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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U05240-1
Contig ID Contig-U05240-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U05240-1 (Contig-U05240-1Q) /CSM_Contig/Contig-U05240-1Q.Seq.d
CATTGGACAACACAAATATATAAAAAAATAAAGAAATAAGAAAGAAAGAA
AGAAAGAAAGAACAAACTAACACATAAATAAATTAACAAACAAACAAACA
AATAAATAAATAAATAAATAAATAAATATACAAATATACAAATAAATAAA
ATGAAATTTAATAAAATAACAATAATATCTATTGTTATTGCATTATTTAC
AATAATATTACAAATTAGTGAAAGTATAACAGTTTCAAATTTAAATAATC
AAAAGGATATTGAATTTACAATGTATCATAATGAAGATCAATCGAAATCA
TGTAAAATTCTATTCAAACCTAAATTAATACCACACTCTACCAATTCTAT
CACTTCTGTTGATTCTATAAATTTTAAAAAAGCAATTCAAATTAAATGTA
AAAATTCATTAACAAAAGAAAGTAGATCATTGTATCAAAAATCATGTGAT
TTATTTAAAACAACAGTTGTATCTGATAAAGATCCAAGTAATTTATCTTT
TTCTTCATTACCAAAGGGTAATTTAAAT
Gap no gap
Contig length 528
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 804082
End point 803554
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05240
List of clone(s) 

est1=SSG461F,1,529
Translated Amino Acid sequence 
hwttqiykkikk*erkkerknklthk*inkqtnk*ink*INKYTNIQINKMKFNKITIIS
IVIALFTIILQISESITVSNLNNQKDIEFTMYHNEDQSKSCKILFKPKLIPHSTNSITSV
DSINFKKAIQIKCKNSLTKESRSLYQKSCDLFKTTVVSDKDPSNLSFSSLPKGNLN
Translated Amino Acid sequence (All Frames) 
Frame A:
hwttqiykkikk*erkkerknklthk*inkqtnk*ink*INKYTNIQINKMKFNKITIIS
IVIALFTIILQISESITVSNLNNQKDIEFTMYHNEDQSKSCKILFKPKLIPHSTNSITSV
DSINFKKAIQIKCKNSLTKESRSLYQKSCDLFKTTVVSDKDPSNLSFSSLPKGNLN


Frame B:
igqhkyikk*rnkkerkkertn*hinkltnkqtnk*ink*iniqiyk*ik*nlik*q*yl
lllhylq*yyklvkv*qfqi*iikrilnlqciimkinrnhvkfysnln*yhtlpilslll
il*ilkkqfklnvkih*qkkvdhciknhviylkqqlylikiqviylflhyqrvi*


Frame C:
ldntni*knkeirkkerkkeqtnt*in*qtnkqink*ink*iykytnk*nei**nnnniy
cyciiynnitn**kynsfkfk*skgy*iynvs**rsieim*nsiqt*inttlyqfyhfc*
fykf*ksnsn*m*kfinkrk*iivskim*fi*nnsci**rsk*fifffitkg*fk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05240-1 (Contig-U05240-1Q)
/CSM_Contig/Contig-U05240-1Q.Seq.d
         (528 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05240-1 (Contig-U05240-1Q) /CSM_Contig/Conti...   696  0.0
Contig-U04923-1 (Contig-U04923-1Q) /CSM_Contig/Conti...    42  6e-04
Contig-U01717-1 (Contig-U01717-1Q) /CSM_Contig/Conti...    42  6e-04
Contig-U14276-1 (Contig-U14276-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U09111-1 (Contig-U09111-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U01835-1 (Contig-U01835-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U12860-1 (Contig-U12860-1Q) /CSM_Contig/Conti...    36  0.037
Contig-U10433-1 (Contig-U10433-1Q) /CSM_Contig/Conti...    36  0.037
Contig-U09374-1 (Contig-U09374-1Q) /CSM_Contig/Conti...    36  0.037
Contig-U09306-1 (Contig-U09306-1Q) /CSM_Contig/Conti...    36  0.037

>Contig-U05240-1 (Contig-U05240-1Q) /CSM_Contig/Contig-U05240-1Q.Seq.d
          Length = 528

 Score =  696 bits (351), Expect = 0.0
 Identities = 351/351 (100%)
 Strand = Plus / Plus

                                                                       
Query: 178 tctattgttattgcattatttacaataatattacaaattagtgaaagtataacagtttca 237
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 178 tctattgttattgcattatttacaataatattacaaattagtgaaagtataacagtttca 237

                                                                       
Query: 238 aatttaaataatcaaaaggatattgaatttacaatgtatcataatgaagatcaatcgaaa 297
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238 aatttaaataatcaaaaggatattgaatttacaatgtatcataatgaagatcaatcgaaa 297

                                                                       
Query: 298 tcatgtaaaattctattcaaacctaaattaataccacactctaccaattctatcacttct 357
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 298 tcatgtaaaattctattcaaacctaaattaataccacactctaccaattctatcacttct 357

                                                                       
Query: 358 gttgattctataaattttaaaaaagcaattcaaattaaatgtaaaaattcattaacaaaa 417
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 358 gttgattctataaattttaaaaaagcaattcaaattaaatgtaaaaattcattaacaaaa 417

                                                                       
Query: 418 gaaagtagatcattgtatcaaaaatcatgtgatttatttaaaacaacagttgtatctgat 477
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 418 gaaagtagatcattgtatcaaaaatcatgtgatttatttaaaacaacagttgtatctgat 477

                                                              
Query: 478 aaagatccaagtaatttatctttttcttcattaccaaagggtaatttaaat 528
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 478 aaagatccaagtaatttatctttttcttcattaccaaagggtaatttaaat 528


>Contig-U04923-1 (Contig-U04923-1Q) /CSM_Contig/Contig-U04923-1Q.Seq.d
          Length = 355

 Score = 42.1 bits (21), Expect = 6e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                
Query: 485 caagtaatttatctttttctt 505
           |||||||||||||||||||||
Sbjct: 197 caagtaatttatctttttctt 177


>Contig-U01717-1 (Contig-U01717-1Q) /CSM_Contig/Contig-U01717-1Q.Seq.d
          Length = 929

 Score = 42.1 bits (21), Expect = 6e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                
Query: 489 taatttatctttttcttcatt 509
           |||||||||||||||||||||
Sbjct: 282 taatttatctttttcttcatt 262


  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: 9775
Number of Sequences: 6905
Number of extensions: 9775
Number of successful extensions: 1301
Number of sequences better than 10.0: 450
length of query: 528
length of database: 5,674,871
effective HSP length: 16
effective length of query: 512
effective length of database: 5,564,391
effective search space: 2848968192
effective search space used: 2848968192
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. 7.15
Homology vs DNA 
Query= Contig-U05240-1 (Contig-U05240-1Q) /CSM_Contig/Contig-U05240-1Q.Seq.d
         (528 letters)

Database: ddbj_B
           105,743,758 sequences; 104,622,809,269 total letters

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

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

(AC117072) Dictyostelium discoideum chromosome 2 map 3879572...   377   e-140  4
(AU073237) Dictyostelium discoideum slug cDNA, clone SSG461.      125   2e-25  2
(CU928732) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    52   0.022  1
(EZ011966) TSA: Acropora millepora SeqIndex13854, mRNA seque...    50   0.088  1
(DY661595) SC_CP_08_F10 SC_CP Senecio cambrensis cDNA 5', mR...    48   0.35   1
(AP005839) Oryza sativa Japonica Group genomic DNA, chromoso...    44   0.42   2
(FI202420) CccaBa022-F12TV CccABa Cajanus cajan genomic clon...    46   1.4    1
(EJ049591) 1095454137551 Global-Ocean-Sampling_GS-26-01-01-1...    46   1.4    1
(CN132698) OX1_7_E03.g1_A002 Oxidatively-stressed leaves and...    46   1.4    1
(CP001184) Ureaplasma urealyticum serovar 10 str. ATCC 33699...    38   1.5    9
(BM170824) EST573347 PyBS Plasmodium yoelii yoelii cDNA clon...    36   1.8    2
(BX208576) Danio rerio genomic clone DKEY-250N24, genomic su...    36   2.3    2
(EJ910710) 1093018536959 Global-Ocean-Sampling_GS-30-02-01-1...    42   2.7    2
(AC007629) Homo sapiens clone NH0443B15a, *** SEQUENCING IN ...    34   2.7    2
(AC007098) Homo sapiens BAC clone RP11-443F16 from 2, comple...    34   2.7    2
(AC079838) Homo sapiens chromosome 2 clone RP11-257N14, WORK...    34   2.7    2
(AL772144) Zebrafish DNA sequence from clone CH211-164J3 in ...    34   3.1    3
(EK397812) 1095469527658 Global-Ocean-Sampling_GS-31-01-01-1...    32   3.6    2
(ER522361) 1093015592894 Global-Ocean-Sampling_GS-35-01-01-1...    32   3.6    2
(AY673996) Gracilaria tenuistipitata var. liui chloroplast, ...    38   4.2    3
(CR533429) Zebrafish DNA sequence from clone CH211-219A4 in ...    44   5.5    1
(BX571780) Zebrafish DNA sequence from clone CH211-139O3 in ...    44   5.5    1
(AP008215) Oryza sativa (japonica cultivar-group) genomic DN...    44   5.5    1
(EA700765) Sequence 79644 from patent US 7365185.                  44   5.5    1
(CS789413) Sequence 669 from Patent WO2005031001.                  44   5.5    1
(GN008955) Sequence 1396 from Patent EP2014669.                    44   5.5    1
(AC162125) Oryctolagus cuniculus clone LB1-187K2, complete s...    44   5.5    1
(AC069454) Homo sapiens chromosome 17, clone RP11-708H21, co...    44   5.5    1
(AC104974) Homo sapiens chromosome 17 clone RP11-145L16 map ...    44   5.5    1
(AC221653) Bos taurus clone CH240-38D12, WORKING DRAFT SEQUE...    44   5.5    1
(AC190290) Macaca mulatta clone CH250-216H15, WORKING DRAFT ...    44   5.5    1
(AC189455) Brassica rapa subsp. pekinensis clone KBrB072L19,...    44   5.5    1
(AC169238) Bos taurus clone CH240-232N5, WORKING DRAFT SEQUE...    44   5.5    1
(FI227150) CccaBa043-H4TV CccABa Cajanus cajan genomic clone...    44   5.5    1
(FI225933) CccaBa055-O10TV CccABa Cajanus cajan genomic clon...    44   5.5    1
(FI209274) CccaBa053-G1TR CccABa Cajanus cajan genomic clone...    44   5.5    1
(ER498953) 1093015391937 Global-Ocean-Sampling_GS-35-01-01-1...    44   5.5    1
(ED281477) AUAC-aay30h08.b1 Ascaris suum whole genome shotgu...    44   5.5    1
(CW660195) OG_BBa0012H08.f OG_BBa Oryza glaberrima genomic c...    44   5.5    1
(CL848257) OR_CBa0075K24.r OR_CBa Oryza rufipogon genomic cl...    44   5.5    1
(CD845552) RFO2.143M16F011228 RFO2 Brassica napus cDNA clone...    44   5.5    1
(CD842030) RFO2.125L19F010622 RFO2 Brassica napus cDNA clone...    44   5.5    1
(CD841374) RFO2.122O08F010618 RFO2 Brassica napus cDNA clone...    44   5.5    1
(CD841063) RFO2.121L04F010608 RFO2 Brassica napus cDNA clone...    44   5.5    1
(FP236602) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    36   5.6    3
(CU302293) Zebrafish DNA sequence from clone DKEY-178I20 in ...    42   6.1    2
(FM921232) Brachionus plicatilis EST 5' end, clone sb103P000...    38   6.5    2
(AC108807) Mus musculus chromosome 14 clone RP23-74M8 map 14...    32   9.6    2
(AC010534) Homo sapiens chromosome 16 clone RP11-259E8, comp...    42   9.6    3
(CU076056) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    30   9.7    2
(AC172751) Mus musculus BAC clone RP23-341F9 from chromosome...    32   9.8    2
(BX284646) Zebrafish DNA sequence from clone CH211-49J11 in ...    30   9.8    2
(AC162784) Danio rerio clone CH211-47A6, WORKING DRAFT SEQUE...    30   9.9    2
(CU606850) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    30   9.9    2

>(AC117072) Dictyostelium discoideum chromosome 2 map 3879572-4071762
              strain AX4, complete sequence.
          Length = 192187

 Score =  377 bits (190), Expect(4) = e-140
 Identities = 190/190 (100%)
 Strand = Plus / Minus


Query: 178    tctattgttattgcattatttacaataatattacaaattagtgaaagtataacagtttca 237
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115851 tctattgttattgcattatttacaataatattacaaattagtgaaagtataacagtttca 115792


Query: 238    aatttaaataatcaaaaggatattgaatttacaatgtatcataatgaagatcaatcgaaa 297
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115791 aatttaaataatcaaaaggatattgaatttacaatgtatcataatgaagatcaatcgaaa 115732


Query: 298    tcatgtaaaattctattcaaacctaaattaataccacactctaccaattctatcacttct 357
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115731 tcatgtaaaattctattcaaacctaaattaataccacactctaccaattctatcacttct 115672


Query: 358    gttgattcta 367
              ||||||||||
Sbjct: 115671 gttgattcta 115662

 Score =  174 bits (88), Expect(4) = e-140
 Identities = 88/88 (100%)
 Strand = Plus / Minus


Query: 430    ttgtatcaaaaatcatgtgatttatttaaaacaacagttgtatctgataaagatccaagt 489
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115437 ttgtatcaaaaatcatgtgatttatttaaaacaacagttgtatctgataaagatccaagt 115378


Query: 490    aatttatctttttcttcattaccaaagg 517
              ||||||||||||||||||||||||||||
Sbjct: 115377 aatttatctttttcttcattaccaaagg 115350

 Score = 28.2 bits (14), Expect(4) = e-140
 Identities = 14/14 (100%)
 Strand = Plus / Minus


Query: 515    agggtaatttaaat 528
              ||||||||||||||
Sbjct: 115209 agggtaatttaaat 115196

 Score = 26.3 bits (13), Expect(4) = e-140
 Identities = 13/13 (100%)
 Strand = Plus / Minus


Query: 1      cattggacaacac 13
              |||||||||||||
Sbjct: 116028 cattggacaacac 116016

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 449,453,966
Number of extensions: 29478055
Number of successful extensions: 2515759
Number of sequences better than 10.0: 54
Length of query: 528
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 505
Effective length of database: 102,190,702,835
Effective search space: 51606304931675
Effective search space used: 51606304931675
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 8. 1
Homology vs Protein 
Query= Contig-U05240-1 (Contig-U05240-1Q) /CSM_Contig/Contig-U05240-1Q.Seq.d
         (528 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BX293980_807(BX293980|pid:none) Mycoplasma mycoides subsp. mycoi...    38   0.18
CR859570_1(CR859570|pid:none) Pongo abelii mRNA; cDNA DKFZp459D1...    36   0.53
(Q7Z570) RecName: Full=Zinc finger protein 804A;  &AY327407_1(AY...    36   0.53
BC136602_1(BC136602|pid:none) Homo sapiens zinc finger protein 8...    36   0.53
AK131402_1(AK131402|pid:none) Homo sapiens cDNA FLJ16500 fis, cl...    36   0.53
CP000117_4313(CP000117|pid:none) Anabaena variabilis ATCC 29413,...    35   0.90
FM864216_232(FM864216|pid:none) Mycoplasma conjunctivae HRC/581T...    35   1.5
L10908_1(L10908|pid:none) Mus musculus Gcap1 mRNA, partial cds.        34   2.0
CP000568_2609(CP000568|pid:none) Clostridium thermocellum ATCC 2...    34   2.0
AK127397_1(AK127397|pid:none) Homo sapiens cDNA FLJ45488 fis, cl...    34   2.6
AP008971_1351(AP008971|pid:none) Finegoldia magna ATCC 29328 DNA...    34   2.6
AE017333_2947(AE017333|pid:none) Bacillus licheniformis DSM 13, ...    33   3.4
AX647813_1(AX647813|pid:none) Sequence 2005 from Patent EP1270724.     33   4.4
AM269894_49(AM269894|pid:none) Eimeria tenella chromosome 1, ord...    33   4.4
CR954247_424(CR954247|pid:none) Pseudoalteromonas haloplanktis s...    33   4.5
AK136747_1(AK136747|pid:none) Mus musculus adult male epididymis...    32   7.5
AL929355_59(AL929355|pid:none) Plasmodium falciparum strain 3D7,...    32   7.6
AJ293568_11(AJ293568|pid:none) Yaba-like disease virus (YLDV), c...    32   7.6
AE001437_2942(AE001437|pid:none) Clostridium acetobutylicum ATCC...    32   7.6
AL844508_60(AL844508|pid:none) Plasmodium falciparum 3D7 chromos...    32   7.6
S72279(S72279;S43896) conserved hypothetical protein 470 - Plasm...    32   9.8
AM412317_3564(AM412317|pid:none) Clostridium botulinum A str. AT...    32   10.0
FM992690_452(FM992690|pid:none) Candida dubliniensis CD36 chromo...    32   10.0
AP003975_13(AP003975|pid:none) Oryza sativa Japonica Group genom...    32   10.0
CP000496_285(CP000496|pid:none) Pichia stipitis CBS 6054 chromos...    32   10.0
AE014187_317(AE014187|pid:none) Plasmodium falciparum 3D7 chromo...    32   10.0
AE017263_507(AE017263|pid:none) Mesoplasma florum L1 complete ge...    32   10.0
CP001581_3792(CP001581|pid:none) Clostridium botulinum A2 str. K...    32   10.0

>BX293980_807(BX293980|pid:none) Mycoplasma mycoides subsp. mycoides
           SC str. PG1, complete genome.
           &BX842644_228(BX842644|pid:none)
          Length = 257

 Score = 37.7 bits (86), Expect = 0.18
 Identities = 29/109 (26%), Positives = 52/109 (47%)
 Frame = +1

Query: 175 ISIVIALFTIILQISESITVSNLNNQKDIEFTMYHNEDQSKSCKILFKPKLIPHSTNSIT 354
           IS+    F  ++  ++   +S LN  + + F    N+D+S S     KPK    S N ++
Sbjct: 148 ISLADINFNSLVSQNKDQWLSKLNGLQTVTF---RNKDKSISIDKTNKPKWFDTSVNKVS 204

Query: 355 SVDSINFKKAIQIKCKNSLTKESRSLYQKSCDLFKTTVVSDKDPSNLSF 501
            +DS+     +  K   +L K ++ +Y  S   F   ++S KD  N++F
Sbjct: 205 IIDSLKLDSMLSSKTDTNL-KINKIVYLVS---FNANILSFKDTKNVAF 249

Lambda     K      H
   0.317    0.129    0.362

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3268448
Number of Hits to DB: 484,779,718
Number of extensions: 7543402
Number of successful extensions: 24574
Number of sequences better than 10.0: 28
Number of HSP's gapped: 24415
Number of HSP's successfully gapped: 28
Length of query: 176
Length of database: 1,061,185,681
Length adjustment: 120
Effective length of query: 56
Effective length of database: 668,971,921
Effective search space: 37462427576
Effective search space used: 37462427576
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: 0.67  gvh: 0.53  alm: 0.17  top: 0.13  tms: 0.07  mit: 0.35  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: 1.00  tyr: 0.29  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 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 24.0 %: cytoplasmic
	 20.0 %: mitochondrial
	 16.0 %: Golgi
	 16.0 %: nuclear
	 16.0 %: endoplasmic reticulum
	  4.0 %: extracellular, including cell wall
	  4.0 %: peroxisomal

>> prediction for Contig-U05240-1 is cyt
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