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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-U02375-1
Contig ID Contig-U02375-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U02375-1 (Contig-U02375-1Q) /CSM_Contig/Contig-U02375-1Q.Seq.d
CTGCTCAGAAGGTAGATGCCCAGAAGAAGATTTCAAGTATCTTAGAAATA
CTGCTAAAGTAAAGAGATGTTATGATGTTGCCAACGTATTCAATGGTTTA
AATATTTTAGAAAAAGTTGGTAAATCTAAAATACACTCTTATCAATGGTG
TGGTGATTTTACAATTCAAGATTGTGAAAATGGTTGCCCATTTGGTCATC
CATTACTTACACCAGGAACTGCATATACAACAAATCCTTCACCCAATCCA
TTCAATCAATTTAGCAATGCATATATCTCTTCATCTGCTCAATCTTCTTT
ATCAAACTCTCCATTCATTCAAGGTGGTTTCCATGGTAACAACAATAATA
GTAATAATAACAATATCAATGGAAATAATATCAATGGAAATAATAACTAT
GGCTATAATAATAATAATAATTATAATAACTACAATAGTAACAATAGCAA
TGGCTTTAATAACNGAAATTCNTTTTTCCAACATACTACA
Gap no gap
Contig length 490
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 1424499
End point 1424989
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U02375
List of clone(s) 

est1=AFA528Z,1,491
Translated Amino Acid sequence 
CSEGRCPEEDFKYLRNTAKVKRCYDVANVFNGLNILEKVGKSKIHSYQWCGDFTIQDCEN
GCPFGHPLLTPGTAYTTNPSPNPFNQFSNAYISSSAQSSLSNSPFIQGGFHGNNNNSNNN
NINGNNINGNNNYGYNNNNNYNNYNSNNSNGFNNXNSFFQHTT
Translated Amino Acid sequence (All Frames) 
Frame A:
llrr*mprrrfqvs*kyc*skeml*ccqriqwfkyfrksw*i*ntllsmvw*fynsrl*k
wlpiwssitytrnciynksftqsiqsi*qciylficsiffiklsihsrwfpw*qq*****
qyqwk*yqwk**lwl*****l**lq**q*qwl**xkfxfptyy


Frame B:
CSEGRCPEEDFKYLRNTAKVKRCYDVANVFNGLNILEKVGKSKIHSYQWCGDFTIQDCEN
GCPFGHPLLTPGTAYTTNPSPNPFNQFSNAYISSSAQSSLSNSPFIQGGFHGNNNNSNNN
NINGNNINGNNNYGYNNNNNYNNYNSNNSNGFNNXNSFFQHTT


Frame C:
aqkvdaqkkissileillk*rdvmmlptysmv*if*kklvnlkytlingvvilqfkivkm
vahlvihylhqelhiqqilhpihsinlamhislhllnllyqtlhsfkvvsmvttiiviit
ismeiismeiitmaiiiiiiiittivtiamaliteixfsnil
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U02375-1 (Contig-U02375-1Q)
/CSM_Contig/Contig-U02375-1Q.Seq.d
         (490 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U02375-1 (Contig-U02375-1Q) /CSM_Contig/Conti...   698  0.0
Contig-U06392-1 (Contig-U06392-1Q) /CSM_Contig/Conti...    36  0.034
Contig-U13222-1 (Contig-U13222-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11867-1 (Contig-U11867-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11589-1 (Contig-U11589-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U09743-1 (Contig-U09743-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U06491-1 (Contig-U06491-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U03714-1 (Contig-U03714-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U14880-1 (Contig-U14880-1Q) /CSM_Contig/Conti...    32  0.53
Contig-U14682-1 (Contig-U14682-1Q) /CSM_Contig/Conti...    32  0.53

>Contig-U02375-1 (Contig-U02375-1Q) /CSM_Contig/Contig-U02375-1Q.Seq.d
          Length = 490

 Score =  698 bits (352), Expect = 0.0
 Identities = 352/352 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ctgctcagaaggtagatgcccagaagaagatttcaagtatcttagaaatactgctaaagt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ctgctcagaaggtagatgcccagaagaagatttcaagtatcttagaaatactgctaaagt 60

                                                                       
Query: 61  aaagagatgttatgatgttgccaacgtattcaatggtttaaatattttagaaaaagttgg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aaagagatgttatgatgttgccaacgtattcaatggtttaaatattttagaaaaagttgg 120

                                                                       
Query: 121 taaatctaaaatacactcttatcaatggtgtggtgattttacaattcaagattgtgaaaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 taaatctaaaatacactcttatcaatggtgtggtgattttacaattcaagattgtgaaaa 180

                                                                       
Query: 181 tggttgcccatttggtcatccattacttacaccaggaactgcatatacaacaaatccttc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tggttgcccatttggtcatccattacttacaccaggaactgcatatacaacaaatccttc 240

                                                                       
Query: 241 acccaatccattcaatcaatttagcaatgcatatatctcttcatctgctcaatcttcttt 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 acccaatccattcaatcaatttagcaatgcatatatctcttcatctgctcaatcttcttt 300

                                                               
Query: 301 atcaaactctccattcattcaaggtggtttccatggtaacaacaataatagt 352
           ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 atcaaactctccattcattcaaggtggtttccatggtaacaacaataatagt 352


 Score = 75.8 bits (38), Expect = 4e-14
 Identities = 44/44 (100%)
 Strand = Plus / Plus

                                                       
Query: 447 gcaatggctttaataacngaaattcntttttccaacatactaca 490
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 447 gcaatggctttaataacngaaattcntttttccaacatactaca 490


>Contig-U06392-1 (Contig-U06392-1Q) /CSM_Contig/Contig-U06392-1Q.Seq.d
          Length = 490

 Score = 36.2 bits (18), Expect = 0.034
 Identities = 24/26 (92%)
 Strand = Plus / Minus

                                     
Query: 153 gtgattttacaattcaagattgtgaa 178
           |||||||||||||| || ||||||||
Sbjct: 481 gtgattttacaattaaacattgtgaa 456


>Contig-U13222-1 (Contig-U13222-1Q) /CSM_Contig/Contig-U13222-1Q.Seq.d
          Length = 640

 Score = 34.2 bits (17), Expect = 0.13
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                
Query: 97  tttaaatattttagaaaaagt 117
           |||||||||||||||| ||||
Sbjct: 425 tttaaatattttagaagaagt 445


  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: 4442
Number of Sequences: 6905
Number of extensions: 4442
Number of successful extensions: 578
Number of sequences better than 10.0: 182
length of query: 490
length of database: 5,674,871
effective HSP length: 16
effective length of query: 474
effective length of database: 5,564,391
effective search space: 2637521334
effective search space used: 2637521334
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 2009. 5.17
Homology vs DNA 
Query= Contig-U02375-1 (Contig-U02375-1Q) /CSM_Contig/Contig-U02375-1Q.Seq.d
         (490 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(BJ340486) Dictyostelium discoideum cDNA clone:dda2g07, 3' e...   666   0.0    2
(AC115607) Dictyostelium discoideum chromosome 2 map 4559693...   666   0.0    1
(BZ494038) BONCZ18TR BO_1.6_2_KB_tot Brassica oleracea genom...    48   0.31   1
(BH996560) oeh19h09.b1 B.oleracea002 Brassica oleracea genom...    48   0.31   1
(DB870264) Lipochromis sp. 'matumbi hunter' cDNA clone:hm747...    48   0.31   1
(DB867391) Lipochromis sp. 'matumbi hunter' cDNA clone:hm713...    48   0.31   1
(ET046954) CHO_OF4537xe10r1.ab1 CHO_OF4 Nicotiana tabacum ge...    46   1.2    1
(EK447054) 1095467050481 Global-Ocean-Sampling_GS-32-01-01-1...    46   1.2    1
(EH056200) THL52h-1744 cDNA library of Tamarix hispida leave...    46   1.2    1
(CK294083) EST756797 Nicotiana benthamiana mixed tissue cDNA...    46   1.2    1
(CK291604) EST754318 Nicotiana benthamiana mixed tissue cDNA...    46   1.2    1
(FG202335) AGN_PNL232df1_a4.trimmed.seq AGN_PNL Nicotiana ta...    46   1.2    1
(AP008934) Staphylococcus saprophyticus subsp. saprophyticus...    46   1.2    1
(AK231044) Sus scrofa mRNA, clone:AMP010085H07, expressed in...    40   4.7    2
(AL136998) Mouse DNA sequence from clone RP21-509E24 on chro...    44   4.9    1
(AP009409) Solanum lycopersicum genomic DNA, chromosome 8, c...    44   4.9    1
(AC093267) Homo sapiens chromosome 5 clone RP11-280F11, comp...    44   4.9    1
(AC156890) Bos taurus clone CH240-65G14, WORKING DRAFT SEQUE...    44   4.9    1
(AC189996) Microcebus murinus clone CH257-127F21, WORKING DR...    44   4.9    1
(AC189650) Brassica rapa subsp. pekinensis clone KBrS011B08,...    44   4.9    1
(AC021463) Homo sapiens clone RP11-280F11, WORKING DRAFT SEQ...    44   4.9    1
(BH536787) BOGYI22TR BOGY Brassica oleracea genomic clone BO...    44   4.9    1
(DX043854) KBrB044K17R KBrB, Brassica rapa BamHI BAC library...    44   4.9    1
(DU870277) 107952 Tomato HindIII BAC Library Solanum lycoper...    44   4.9    1
(CC485409) CH240_314B18.TARBAC13P2 CHORI-240 Bos taurus geno...    44   4.9    1
(BY906976) Cryptomeria japonica cDNA clone: CMFL031_P02, 3'e...    44   4.9    1
(BY889182) Cryptomeria japonica cDNA clone: CMFL031_P02, 5'e...    44   4.9    1
(EX314727) GQ02807.SP6_I05 GQ028 - Cambium / phloem scrappin...    44   4.9    1
(EX314403) GQ02807.B7_I05 GQ028 - Cambium / phloem scrapping...    44   4.9    1
(EX127535) BR111365 etiolated mature leaf cDNA library KHLW ...    44   4.9    1
(EK151194) 1095456052357 Global-Ocean-Sampling_GS-31-01-01-1...    38   8.0    2

>(BJ340486) Dictyostelium discoideum cDNA clone:dda2g07, 3' end,
           single read.
          Length = 491

 Score =  666 bits (336), Expect(2) = 0.0
 Identities = 336/336 (100%)
 Strand = Plus / Minus


Query: 1   ctgctcagaaggtagatgcccagaagaagatttcaagtatcttagaaatactgctaaagt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 491 ctgctcagaaggtagatgcccagaagaagatttcaagtatcttagaaatactgctaaagt 432


Query: 61  aaagagatgttatgatgttgccaacgtattcaatggtttaaatattttagaaaaagttgg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 431 aaagagatgttatgatgttgccaacgtattcaatggtttaaatattttagaaaaagttgg 372


Query: 121 taaatctaaaatacactcttatcaatggtgtggtgattttacaattcaagattgtgaaaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 371 taaatctaaaatacactcttatcaatggtgtggtgattttacaattcaagattgtgaaaa 312


Query: 181 tggttgcccatttggtcatccattacttacaccaggaactgcatatacaacaaatccttc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 311 tggttgcccatttggtcatccattacttacaccaggaactgcatatacaacaaatccttc 252


Query: 241 acccaatccattcaatcaatttagcaatgcatatatctcttcatctgctcaatcttcttt 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 acccaatccattcaatcaatttagcaatgcatatatctcttcatctgctcaatcttcttt 192


Query: 301 atcaaactctccattcattcaaggtggtttccatgg 336
           ||||||||||||||||||||||||||||||||||||
Sbjct: 191 atcaaactctccattcattcaaggtggtttccatgg 156

 Score = 46.1 bits (23), Expect(2) = 0.0
 Identities = 26/26 (100%)
 Strand = Plus / Minus


Query: 465 gaaattcntttttccaacatactaca 490
           ||||||||||||||||||||||||||
Sbjct: 27  gaaattcntttttccaacatactaca 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 447,773,490
Number of extensions: 26350587
Number of successful extensions: 2134530
Number of sequences better than 10.0: 32
Length of query: 490
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 467
Effective length of database: 99,442,330,388
Effective search space: 46439568291196
Effective search space used: 46439568291196
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.19
Homology vs Protein 
Query= Contig-U02375-1 (Contig-U02375-1Q) /CSM_Contig/Contig-U02375-1Q.Seq.d
         (490 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BT061185_1(BT061185|pid:none) Zea mays full-length cDNA clone ZM...    42   0.010
AP005112_14(AP005112|pid:none) Oryza sativa Japonica Group genom...    38   0.15
BC070864_1(BC070864|pid:none) Xenopus laevis hypothetical protei...    38   0.15
BX072538_2(BX072538|pid:none) Zebrafish DNA sequence from clone ...    37   0.19
AB074532_1(AB074532|pid:none) Arabidopsis thaliana mRNA for E2F-...    37   0.33
AC010676_4(AC010676|pid:none) Arabidopsis thaliana chromosome II...    37   0.33
AB480826_1(AB480826|pid:none) Porphyra yezoensis PyDEL1 mRNA for...    35   0.95
DQ353854_1(DQ353854|pid:none) Triticum aestivum transcription re...    35   1.2
AL031627_12(AL031627|pid:none) Caenorhabditis elegans YAC Y102A5...    34   1.6
EU964535_1(EU964535|pid:none) Zea mays clone 279700 unknown mRNA.      34   2.1
AC136839_10(AC136839|pid:none) Medicago truncatula clone mth2-13...    33   2.8
AJ417836_1(AJ417836|pid:none) Arabidopsis thaliana mRNA for tran...    33   3.6
AB074533_1(AB074533|pid:none) Arabidopsis thaliana mRNA for E2F-...    33   3.6
AY028167_1(AY028167|pid:none) Caenorhabditis elegans EFL-2 (efl-...    33   4.7
BC086675_1(BC086675|pid:none) Mus musculus E2F transcription fac...    32   6.1
(A0AVK6) RecName: Full=Transcription factor E2F8;          Short...    32   6.1

>BT061185_1(BT061185|pid:none) Zea mays full-length cDNA clone
           ZM_BFb0119O11 mRNA, complete cds.
          Length = 223

 Score = 41.6 bits (96), Expect = 0.010
 Identities = 21/51 (41%), Positives = 33/51 (64%), Gaps = 2/51 (3%)
 Frame = +2

Query: 56  KVKRCYDVANVFNGLNILEKV--GKSKIHSYQWCGDFTIQDCENGCPFGHP 202
           KV+R YD+ANV + LN++EK+  G S+  +++W G  T+ + ENG     P
Sbjct: 28  KVRRLYDIANVLSSLNLIEKIHQGDSRKPAFRWLGRATL-NTENGVTVAVP 77

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: 599,466,814
Number of extensions: 10218405
Number of successful extensions: 16335
Number of sequences better than 10.0: 16
Number of HSP's gapped: 16335
Number of HSP's successfully gapped: 16
Length of query: 163
Length of database: 1,051,180,864
Length adjustment: 118
Effective length of query: 45
Effective length of database: 669,266,902
Effective search space: 30117010590
Effective search space used: 30117010590
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: 30 (16.2 bits)
PSORT 

 psg: 0.75  gvh: 0.20  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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
	 32.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: vacuolar

>> prediction for Contig-U02375-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 1
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