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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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-U05528-1
Contig ID Contig-U05528-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U05528-1 (Contig-U05528-1Q) /CSM_Contig/Contig-U05528-1Q.Seq.d
CAAAACCACAAACAAAAAATCAATTTTTTTTTTTAAAATTACAAATAATC
ATCAACAATTGTGATTGCAAATAAAATAAAAATAAATTTTATTATATTTT
TTTTTTTATTTTTTCAATATTATTTCAAAAATCAAATTTACCAATATTAA
GCATTAATAATAATAATAAAAAATAAATAACCTCAATTAAAATAATAATA
ACTTTTAGAAAAAAAAAAAAAAAGAAAAAGAAAAACAAAAACAAAAATTC
AAAGAAACACTTGCCACCAAATATTTTAAAATTTACACTTTATAATTTAT
TCTTTTTCTCTTTTATTGAAACGATTGTATCCAAACAAATT
Gap no gap
Contig length 341
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 2177797
End point 2177456
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05528
List of clone(s) 

est1=SSJ306E,1,342
Translated Amino Acid sequence 
kpqtknqffflklqiiinncdck*nknkfyyifffifsilfqksnlpilsinnnnkk*IT
SIKIIITFRKKKKKKKKNKNKNSKKHLPPNILKFTLYNLFFFSFIETIVSKQI
Translated Amino Acid sequence (All Frames) 
Frame A:
qnhkqkinfff*nyk*sstiviankikinfiiffflffqyyfknqiyqy*aliiiiknk*
pqlk***llekkkkrkrktktkiqrntchqif*nlhfiiysfslllkrlypnk


Frame B:
kttnkksifffkitnnhqql*lqik*k*illyfffyffniiskikftnikh*****kinn
ln*nnnnf*kkkkkekekqkqkfketlatkyfkiytl*filflfy*ndciqtn


Frame C:
kpqtknqffflklqiiinncdck*nknkfyyifffifsilfqksnlpilsinnnnkk*IT
SIKIIITFRKKKKKKKKNKNKNSKKHLPPNILKFTLYNLFFFSFIETIVSKQI
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05528-1 (Contig-U05528-1Q)
/CSM_Contig/Contig-U05528-1Q.Seq.d
         (341 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05528-1 (Contig-U05528-1Q) /CSM_Contig/Conti...   186  1e-47
Contig-U13389-1 (Contig-U13389-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U09252-1 (Contig-U09252-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U07510-1 (Contig-U07510-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U07033-1 (Contig-U07033-1Q) /CSM_Contig/Conti...    40  0.001
Contig-U11535-1 (Contig-U11535-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U10965-1 (Contig-U10965-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U06566-1 (Contig-U06566-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U06395-1 (Contig-U06395-1Q) /CSM_Contig/Conti...    38  0.006
Contig-U06353-1 (Contig-U06353-1Q) /CSM_Contig/Conti...    38  0.006

>Contig-U05528-1 (Contig-U05528-1Q) /CSM_Contig/Contig-U05528-1Q.Seq.d
          Length = 341

 Score =  186 bits (94), Expect = 1e-47
 Identities = 94/94 (100%)
 Strand = Plus / Plus

                                                                       
Query: 248 ttcaaagaaacacttgccaccaaatattttaaaatttacactttataatttattcttttt 307
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 248 ttcaaagaaacacttgccaccaaatattttaaaatttacactttataatttattcttttt 307

                                             
Query: 308 ctcttttattgaaacgattgtatccaaacaaatt 341
           ||||||||||||||||||||||||||||||||||
Sbjct: 308 ctcttttattgaaacgattgtatccaaacaaatt 341


 Score =  125 bits (63), Expect = 3e-29
 Identities = 85/96 (88%)
 Strand = Plus / Plus

                                                                      
Query: 1  caaaaccacaaacaaaaaatcaannnnnnnnnnnaaaattacaaataatcatcaacaatt 60
          |||||||||||||||||||||||           ||||||||||||||||||||||||||
Sbjct: 1  caaaaccacaaacaaaaaatcaatttttttttttaaaattacaaataatcatcaacaatt 60

                                              
Query: 61 gtgattgcaaataaaataaaaataaattttattata 96
          ||||||||||||||||||||||||||||||||||||
Sbjct: 61 gtgattgcaaataaaataaaaataaattttattata 96


>Contig-U13389-1 (Contig-U13389-1Q) /CSM_Contig/Contig-U13389-1Q.Seq.d
          Length = 207

 Score = 42.1 bits (21), Expect = 4e-04
 Identities = 24/25 (96%)
 Strand = Plus / Plus

                                    
Query: 72  taaaataaaaataaattttattata 96
           ||||||||||||||| |||||||||
Sbjct: 119 taaaataaaaataaaatttattata 143


>Contig-U09252-1 (Contig-U09252-1Q) /CSM_Contig/Contig-U09252-1Q.Seq.d
          Length = 524

 Score = 40.1 bits (20), Expect = 0.001
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 69  aaataaaataaaaataaatt 88
           ||||||||||||||||||||
Sbjct: 493 aaataaaataaaaataaatt 512


  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: 11,421
Number of Sequences: 6905
Number of extensions: 11421
Number of successful extensions: 3601
Number of sequences better than 10.0: 1218
length of query: 341
length of database: 5,674,871
effective HSP length: 15
effective length of query: 326
effective length of database: 5,571,296
effective search space: 1816242496
effective search space used: 1816242496
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. 7.29
Homology vs DNA 
Query= Contig-U05528-1 (Contig-U05528-1Q) /CSM_Contig/Contig-U05528-1Q.Seq.d
         (341 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

(C90915) Dictyostelium discoideum slug cDNA, clone SSJ306.        186   6e-64  3
(AC170053) Oryctolagus cuniculus clone LB1-219P1, WORKING DR...    48   0.22   1
(DU964894) 234892 Tomato MboI BAC Library Solanum lycopersic...    48   0.22   1
(DE101461) Oryzias latipes DNA, clone: ola1-134K06.F, genomi...    48   0.22   1
(AC112944) Mus musculus chromosome 5, clone RP23-411F8, comp...    40   0.44   3
(AL669979) Mouse DNA sequence from clone RP23-93O11 on chrom...    34   0.48   2
(AM442556) Vitis vinifera contig VV78X024166.3, whole genome...    34   0.54   2
(AM460389) Vitis vinifera contig VV78X111522.6, whole genome...    34   0.57   2
(AK319896) Solanum lycopersicum cDNA, clone: LEFL1003AF09, H...    34   0.62   2
(AC203599) Homo sapiens FOSMID clone ABC10-43645800E4 from c...    46   0.87   1
(AC008035) Homo sapiens 12 BAC RP11-446N19 (Roswell Park Can...    46   0.87   1
(AC154083) Dasypus novemcinctus clone VMRC5-309H24, WORKING ...    46   0.87   1
(AC118531) Rattus norvegicus clone CH230-328I20, *** SEQUENC...    46   0.87   1
(AC115479) Rattus norvegicus clone CH230-236B21, *** SEQUENC...    46   0.87   1
(AC097682) Rattus norvegicus clone CH230-66O13, WORKING DRAF...    46   0.87   1
(DH796484) Rattus norvegicus DNA, BAC clone: RNB1-390E06, 5'...    46   0.87   1
(ED053590) AUAC-aaj09h04.g1 Ascaris suum whole genome shotgu...    34   0.99   2
(CU468277) M.truncatula DNA sequence *** SEQUENCING CANCELLE...    38   1.4    3
(CU463296) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   1.6    3
(AX346453) Sequence 1524 from Patent WO0200928.                    36   1.7    2
(AC165687) Bos taurus clone CH240-165O2, WORKING DRAFT SEQUE...    34   1.7    2
(AC184284) Strongylocentrotus purpuratus clone R3-56M1, WORK...    34   1.8    2
(AC201121) Strongylocentrotus purpuratus clone R3-13O9, WORK...    34   1.8    2
(AC188382) Medicago truncatula clone mth2-167o13, WORKING DR...    36   2.3    3
(AC174299) Medicago truncatula clone mth2-80e19, complete se...    36   2.3    3
(AC068124) Homo sapiens chromosome 11 clone RP11-325I16, WOR...    38   2.3    2
(EI295019) GM_WBc0018I19.r GM_WBc Glycine max genomic clone ...    36   2.8    2
(AC095998) Rattus norvegicus clone CH230-22A23, *** SEQUENCI...    44   2.9    2
(AC155783) Papio anubis clone RP41-135B18, WORKING DRAFT SEQ...    44   3.1    3
(AC147719) Gallus gallus BAC clone CH261-22J12 from chromoso...    44   3.4    1
(CT030155) Mouse DNA sequence from clone RP23-425N11 on chro...    44   3.4    1
(AL671887) Mouse DNA sequence from clone RP23-197O15 on chro...    44   3.4    1
(AC167166) Mus musculus chromosome 1, clone RP23-133G16, com...    44   3.4    1
(AC156983) Mus musculus chromosome 1, clone RP23-236I14, com...    44   3.4    1
(AC154557) Mus musculus BAC clone RP23-425M9 from 17, comple...    44   3.4    1
(AC156127) Bos taurus clone CH240-47D7, WORKING DRAFT SEQUEN...    44   3.4    1
(AC146486) Gallus gallus clone CH261-61E4, WORKING DRAFT SEQ...    44   3.4    1
(AC141178) Rattus norvegicus clone CH230-424K9, WORKING DRAF...    44   3.4    1
(AC140955) Didelphis virginiana clone LB3-197O4, WORKING DRA...    44   3.4    1
(AC129041) Rattus norvegicus clone CH230-106J6, *** SEQUENCI...    44   3.4    1
(AC118579) Didelphis virginiana clone LB3-54P21, WORKING DRA...    44   3.4    1
(AC095729) Rattus norvegicus clone CH230-9A9, *** SEQUENCING...    44   3.4    1
(AC095296) Rattus norvegicus clone CH230-12A10, *** SEQUENCI...    44   3.4    1
(AC224179) Bos taurus clone CH240-447D6, WORKING DRAFT SEQUE...    44   3.4    1
(AC188916) Colobus guereza clone CH272-132M20, WORKING DRAFT...    44   3.4    1
(AC178205) Strongylocentrotus purpuratus clone R3-3085E21, W...    44   3.4    1
(AC177965) Strongylocentrotus purpuratus clone R3-3049J4, WO...    44   3.4    1
(EJ180475) 1092344119479 Global-Ocean-Sampling_GS-27-01-01-1...    44   3.4    1
(EI478530) PV_GBa0090C08.r PV_GBa Phaseolus vulgaris genomic...    44   3.4    1
(CR827721) GR0AAA59DB10FM1 INRA BAC Bos taurus genomic clone...    44   3.4    1
(AG839356) Oryza sativa Indica Group genomic DNA, BAC end se...    44   3.4    1
(CC590874) CH240_390J22.TARBAC13P2 CHORI-240 Bos taurus geno...    44   3.4    1
(BZ233710) CH230-427K20.TJ CHORI-230 Segment 2 Rattus norveg...    44   3.4    1
(EH176578) LB01738.CR_A21 GC_BGC-17 Bos taurus cDNA clone IM...    44   3.4    1
(EH174792) LB01652.CR_K04 GC_BGC-16 Bos taurus cDNA clone IM...    44   3.4    1
(EH169340) LB01636.CR.1_H23 GC_BGC-16 Bos taurus cDNA clone ...    44   3.4    1
(DV892037) LB02722.CR_F16 GC_BGC-27 Bos taurus cDNA clone IM...    44   3.4    1
(DV795979) 10-24-24 Bos taurus CF-24-HW loin cDNA library Bo...    44   3.4    1
(DV794556) Hw_loin_54_050811_A04 Bos taurus CF-24-HW loin cD...    44   3.4    1
(DT809255) LB0163.CR_B03 GC_BGC-16 Bos taurus cDNA clone IMA...    44   3.4    1
(CN791323) 4126027 BARC 8BOV Bos taurus cDNA clone 8BOV_41O1...    44   3.4    1
(EW684947) LB02743.CR.1_M12 GC_BGC-27 Bos taurus cDNA clone ...    44   3.4    1
(CP000111) Prochlorococcus marinus str. MIT 9312, complete g...    44   3.4    1
(FH065206) CHO_OF3599xf16f1.ab1 CHO_OF3 Nicotiana tabacum ge...    34   3.5    2
(BX005066) Zebrafish DNA sequence from clone CH211-152F23 in...    40   3.7    3
(AC205877) Pan troglodytes BAC clone CH251-412K5 from chromo...    32   3.8    6
(CW794474) WiscDsLox363A07 Arabidopsis thaliana T-DNA insert...    34   3.8    2
(AL162831) Human chromosome 14 DNA sequence BAC R-1077A2 of ...    40   5.1    3
(AC087824) Homo sapiens chromosome 11 clone RP1-187A11 map 1...    38   5.8    2
(AC226514) Solanum lycopersicum chromosome 2 clone C02SLe002...    38   6.2    2
(AC111433) Rattus norvegicus clone CH230-170A7, WORKING DRAF...    30   6.3    2
(AC119474) Rattus norvegicus clone CH230-424C21, *** SEQUENC...    30   6.4    2
(AC162524) Mus musculus chromosome 5 clone RP24-135A18, WORK...    40   6.5    2
(ET932881) CHO_OF122xg15r1.ab1 CHO_OF Nicotiana tabacum geno...    34   7.4    2
(FH624088) CHO_OF4548xj01f1.ab1 CHO_OF4 Nicotiana tabacum ge...    34   7.9    2
(AX509545) Sequence 4240 from Patent WO0216655.                    34   8.4    2
(CL513910) SAIL_880_F11.v1 SAIL Collection Arabidopsis thali...    30   8.4    2
(FT034169) Rattus norvegicus DNA, BAC clone: RNB2-049D10, 5'...    30   8.4    2
(AG305106) Mus musculus molossinus DNA, clone:MSMg01-085I24....    32   8.4    2
(DB771915) Apis mellifera head cDNA, RIKEN full-length enric...    32   8.8    2
(DB773122) Apis mellifera head cDNA, RIKEN full-length enric...    32   8.8    2
(DB756808) Apis mellifera head cDNA, RIKEN full-length enric...    32   8.8    2
(DB762412) Apis mellifera head cDNA, RIKEN full-length enric...    32   8.8    2
(FH573753) CHO_OF4279xa03r2.ab1 CHO_OF4 Nicotiana tabacum ge...    34   8.8    2
(AC168885) Bos taurus clone CH240-245F21, WORKING DRAFT SEQU...    38   9.0    2
(CL634194) CH243-6C22.SP6 CHORI-243 Ovis aries genomic clone...    38   9.1    2
(CU928722) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   9.2    2
(CU062401) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    38   9.6    2

>(C90915) Dictyostelium discoideum slug cDNA, clone SSJ306.
          Length = 342

 Score =  186 bits (94), Expect(3) = 6e-64
 Identities = 94/94 (100%)
 Strand = Plus / Plus


Query: 248 ttcaaagaaacacttgccaccaaatattttaaaatttacactttataatttattcttttt 307
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 248 ttcaaagaaacacttgccaccaaatattttaaaatttacactttataatttattcttttt 307


Query: 308 ctcttttattgaaacgattgtatccaaacaaatt 341
           ||||||||||||||||||||||||||||||||||
Sbjct: 308 ctcttttattgaaacgattgtatccaaacaaatt 341

 Score = 67.9 bits (34), Expect(3) = 6e-64
 Identities = 34/34 (100%)
 Strand = Plus / Plus


Query: 35 aaaattacaaataatcatcaacaattgtgattgc 68
          ||||||||||||||||||||||||||||||||||
Sbjct: 35 aaaattacaaataatcatcaacaattgtgattgc 68

 Score = 46.1 bits (23), Expect(3) = 6e-64
 Identities = 23/23 (100%)
 Strand = Plus / Plus


Query: 1  caaaaccacaaacaaaaaatcaa 23
          |||||||||||||||||||||||
Sbjct: 1  caaaaccacaaacaaaaaatcaa 23

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 294,841,572
Number of extensions: 24407928
Number of successful extensions: 2373254
Number of sequences better than 10.0: 89
Length of query: 341
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 318
Effective length of database: 102,190,702,835
Effective search space: 32496643501530
Effective search space used: 32496643501530
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 8. 2
Homology vs Protein 
Query= Contig-U05528-1 (Contig-U05528-1Q) /CSM_Contig/Contig-U05528-1Q.Seq.d
         (341 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 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: 3268448
Number of Hits to DB: 254,931,068
Number of extensions: 2653403
Number of successful extensions: 2060
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2060
Number of HSP's successfully gapped: 0
Length of query: 113
Length of database: 1,061,185,681
Length adjustment: 80
Effective length of query: 33
Effective length of database: 799,709,841
Effective search space: 26390424753
Effective search space used: 26390424753
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: 28 (15.4 bits)
PSORT 

 psg: 0.03  gvh: 0.54  alm: 0.39  top: 0.53  tms: 0.00  mit: 0.39  mip: 0.00
 nuc: 0.43  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 

	 64.0 %: nuclear
	 20.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U05528-1 is nuc
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