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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-U07107-1
Contig ID Contig-U07107-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Contig-U07107-1Q.Seq.d
CCACGNGNCCGATTAAACGATATGGATAAAGTTTTTAATGTTGGTAAATT
AGTTGATTTTCAATGGAAATTGGGCGTTTCAATTGCTTCAAATCACTCTT
CTCAATTAAATACACCATTCATTACAGTTTTTGTTAAAGTTTTAGATTCA
AATAGTGAAGTAACATCACATTCTTTTGAATTAACTATACCAGAATTTAA
GAATTTTGCACAACAATTTAAAGATATGTCAAACATGATTGAAACCTTAT
AAAAGAAAGGAAAGTTATTGTTATATTAGAAAAATAAAAAAAAAATAAAA
AAAAAATAAAAATAGAAATAATAGTGATATATAAATGAAATTAAAAAAAT
TACTCTAGGGTTGACAAAGGAGTTAATATGTTTCAATGAATAAAAAAATG
GTAGATGTGACAGGGTTGAGTTTAAT
Gap no gap
Contig length 426
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4033924
End point 4034332
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U07107
List of clone(s) 

est1=VSK428Z,1,427
est2=VSK428F,12,310
Translated Amino Acid sequence 
PRXRLNDMDKVFNVGKLVDFQWKLGVSIASNHSSQLNTPFITVFVKVLDSNSEVTSHSFE
LTIPEFKNFAQQFKDMSNMIETL*kkgkllly*knkkkikkk*k*k***yineikkitlg
ltkelicfne*kngrcdrvefn
Translated Amino Acid sequence (All Frames) 
Frame A:
PRXRLNDMDKVFNVGKLVDFQWKLGVSIASNHSSQLNTPFITVFVKVLDSNSEVTSHSFE
LTIPEFKNFAQQFKDMSNMIETL*kkgkllly*knkkkikkk*k*k***yineikkitlg
ltkelicfne*kngrcdrvefn


Frame B:
hxxd*tiwikflmlvn*lifngnwafqllqitlln*ihhslqfllkf*iqivk*hhilln
*lyqnlrilhnnlkicqt*lkpykrkesycyirkikkk*kknknrnnsdi*mklkkll*g
*qrs*yvsmnkkmvdvtglsl


Frame C:
txpikryg*sf*cw*is*fsmeigrfncfkslfsikytihysfc*sfrfk**snitff*i
nytri*efctti*ryvkhd*nlikerkvivilek*kknkkkikieiiviyk*n*knysrv
dkgvnmfq*ikkw*m*qg*v*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07107-1 (Contig-U07107-1Q)
/CSM_Contig/Contig-U07107-1Q.Seq.d
         (426 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Conti...   541  e-154
Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U13931-1 (Contig-U13931-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U09792-1 (Contig-U09792-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U08104-1 (Contig-U08104-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U12176-1 (Contig-U12176-1Q) /CSM_Contig/Conti...    32  0.46
Contig-U11288-1 (Contig-U11288-1Q) /CSM_Contig/Conti...    32  0.46
Contig-U10403-1 (Contig-U10403-1Q) /CSM_Contig/Conti...    32  0.46
Contig-U09114-1 (Contig-U09114-1Q) /CSM_Contig/Conti...    32  0.46
Contig-U07084-1 (Contig-U07084-1Q) /CSM_Contig/Conti...    32  0.46

>Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Contig-U07107-1Q.Seq.d
          Length = 426

 Score =  541 bits (273), Expect = e-154
 Identities = 279/279 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ccacgngnccgattaaacgatatggataaagtttttaatgttggtaaattagttgatttt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ccacgngnccgattaaacgatatggataaagtttttaatgttggtaaattagttgatttt 60

                                                                       
Query: 61  caatggaaattgggcgtttcaattgcttcaaatcactcttctcaattaaatacaccattc 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  caatggaaattgggcgtttcaattgcttcaaatcactcttctcaattaaatacaccattc 120

                                                                       
Query: 121 attacagtttttgttaaagttttagattcaaatagtgaagtaacatcacattcttttgaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 attacagtttttgttaaagttttagattcaaatagtgaagtaacatcacattcttttgaa 180

                                                                       
Query: 181 ttaactataccagaatttaagaattttgcacaacaatttaaagatatgtcaaacatgatt 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 ttaactataccagaatttaagaattttgcacaacaatttaaagatatgtcaaacatgatt 240

                                                  
Query: 241 gaaaccttataaaagaaaggaaagttattgttatattag 279
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 241 gaaaccttataaaagaaaggaaagttattgttatattag 279


 Score =  143 bits (72), Expect = 2e-34
 Identities = 100/114 (87%)
 Strand = Plus / Plus

                                                                       
Query: 313 tagaaataatagtgatatataaatgaaattnnnnnnnttactctagggttgacaaaggag 372
           ||||||||||||||||||||||||||||||       |||||||||||||||||||||||
Sbjct: 313 tagaaataatagtgatatataaatgaaattaaaaaaattactctagggttgacaaaggag 372

                                                                 
Query: 373 ttaatatgtttcaatgaatnnnnnnntggtagatgtgacagggttgagtttaat 426
           |||||||||||||||||||       ||||||||||||||||||||||||||||
Sbjct: 373 ttaatatgtttcaatgaataaaaaaatggtagatgtgacagggttgagtttaat 426


>Contig-U11185-1 (Contig-U11185-1Q) /CSM_Contig/Contig-U11185-1Q.Seq.d
          Length = 961

 Score = 36.2 bits (18), Expect = 0.029
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 141 tttagattcaaatagtga 158
           ||||||||||||||||||
Sbjct: 887 tttagattcaaatagtga 904


>Contig-U13931-1 (Contig-U13931-1Q) /CSM_Contig/Contig-U13931-1Q.Seq.d
          Length = 1359

 Score = 34.2 bits (17), Expect = 0.12
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 77  tttcaattgcttcaaat 93
           |||||||||||||||||
Sbjct: 261 tttcaattgcttcaaat 245


  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: 5124
Number of Sequences: 6905
Number of extensions: 5124
Number of successful extensions: 551
Number of sequences better than 10.0: 181
length of query: 426
length of database: 5,674,871
effective HSP length: 16
effective length of query: 410
effective length of database: 5,564,391
effective search space: 2281400310
effective search space used: 2281400310
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 2008.11.11
Homology vs DNA 
Query= Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Contig-U07107-1Q.Seq.d
         (426 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

(AU271178) Dictyostelium discoideum vegetative cDNA clone:VS...   470   e-155  3
(AU271177) Dictyostelium discoideum vegetative cDNA clone:VS...   531   e-147  1
(AC095229) Rattus norvegicus clone CH230-9D21, *** SEQUENCIN...    50   0.064  1
(AC110391) Rattus norvegicus clone CH230-30H5, *** SEQUENCIN...    48   0.25   1
(BV070763) S209P6350FG2.T0 C3H/HeJ Mus musculus STS genomic,...    40   1.1    2
(BD453051) Diagnosis of Diseases Associated with tumor suppr...    34   1.5    3
(AX251530) Sequence 498 from Patent WO0168912.                     34   1.5    3
(CQ584907) Sequence 12665 from Patent WO0171042.                   44   4.0    1
(CQ584906) Sequence 12664 from Patent WO0171042.                   44   4.0    1
(AE014296) Drosophila melanogaster chromosome 3L, complete s...    44   4.0    1
(AC105263) Drosophila melanogaster 3L BAC RP98-48G3 (Roswell...    44   4.0    1
(AP003693) Homo sapiens genomic DNA, chromosome 8q23, clone:...    44   4.0    1
(AP003547) Homo sapiens genomic DNA, chromosome 8q23, clone:...    44   4.0    1
(AC090819) Homo sapiens chromosome 8, clone CTD-2544L4, comp...    44   4.0    1
(AC026798) Homo sapiens chromosome 5 clone CTD-2312P21, comp...    44   4.0    1
(AC015105) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    44   4.0    1
(AC006492) Drosophila melanogaster strain y chromosome 3 clo...    44   4.0    1
(AM605403) Entamoeba invadens IP1 GSS, clone inv048f08.p1k.        44   4.0    1
(CZ213619) AIAA-aah38k07.g1 Ancylostoma caninum whole genome...    44   4.0    1
(BZ387261) EINCQ60TF EI_10_12_KB Entamoeba invadens genomic ...    44   4.0    1
(CU424487) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   4.6    2
(AC131399) Rattus norvegicus clone CH230-102I19, WORKING DRA...    36   4.7    3
(BH095374) RPCI-24-297N22.TV RPCI-24 Mus musculus genomic cl...    40   4.8    2
(AC163882) Bos taurus clone CH240-130P24, WORKING DRAFT SEQU...    32   7.2    2
(AC168417) Strongylocentrotus purpuratus clone R3-4002B10, W...    32   8.3    5

>(AU271178) Dictyostelium discoideum vegetative cDNA clone:VSK428,
           3' end single read.
          Length = 427

 Score =  470 bits (237), Expect(3) = e-155
 Identities = 267/279 (95%)
 Strand = Plus / Plus


Query: 1   ccacgngnccgattaaacgatatggataaagtttttaatgttggtaaattagttgatttt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ccacgngnccgattaaacgatatggataaagtttttaatgttggtaaattagttgatttt 60


Query: 61  caatggaaattgggcgtttcaattgcttcaaatcactcttctcaattaaatacaccattc 120
           |||||||||||||| ||||||||||||||||||| ||||| ||||||||| || ||||||
Sbjct: 61  caatggaaattgggngtttcaattgcttcaaatcnctcttntcaattaaanacnccattc 120


Query: 121 attacagtttttgttaaagttttagattcaaatagtgaagtaacatcacattcttttgaa 180
           |||||||||||||||||||||||||||||||| ||||||| |||||| ||||||||||||
Sbjct: 121 attacagtttttgttaaagttttagattcaaanagtgaagnaacatcncattcttttgaa 180


Query: 181 ttaactataccagaatttaagaattttgcacaacaatttaaagatatgtcaaacatgatt 240
           ||||||| ||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct: 181 ttaactanaccagaatttaagaattttgcncaacaatttaaagatatgtcaaacatgatt 240


Query: 241 gaaaccttataaaagaaaggaaagttattgttatattag 279
           ||||||||| |||| ||||||||||||||||||||||||
Sbjct: 241 gaaaccttanaaaanaaaggaaagttattgttatattag 279

 Score = 81.8 bits (41), Expect(3) = e-155
 Identities = 41/41 (100%)
 Strand = Plus / Plus


Query: 351 tactctagggttgacaaaggagttaatatgtttcaatgaat 391
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 351 tactctagggttgacaaaggagttaatatgtttcaatgaat 391

 Score = 56.0 bits (28), Expect(3) = e-155
 Identities = 28/28 (100%)
 Strand = Plus / Plus


Query: 399 tggtagatgtgacagggttgagtttaat 426
           ||||||||||||||||||||||||||||
Sbjct: 399 tggtagatgtgacagggttgagtttaat 426

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 415,503,369
Number of extensions: 24882931
Number of successful extensions: 2101789
Number of sequences better than 10.0: 25
Length of query: 426
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 403
Effective length of database: 93,106,754,628
Effective search space: 37522022115084
Effective search space used: 37522022115084
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Contig-U07107-1Q.Seq.d
         (426 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54MA5) RecName: Full=COMM domain-containing protein 6;              152   5e-36
AY626040_1(AY626040|pid:none) Branchiostoma belcheri tsingtaunes...    84   1e-15
BC171118_1(BC171118|pid:none) Xenopus tropicalis COMM domain con...    84   1e-15
BT075212_1(BT075212|pid:none) Osmerus mordax clone omor-eva-513-...    78   1e-13
(Q3V4B5) RecName: Full=COMM domain-containing protein 6;  &AK004...    77   1e-13
(Q7Z4G1) RecName: Full=COMM domain-containing protein 6;  &AF169...    74   2e-12
AL137244_2(AL137244|pid:none) Human DNA sequence from clone RP11...    64   1e-09
BC063343_1(BC063343|pid:none) Xenopus tropicalis COMM domain con...    41   0.015
BT073299_1(BT073299|pid:none) Oncorhynchus mykiss clone omyk-evn...    41   0.015
(Q550I8) RecName: Full=COMM domain-containing protein 4;               39   0.044
AK008447_1(AK008447|pid:none) Mus musculus adult male small inte...    39   0.057
BT075251_1(BT075251|pid:none) Osmerus mordax clone omor-eva-007-...    37   0.17
(Q3MHX1) RecName: Full=COMM domain-containing protein 7;  &BC104...    37   0.17
AY542162_1(AY542162|pid:none) Homo sapiens COMMD7 mRNA, complete...    37   0.22
(Q86VX2) RecName: Full=COMM domain-containing protein 7;  &AK027...    37   0.22
BC003310_1(BC003310|pid:none) Mus musculus COMM domain containin...    36   0.37
AL929021_2(AL929021|pid:none) Mouse DNA sequence from clone RP23...    36   0.37
AK089926_1(AK089926|pid:none) Mus musculus B cells CRL-1669 BCL1...    36   0.37
AF182421_1(AF182421|pid:none) Homo sapiens MDS022 (MDS022) mRNA,...    35   0.63
BC078326_1(BC078326|pid:none) Danio rerio zgc:101056, mRNA (cDNA...    35   0.63
(Q86I14) RecName: Full=COMM domain-containing protein 7;  &AC116...    35   0.63
(Q9NX08) RecName: Full=COMM domain-containing protein 8;  &AK000...    35   0.63
BC099753_1(BC099753|pid:none) Rattus norvegicus COMM domain cont...    35   1.1
BC019826_1(BC019826|pid:none) Homo sapiens COMM domain containin...    34   1.4
AJ719495_1(AJ719495|pid:none) Gallus gallus mRNA for hypothetica...    34   1.8
AE017348_132(AE017348|pid:none) Cryptococcus neoformans var. neo...    33   4.1
CP000499_45(CP000499|pid:none) Pichia stipitis CBS 6054 chromoso...    33   4.1
CR761140_1(CR761140|pid:none) Xenopus tropicalis finished cDNA, ...    32   6.9
(Q54QK4) RecName: Full=COMM domain-containing protein 3;               32   6.9
(P62371) RecName: Full=Histidyl-tRNA synthetase;          EC=6.1...    32   9.1
BT074294_1(BT074294|pid:none) Oncorhynchus mykiss clone omyk-evo...    32   9.1
BC084128_1(BC084128|pid:none) Xenopus laevis hypothetical LOC495...    32   9.1

>(Q54MA5) RecName: Full=COMM domain-containing protein 6;
          Length = 76

 Score =  152 bits (383), Expect = 5e-36
 Identities = 75/75 (100%), Positives = 75/75 (100%)
 Frame = +1

Query: 22  MDKVFNVGKLVDFQWKLGVSIASNHSSQLNTPFITVFVKVLDSNSEVTSHSFELTIPEFK 201
           MDKVFNVGKLVDFQWKLGVSIASNHSSQLNTPFITVFVKVLDSNSEVTSHSFELTIPEFK
Sbjct: 1   MDKVFNVGKLVDFQWKLGVSIASNHSSQLNTPFITVFVKVLDSNSEVTSHSFELTIPEFK 60

Query: 202 NFAQQFKDMSNMIET 246
           NFAQQFKDMSNMIET
Sbjct: 61  NFAQQFKDMSNMIET 75

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: 504,105,276
Number of extensions: 7445164
Number of successful extensions: 13543
Number of sequences better than 10.0: 32
Number of HSP's gapped: 13534
Number of HSP's successfully gapped: 32
Length of query: 142
Length of database: 1,040,966,779
Length adjustment: 105
Effective length of query: 37
Effective length of database: 704,516,854
Effective search space: 26067123598
Effective search space used: 26067123598
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: 29 (15.8 bits)
PSORT 

 psg: 0.77  gvh: 0.49  alm: 0.49  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.02
 nuc: 0.00  erl: 0.00  erm: 0.40  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 

	 36.0 %: cytoplasmic
	 28.0 %: nuclear
	 20.0 %: mitochondrial
	  8.0 %: vacuolar
	  4.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U07107-1 is cyt
VS (DIR, S) 1
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) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0