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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U10043-1
Contig ID Contig-U10043-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Contig-U10043-1Q.Seq.d
AGCTTAAATGACAAATTTAAGGTTTAAGGGGAAAAGATAGGAGAAATTGA
AGAGGAACCAGAAAAAAAACCAACTAAAAGCAGATCAAGATCATCTTTAG
CCGCTGCAACAAAAACTGTAGCTAAAACCCCAACTAGATCAAAATCATCA
CTTAAAGAAAATGAAACTAAAGAAAAAGAAACCAAAGAAACCAAAGAAAA
AGAAGCTAAAGAAAAAGAAGCTAAAGAAAAAGAAGCTAAAGAAAAAGAAA
CCAAAGAAAATGAAACAAAAGAAAAACCAAAAGGTAAAGGAAAAGAAACA
AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAA
AGAAAAAGAAAAAGAAAAGGAAAAGGAAAAGGAAAAGGAAAAAGAAAAAG
AAAAAGAAAAAGAAAAGGAAAAGGAAAAAGAAAAGGAAAAAGAAAAAGAA
AAACTAAAGGAAAAAGAAAAAGAAAAAGAAAAAGAAGCATCAGAGGGATC
AGATTCAGATTCAGAAACTAAAGAATCTGGTAAAAAGAGAAAATCACCAT
CAACAACAGCATCAAAAAAGAAAGCAAAGGTCACAGCCTCTCGTTCAAAT
GTTACTAATAACACCAAAGAAGAGAGTGGTTCTTCAAACTGATACTGATG
CTTCCTCAGCATCCGATAGTACTGCTCCAGAAGCATCCACTACCACCACC
ACTACCGAACCAAAGAAATCAATTCCAATGCCATCAAAATCTGCTGTC
Gap no gap
Contig length 748
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 4165369
End point 4166069
Strand (PLUS/MINUS) PLUS
Number of clones 5
Number of EST 5
Link to clone list U10043
List of clone(s) 

est1=VSE117E,1,461
est2=VFK339Z,169,749
est3=VFA439Z,175,749
est4=VFK882Z,175,749
est5=CFA635Z,267,746
Translated Amino Acid sequence 
slndkfkv*GEKIGEIEEEPEKKPTKSRSRSSLAAATKTVAKTPTRSKSSLKENETKEKE
TKETKEKEAKEKEAKEKEAKEKETKENETKEKPKGKGKETKEKEKEKEKEKEKEKEKEKE
KEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKLKEKEKEKEKEASEGSDSDSETKESGKKR
KSPSTTASKKKAKVTASRSNVTNNTKEESGSSN*y*cflsir*ycsrsihyhhhyrtkei
nsnaikicc
Translated Amino Acid sequence (All Frames) 
Frame A:
slndkfkv*GEKIGEIEEEPEKKPTKSRSRSSLAAATKTVAKTPTRSKSSLKENETKEKE
TKETKEKEAKEKEAKEKEAKEKETKENETKEKPKGKGKETKEKEKEKEKEKEKEKEKEKE
KEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKLKEKEKEKEKEASEGSDSDSETKESGKKR
KSPSTTASKKKAKVTASRSNVTNNTKEESGSSN*y*cflsir*ycsrsihyhhhyrtkei
nsnaikicc


Frame B:
a*mtnlrfkgkr*eklkrnqkknqlkadqdhl*plqqkl*lkpqldqnhhlkkmklkkkk
pkkpkkkklkkkklkkkklkkkkpkkmkqkknqkvkekkqkkkkkkkkkkkkkkkkkkkk
kkrkrkrkrkkkkkkkkkrkrkkkrkkkkkn*rkkkkkkkkkhqrdqiqiqklknlvkre
nhhqqqhqkrkqrsqplvqmllitpkkrvvlqtdtdassasdstapeasttttttepkks
ipmpsksav


Frame C:
lk*qi*glrgkdrrn*rgtrkktn*kqikiifsrcnkncs*npn*ikiit*rk*n*rkrn
qrnqrkrs*rkrs*rkrs*rkrnqrk*nkrktkr*rkrnkrkrkrkrkrkrkrkrkrkrk
rkgkgkgkgkrkrkrkrkgkgkrkgkrkrktkgkrkrkrkrsirgirfrfrn*riw*kek
itinnsikkeskghslsfkcy**hqrrewffklilmlpqhpivllqkhplppplpnqrnq
fqchqnll
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10043-1 (Contig-U10043-1Q)
/CSM_Contig/Contig-U10043-1Q.Seq.d
         (748 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Conti...   525  e-149
Contig-U14632-1 (Contig-U14632-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U13396-1 (Contig-U13396-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U12120-1 (Contig-U12120-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U09072-1 (Contig-U09072-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U13922-1 (Contig-U13922-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U12945-1 (Contig-U12945-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U11177-1 (Contig-U11177-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U11146-1 (Contig-U11146-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U06233-1 (Contig-U06233-1Q) /CSM_Contig/Conti...    38  0.013

>Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Contig-U10043-1Q.Seq.d
          Length = 748

 Score =  525 bits (265), Expect = e-149
 Identities = 265/265 (100%)
 Strand = Plus / Plus

                                                                       
Query: 484 gaagcatcagagggatcagattcagattcagaaactaaagaatctggtaaaaagagaaaa 543
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 484 gaagcatcagagggatcagattcagattcagaaactaaagaatctggtaaaaagagaaaa 543

                                                                       
Query: 544 tcaccatcaacaacagcatcaaaaaagaaagcaaaggtcacagcctctcgttcaaatgtt 603
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 544 tcaccatcaacaacagcatcaaaaaagaaagcaaaggtcacagcctctcgttcaaatgtt 603

                                                                       
Query: 604 actaataacaccaaagaagagagtggttcttcaaactgatactgatgcttcctcagcatc 663
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 604 actaataacaccaaagaagagagtggttcttcaaactgatactgatgcttcctcagcatc 663

                                                                       
Query: 664 cgatagtactgctccagaagcatccactaccaccaccactaccgaaccaaagaaatcaat 723
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 664 cgatagtactgctccagaagcatccactaccaccaccactaccgaaccaaagaaatcaat 723

                                    
Query: 724 tccaatgccatcaaaatctgctgtc 748
           |||||||||||||||||||||||||
Sbjct: 724 tccaatgccatcaaaatctgctgtc 748


 Score =  220 bits (111), Expect = 2e-57
 Identities = 127/135 (94%)
 Strand = Plus / Plus

                                                                       
Query: 1   agcttaaatgacaaatttaaggtttaaggggaaaagataggagaaattgaagaggaacca 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   agcttaaatgacaaatttaaggtttaaggggaaaagataggagaaattgaagaggaacca 60

                                                                       
Query: 61  gnnnnnnnnccaactaaaagcagatcaagatcatctttagccgctgcaacaaaaactgta 120
           |        |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gaaaaaaaaccaactaaaagcagatcaagatcatctttagccgctgcaacaaaaactgta 120

                          
Query: 121 gctaaaaccccaact 135
           |||||||||||||||
Sbjct: 121 gctaaaaccccaact 135


>Contig-U14632-1 (Contig-U14632-1Q) /CSM_Contig/Contig-U14632-1Q.Seq.d
          Length = 652

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 508 gattcagaaactaaagaatc 527
           ||||||||||||||||||||
Sbjct: 152 gattcagaaactaaagaatc 171


>Contig-U13396-1 (Contig-U13396-1Q) /CSM_Contig/Contig-U13396-1Q.Seq.d
          Length = 262

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Minus

                               
Query: 687 ccactaccaccaccactacc 706
           ||||||||||||||||||||
Sbjct: 215 ccactaccaccaccactacc 196


  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: 5638
Number of Sequences: 6905
Number of extensions: 5638
Number of successful extensions: 901
Number of sequences better than 10.0: 184
length of query: 748
length of database: 5,674,871
effective HSP length: 16
effective length of query: 732
effective length of database: 5,564,391
effective search space: 4073134212
effective search space used: 4073134212
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.11.18
Homology vs DNA 
Query= Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Contig-U10043-1Q.Seq.d
         (748 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

(BJ428840) Dictyostelium discoideum cDNA clone:ddv1n10, 3' e...   511   e-140  1
(BJ433319) Dictyostelium discoideum cDNA clone:ddv21n09, 3' ...   299   e-135  2
(BJ433734) Dictyostelium discoideum cDNA clone:ddv22d22, 3' ...   299   e-135  2
(BJ373236) Dictyostelium discoideum cDNA clone:ddc2e10, 3' e...   240   6e-59  1
(AU262882) Dictyostelium discoideum vegetative cDNA clone:VS...   121   2e-49  2
(D16466) Dictyostelium discoideum mitochondrial genes for la...   100   1e-16  1
(AB000109) Dictyostelium discoideum mitochondrial DNA, compl...   100   1e-16  1
(AU266104) Dictyostelium discoideum vegetative cDNA clone:VS...   100   1e-16  1
(AU061840) Dictyostelium discoideum slug cDNA, clone SLG289.      100   1e-16  1
(AU271030) Dictyostelium discoideum vegetative cDNA clone:VS...    98   6e-16  1
(AU262222) Dictyostelium discoideum vegetative cDNA clone:VS...    98   6e-16  1
(AU261387) Dictyostelium discoideum vegetative cDNA clone:VS...    98   6e-16  1
(AU264639) Dictyostelium discoideum vegetative cDNA clone:VS...    82   3e-11  1
(AU264638) Dictyostelium discoideum vegetative cDNA clone:VS...    80   1e-10  1
(AL138958) Human DNA sequence from clone RP11-206I15 on chro...    48   0.48   1
(AQ678528) HS_2130_B2_G01_T7C CIT Approved Human Genomic Spe...    48   0.48   1
(AF125464) Caenorhabditis elegans cosmid Y48A5B, complete se...    42   2.1    2
(FG080259) UI-FF-IH0-aau-o-05-0-UI.r1 Ceratitis capitata adu...    40   3.9    2
(DQ121025) Hucho taimen clone ZA-23 microsatellite sequence.       42   4.4    2
(EH066425) PMDCB68TR Perkinsus marinus small insert cDNA lib...    38   4.4    2
(EH073085) PMDAV58TR Perkinsus marinus small insert cDNA lib...    38   4.6    2
(G76869) S208P6680FH6.T0 129S1/SvImJ Mus musculus STS genomi...    44   7.4    1
(AC158973) Mus musculus chromosome 15, clone RP24-236A19, co...    44   7.4    1
(AC124543) Mus musculus BAC clone RP23-264A21 from chromosom...    44   7.4    1
(AC138130) Medicago truncatula clone mth2-31d24, complete se...    44   7.4    1
(CU928775) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   7.4    1
(AC207632) Zea mays chromosome 10 clone CH201-167A8; ZMMBBc0...    44   7.4    1
(AC180160) Strongylocentrotus purpuratus clone R3-4003B3, WO...    44   7.4    1
(CZ590080) OA_BBa0183M20.f OA_BBa Oryza alta genomic clone O...    44   7.4    1
(CG927077) MBEFH90TF mth2 Medicago truncatula genomic clone ...    44   7.4    1
(CC002870) PUDJM85TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    44   7.4    1
(DY290874) IC0AAA76CE08RM1 CitNFL Citrus clementina cDNA 5',...    44   7.4    1
(DY278886) IC0AAA47DE04RM1 CitNFL Citrus clementina cDNA 5',...    44   7.4    1
(CX672396) UCRCS10_16F10_g Madame Vinous Sweet Orange Multip...    44   7.4    1
(CX526193) s13dNF29C03AT022_510130 Aphid-Infected Shoots Med...    44   7.4    1
(CK933118) CGF1004347_E10 Developing fruit juice sac at 38 D...    44   7.4    1
(FE896705) C1-I21 Adult juvenile early flowering trifoliate ...    44   7.4    1
(FE896704) C1-H21 Adult juvenile early flowering trifoliate ...    44   7.4    1
(EY976973) C1I21 Juvenile early flowering trifoliate orange ...    44   7.4    1
(EY883283) LT33-C1-003-082-G05-CT.F Tahiti lime leaf, greenh...    44   7.4    1
(EY800843) CR05-C3-701-079-A05-CT.F Mandarin fruit, developm...    44   7.4    1
(EY793741) CR05-C3-701-010-B06-CT.F Mandarin fruit, developm...    44   7.4    1
(EY776207) CR05-C1-103-015-C07-CT.F Mandarin leaf, infected ...    44   7.4    1
(EY670822) CS00-C1-102-079-G01-CT.F Sweet orange leaf, infec...    44   7.4    1
(EY669882) CS00-C1-102-052-F06-CT.F Sweet orange leaf, infec...    44   7.4    1
(EY665649) CS00-C1-102-092-A07-CT.F Sweet orange leaf, infec...    44   7.4    1
(EY650696) CS00-C1-100-013-G10-CT.F Sweet orange leaf, green...    44   7.4    1
(EY433437) 1I21 Poncirus trifoliata Suppression Subtractive ...    44   7.4    1
(EY433436) C1H21 Poncirus trifoliata Suppression Subtractive...    44   7.4    1
(EY348140) CAWZ16333.fwd CAWZ Helobdella robusta Primary Lat...    44   7.4    1
(EY341956) CAWZ11448.fwd CAWZ Helobdella robusta Primary Lat...    44   7.4    1
(EY308522) CAWX21078.fwd CAWX Helobdella robusta Primary Ear...    44   7.4    1
(EY308360) CAWX20987.fwd CAWX Helobdella robusta Primary Ear...    44   7.4    1
(EY297217) CAWX13241.fwd CAWX Helobdella robusta Primary Ear...    44   7.4    1
(EY079345) CAZI13759.rev CAZI Artemisia annua normalized lea...    44   7.4    1
(EY077116) CAZI12633.rev CAZI Artemisia annua normalized lea...    44   7.4    1
(BJ364380) Dictyostelium discoideum cDNA clone:ddc31c16, 5' ...    34   9.9    2

>(BJ428840) Dictyostelium discoideum cDNA clone:ddv1n10, 3' end,
           single read.
          Length = 577

 Score =  511 bits (258), Expect = e-140
 Identities = 260/261 (99%)
 Strand = Plus / Minus


Query: 488 catcagagggatcagattcagattcagaaactaaagaatctggtaaaaagagaaaatcac 547
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 262 catcagagggatcagattcagattcagaaactaaagaatctggtaaaaagagaaaatcac 203


Query: 548 catcaacaacagcatcaaaaaagaaagcaaaggtcacagcctctcgttcaaatgttacta 607
           ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 202 catcaacaacagcatcaaaaaagaaagcaaaggtcncagcctctcgttcaaatgttacta 143


Query: 608 ataacaccaaagaagagagtggttcttcaaactgatactgatgcttcctcagcatccgat 667
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 142 ataacaccaaagaagagagtggttcttcaaactgatactgatgcttcctcagcatccgat 83


Query: 668 agtactgctccagaagcatccactaccaccaccactaccgaaccaaagaaatcaattcca 727
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82  agtactgctccagaagcatccactaccaccaccactaccgaaccaaagaaatcaattcca 23


Query: 728 atgccatcaaaatctgctgtc 748
           |||||||||||||||||||||
Sbjct: 22  atgccatcaaaatctgctgtc 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 473,124,317
Number of extensions: 31663982
Number of successful extensions: 2771460
Number of sequences better than 10.0: 59
Length of query: 748
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 724
Effective length of database: 97,308,875,965
Effective search space: 70451626198660
Effective search space used: 70451626198660
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.27
Homology vs Protein 
Query= Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Contig-U10043-1Q.Seq.d
         (748 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 309,869,351
Number of extensions: 3003350
Number of successful extensions: 5718
Number of sequences better than 10.0: 0
Number of HSP's gapped: 5666
Number of HSP's successfully gapped: 0
Length of query: 249
Length of database: 1,040,966,779
Length adjustment: 125
Effective length of query: 124
Effective length of database: 640,431,154
Effective search space: 79413463096
Effective search space used: 79413463096
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: 31 (16.5 bits)
PSORT 

 psg: 0.75  gvh: 0.42  alm: 0.64  top: 0.53  tms: 0.00  mit: 0.20  mip: 0.00
 nuc: 0.35  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 

	 76.0 %: nuclear
	 12.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: cytoplasmic
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U10043-1 is nuc
VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 3
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