Madrid E, complete g...    42   6.3    1
(AC178742) Strongylocentrotus purpuratus clone R3-14A04, WOR...    34   6.8    3
(AC187948) Atelerix albiventris clone LB4-89D3, WORKING DRAF...    38   7.7    2
(AC007474) Drosophila melanogaster, chromosome 2R, region 49...    40   7.7    3
(AC173936) Atelerix albiventris clone LB4-66O19, WORKING DRA...    38   7.7    2
(AC020286) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    40   7.8    3
(AC095088) Rattus norvegicus clone CH230-7J15, *** SEQUENCIN...    34   8.2    4
(AC090572) Homo sapiens chromosome 8, clone RP11-386D6, comp...    36   9.0    2
(CU467542) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    32   9.0    5
(CP000107) Ehrlichia canis str. Jake, complete genome.             32   9.7    2
(DN565603) 90146690 Sea Urchin primary mesenchyme cell cDNA ...    38   9.7    2

>(BJ336157) Dictyostelium discoideum cDNA clone:dda52n21, 5' end,
           single read.
          Length = 179

 Score =  240 bits (121), Expect = 1e-59
 Identities = 121/121 (100%)
 Strand = Plus / Plus


Query: 1   caatttctttttatattttcgttagtagaaaagtaaaataagagaaagtatttataaatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caatttctttttatattttcgttagtagaaaagtaaaataagagaaagtatttataaatt 60


Query: 61  tttagtaatgtttgttggtacattggtcattattatatgcacgacattgatcattattat 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tttagtaatgtttgttggtacattggtcattattatatgcacgacattgatcattattat 120


Query: 121 t 121
           |
Sbjct: 121 t 121

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 203,192,923
Number of extensions: 14196029
Number of successful extensions: 4441948
Number of sequences better than 10.0: 101
Length of query: 184
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 162
Effective length of database: 93,199,600,587
Effective search space: 15098335295094
Effective search space used: 15098335295094
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 4
Homology vs Protein 
Query= Contig-U12677-1 (Contig-U12677-1Q) /CSM_Contig/Contig-U12677-1Q.Seq.d
         (184 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: 127,287,462
Number of extensions: 1007810
Number of successful extensions: 1028
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1028
Number of HSP's successfully gapped: 0
Length of query: 61
Length of database: 1,051,180,864
Length adjustment: 33
Effective length of query: 28
Effective length of database: 944,374,417
Effective search space: 26442483676
Effective search space used: 26442483676
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: 0.97  gvh: 0.47  alm: 0.14  top: 0.67  tms: 0.07  mit: 0.35  mip: 0.07
 nuc: 0.23  erl: 0.00  erm: 1.20  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 %: cytoplasmic
	 24.0 %: mitochondrial
	 24.0 %: nuclear
	  8.0 %: plasma membrane
	  8.0 %: endoplasmic reticulum
	  4.0 %: vesicles of secretory system
	  4.0 %: peroxisomal

>> prediction for Contig-U12677-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 5
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