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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-U06822-1
Contig ID Contig-U06822-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06822-1 (Contig-U06822-1Q) /CSM_Contig/Contig-U06822-1Q.Seq.d
ATATTATTCTATTCACTCGTAATAATACATATAAATTGATATCAATCAGA
AAAACAAACAAACAAACAAACAAGCAAATAAACAAACAAAAAAAACGAAC
AAACAAAAAACGAACAACAATAAAATAAATAATAAATAAATAAATATATA
TAAATAAAAAATGAATAATTTAATTCGTAGATCATTATTAAATCAAATAA
ATTTAAATAGAGCAGGTCAAAAATTTAGACAATCAATAGGACTTGCCAGA
AGTGGTAATGAAGATGGTCCACTTCATGATTTACCAGATTTTCATTTTGC
TAATGGTGAGTTCCCAGCTTTAACAGATACACAAAAGAAATGGATGAAAA
CAAGAATTAATGAAGCAAAGATTTTAAATAAAATTGTAAATGATGTTGAA
ACTCAAAGAAATAAAGTTATTGGTGCTATTAAGACTTTGGAGCAAAAAAC
TAACAAATCAATTCAAAA
Gap no gap
Contig length 468
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 438742
End point 439211
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U06822
List of clone(s) 

est1=VSG715F,1,469
Translated Amino Acid sequence 
yysihs**yi*idinqknkqtnkqankqtkktnkqktnnnkinnk*iniyk*KMNNLIRR
SLLNQINLNRAGQKFRQSIGLARSGNEDGPLHDLPDFHFANGEFPALTDTQKKWMKTRIN
EAKILNKIVNDVETQRNKVIGAIKTLEQKTNKSIQ
Translated Amino Acid sequence (All Frames) 
Frame A:
ilfyslviihin*yqsekqtnkqtsk*tnkkneqtkneqq*nk**inkyi*ikne*fns*
iiiksnkfk*srski*tinrtcqkw**rwsts*ftrfsfc*w*vpsfnrytkemdenkn*
*skdfk*nck*c*nskk*sywcy*dfgakn*qinsk


Frame B:
yysihs**yi*idinqknkqtnkqankqtkktnkqktnnnkinnk*iniyk*KMNNLIRR
SLLNQINLNRAGQKFRQSIGLARSGNEDGPLHDLPDFHFANGEFPALTDTQKKWMKTRIN
EAKILNKIVNDVETQRNKVIGAIKTLEQKTNKSIQ


Frame C:
iilftrnntyklisirktnkqtnkqinkqkkrtnkkrttik*iink*iyinkk*ii*fvd
hy*ik*i*ieqvknldnq*dlpevvmkmvhfmiyqifillmvssql*qihkrng*kqelm
kqrf*ikl*mmlklkeikllvllrlwskkltnqfk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06822-1 (Contig-U06822-1Q)
/CSM_Contig/Contig-U06822-1Q.Seq.d
         (468 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06822-1 (Contig-U06822-1Q) /CSM_Contig/Conti...   593  e-170
Contig-U01796-1 (Contig-U01796-1Q) /CSM_Contig/Conti...    38  0.008
Contig-U13903-1 (Contig-U13903-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U12547-1 (Contig-U12547-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U06302-1 (Contig-U06302-1Q) /CSM_Contig/Conti...    36  0.032
Contig-U14800-1 (Contig-U14800-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U14003-1 (Contig-U14003-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U13665-1 (Contig-U13665-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11642-1 (Contig-U11642-1Q) /CSM_Contig/Conti...    34  0.13
Contig-U11377-1 (Contig-U11377-1Q) /CSM_Contig/Conti...    34  0.13

>Contig-U06822-1 (Contig-U06822-1Q) /CSM_Contig/Contig-U06822-1Q.Seq.d
          Length = 468

 Score =  593 bits (299), Expect = e-170
 Identities = 299/299 (100%)
 Strand = Plus / Plus

                                                                       
Query: 170 ttaattcgtagatcattattaaatcaaataaatttaaatagagcaggtcaaaaatttaga 229
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 170 ttaattcgtagatcattattaaatcaaataaatttaaatagagcaggtcaaaaatttaga 229

                                                                       
Query: 230 caatcaataggacttgccagaagtggtaatgaagatggtccacttcatgatttaccagat 289
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 230 caatcaataggacttgccagaagtggtaatgaagatggtccacttcatgatttaccagat 289

                                                                       
Query: 290 tttcattttgctaatggtgagttcccagctttaacagatacacaaaagaaatggatgaaa 349
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 290 tttcattttgctaatggtgagttcccagctttaacagatacacaaaagaaatggatgaaa 349

                                                                       
Query: 350 acaagaattaatgaagcaaagattttaaataaaattgtaaatgatgttgaaactcaaaga 409
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 350 acaagaattaatgaagcaaagattttaaataaaattgtaaatgatgttgaaactcaaaga 409

                                                                      
Query: 410 aataaagttattggtgctattaagactttggagcaaaaaactaacaaatcaattcaaaa 468
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 410 aataaagttattggtgctattaagactttggagcaaaaaactaacaaatcaattcaaaa 468


 Score = 97.6 bits (49), Expect = 1e-20
 Identities = 49/49 (100%)
 Strand = Plus / Plus

                                                           
Query: 1  atattattctattcactcgtaataatacatataaattgatatcaatcag 49
          |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atattattctattcactcgtaataatacatataaattgatatcaatcag 49


>Contig-U01796-1 (Contig-U01796-1Q) /CSM_Contig/Contig-U01796-1Q.Seq.d
          Length = 947

 Score = 38.2 bits (19), Expect = 0.008
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 377 aataaaattgtaaatgatg 395
           |||||||||||||||||||
Sbjct: 154 aataaaattgtaaatgatg 172


>Contig-U13903-1 (Contig-U13903-1Q) /CSM_Contig/Contig-U13903-1Q.Seq.d
          Length = 1303

 Score = 36.2 bits (18), Expect = 0.032
 Identities = 24/26 (92%)
 Strand = Plus / Plus

                                      
Query: 371  attttaaataaaattgtaaatgatgt 396
            |||||||||  |||||||||||||||
Sbjct: 1058 attttaaattcaattgtaaatgatgt 1083


  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: 7652
Number of Sequences: 6905
Number of extensions: 7652
Number of successful extensions: 1000
Number of sequences better than 10.0: 297
length of query: 468
length of database: 5,674,871
effective HSP length: 16
effective length of query: 452
effective length of database: 5,564,391
effective search space: 2515104732
effective search space used: 2515104732
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 2008.11.10
Homology vs DNA 
Query= Contig-U06822-1 (Contig-U06822-1Q) /CSM_Contig/Contig-U06822-1Q.Seq.d
         (468 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

(AU266746) Dictyostelium discoideum vegetative cDNA clone:VS...   513   e-163  2
(AM615221) Entamoeba invadens IP1 GSS, clone inv059e07.p1k.        50   0.071  1
(AC134655) Rattus norvegicus clone CH230-12A24, *** SEQUENCI...    34   0.59   2
(AC214852) Pan troglodytes BAC clone CH251-599M5 from chromo...    44   0.86   3
(AM430260) Vitis vinifera contig VV78X203763.10, whole genom...    46   1.1    1
(AZ568194) 244PvC02 Pv MBN #30 Plasmodium vivax genomic 3', ...    46   1.1    1
(CT033765) Medicago truncatula chromosome 5 clone mth2-105d2...    38   1.5    3
(FG747469) G1146P39RC21.T0 Anolis carolinensis pooled normal...    42   1.7    2
(AC027359) Homo sapiens chromosome 18, clone RP11-13L18, com...    36   2.1    3
(AC021401) Homo sapiens clone RP11-28P8, WORKING DRAFT SEQUE...    42   2.3    3
(AC073520) Homo sapiens BAC clone RP11-792H4 from 7, complet...    44   2.3    2
(DT740888) EST1174737 Aquilegia cDNA library Aquilegia formo...    34   2.5    2
(AC109314) Homo sapiens chromosome 18, clone CTD-3135I6, com...    36   3.7    3
(BX119918) Zebrafish DNA sequence from clone CH211-202H22 in...    44   4.4    1
(AC154531) Mus musculus BAC clone RP23-468B10 from chromosom...    44   4.4    1
(AC147213) Pan troglodytes BAC clone RP43-127I22 from chromo...    44   4.4    1
(DD121863) STAPHYLOCOCCUS AUREUS PROTEINS AND NUCLEIC ACIDS.       44   4.4    1
(CS712499) Sequence 5039 from Patent EP1829892.                    44   4.4    1
(AX622076) Sequence 5039 from Patent WO02094868.                   44   4.4    1
(AR535608) Sequence 170 from patent US 6737248.                    44   4.4    1
(AR411573) Sequence 20 from patent US 6638718.                     44   4.4    1
(AR405027) Sequence 20 from patent US 6630303.                     44   4.4    1
(AR354052) Sequence 170 from patent US 6593114.                    44   4.4    1
(AR149317) Sequence 20 from patent US 6228588.                     44   4.4    1
(AL139237) Human DNA sequence from clone RP11-168P8 on chrom...    44   4.4    1
(AC094590) Rattus norvegicus clone CH230-4D8, *** SEQUENCING...    44   4.4    1
(CU915556) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.4    1
(AL390714) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    44   4.4    1
(AC021540) Homo sapiens chromosome 10 clone RP11-477E6 map 1...    44   4.4    1
(EK085298) 1092961143051 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.4    1
(EK011797) 1092955196836 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.4    1
(ED810655) ML__Ba0055O06f ML__Ba Mimulus lewisii genomic, ge...    44   4.4    1
(AG667114) Macaca fuscata fuscata DNA, clone: MSB2-089C02_R,...    44   4.4    1
(CT848495) Oryza sativa Indica Group EST sequence:CONTIG4740.      44   4.4    1
(CD859072) CNE.007E11F010726 CNE Pisum sativum cDNA clone CN...    44   4.4    1
(EX566046) AIAE-aaa51h08.b1 Ancylostoma_caninum_EST_Female_p...    44   4.4    1
(CP000736) Staphylococcus aureus subsp. aureus JH1, complete...    44   4.4    1
(CP000730) Staphylococcus aureus subsp. aureus USA300_TCH151...    44   4.4    1
(CP000703) Staphylococcus aureus subsp. aureus JH9, complete...    44   4.4    1
(CP000255) Staphylococcus aureus subsp. aureus USA300_FPR375...    44   4.4    1
(CP000253) Staphylococcus aureus subsp. aureus NCTC 8325, co...    44   4.4    1
(CP000046) Staphylococcus aureus subsp. aureus COL, complete...    44   4.4    1
(BX571857) Staphylococcus aureus strain MSSA476, complete ge...    44   4.4    1
(BX571856) Staphylococcus aureus subsp. aureus strain MRSA25...    44   4.4    1
(BA000033) Staphylococcus aureus subsp. aureus MW2 DNA, comp...    44   4.4    1
(BA000018) Staphylococcus aureus subsp. aureus N315 DNA, com...    44   4.4    1
(BA000017) Staphylococcus aureus subsp. aureus Mu50 DNA, com...    44   4.4    1
(AP009351) Staphylococcus aureus subsp. aureus str. Newman D...    44   4.4    1
(AP009324) Staphylococcus aureus subsp. aureus Mu3 DNA, comp...    44   4.4    1
(AJ938182) Staphylococcus aureus RF122 complete genome.            44   4.4    1
(AC164335) Bos taurus clone CH240-145K5, *** SEQUENCING IN P...    40   4.8    3
(AC093263) Homo sapiens chromosome 5 clone RP11-259G23, comp...    42   5.9    3
(AC019088) Homo sapiens chromosome 11 clone RP11-364G22, WOR...    42   6.9    4
(EJ986305) 1093023013133 Global-Ocean-Sampling_GS-30-02-01-1...    38   7.1    2
(AL357393) Human DNA sequence *** SEQUENCING CANCELLED *** f...    38   7.1    3
(EJ928026) 1093018790578 Global-Ocean-Sampling_GS-30-02-01-1...    38   7.8    2
(AC139812) Homo sapiens chromosome 5 clone RP11-1375M22, WOR...    42   8.0    4
(AC187478) Gossypium hirsutum chromosome UNKNOWN clone ZMMBB...    30   8.2    2
(AC139804) Homo sapiens chromosome 5 clone RP11-1349B19, WOR...    42   9.0    4
(AC215724) Zea mays chromosome 2 clone CH201-478E21; ZMMBBc0...    38   9.4    3
(AC205577) Zea mays chromosome 3 clone CH201-123K3; ZMMBBc01...    38   9.9    3

>(AU266746) Dictyostelium discoideum vegetative cDNA clone:VSG715,
           5' end single read.
          Length = 469

 Score =  513 bits (259), Expect(2) = e-163
 Identities = 259/259 (100%)
 Strand = Plus / Plus


Query: 210 gagcaggtcaaaaatttagacaatcaataggacttgccagaagtggtaatgaagatggtc 269
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 210 gagcaggtcaaaaatttagacaatcaataggacttgccagaagtggtaatgaagatggtc 269


Query: 270 cacttcatgatttaccagattttcattttgctaatggtgagttcccagctttaacagata 329
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 270 cacttcatgatttaccagattttcattttgctaatggtgagttcccagctttaacagata 329


Query: 330 cacaaaagaaatggatgaaaacaagaattaatgaagcaaagattttaaataaaattgtaa 389
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 330 cacaaaagaaatggatgaaaacaagaattaatgaagcaaagattttaaataaaattgtaa 389


Query: 390 atgatgttgaaactcaaagaaataaagttattggtgctattaagactttggagcaaaaaa 449
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 390 atgatgttgaaactcaaagaaataaagttattggtgctattaagactttggagcaaaaaa 449


Query: 450 ctaacaaatcaattcaaaa 468
           |||||||||||||||||||
Sbjct: 450 ctaacaaatcaattcaaaa 468

 Score = 97.6 bits (49), Expect(2) = e-163
 Identities = 49/49 (100%)
 Strand = Plus / Plus


Query: 1  atattattctattcactcgtaataatacatataaattgatatcaatcag 49
          |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atattattctattcactcgtaataatacatataaattgatatcaatcag 49

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 436,128,834
Number of extensions: 28426420
Number of successful extensions: 2485172
Number of sequences better than 10.0: 61
Length of query: 468
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 445
Effective length of database: 93,106,754,628
Effective search space: 41432505809460
Effective search space used: 41432505809460
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06822-1 (Contig-U06822-1Q) /CSM_Contig/Contig-U06822-1Q.Seq.d
         (468 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q4V7Q1) RecName: Full=39S ribosomal protein L52, mitochondrial;...    42   0.005
DQ440494_1(DQ440494|pid:none) Aedes aegypti clone AET-8464 mitoc...    42   0.007
(Q290P4) RecName: Full=39S ribosomal protein L52, mitochondrial;...    38   0.097
BC166922_1(BC166922|pid:none) Rattus norvegicus mitochondrial ri...    34   1.4
AY961510_1(AY961510|pid:none) Lysiphlebus testaceipes putative m...    34   1.8
AY815437_1(AY815437|pid:none) Schistosoma japonicum SJCHGC09519 ...    34   1.8
CP000768_1158(CP000768|pid:none) Campylobacter jejuni subsp. doy...    33   4.1
(P0C2B7) RecName: Full=39S ribosomal protein L52, mitochondrial;...    33   4.1
CP000814_500(CP000814|pid:none) Campylobacter jejuni subsp. jeju...    32   5.3
AY181031_2(AY181031|pid:none) Vibrio fischeri strain CIP 103206 ...    32   5.3
AL111168_506(AL111168|pid:none) Campylobacter jejuni subsp. jeju...    32   7.0
CP000025_631(CP000025|pid:none) Campylobacter jejuni RM1221, com...    32   7.0
FN318664_1(FN318664|pid:none) Schistosoma japonicum isolate Anhu...    32   9.1

>(Q4V7Q1) RecName: Full=39S ribosomal protein L52, mitochondrial;
                 Short=L52mt;          Short=MRP-L52; Flags:
           Precursor;  &BC097777_1(BC097777|pid:none)
          Length = 145

 Score = 42.4 bits (98), Expect = 0.005
 Identities = 21/35 (60%), Positives = 25/35 (71%)
 Frame = +2

Query: 203 LNRAGQKFRQSIGLARSGNEDGPLHDLPDFHFANG 307
           L  AGQ +R   G ARSG+E GPL DLPD+ FA+G
Sbjct: 43  LRCAGQDWRVRRGFARSGSEYGPLTDLPDWSFADG 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: 3204285
Number of Hits to DB: 449,961,967
Number of extensions: 6911886
Number of successful extensions: 17331
Number of sequences better than 10.0: 13
Number of HSP's gapped: 17324
Number of HSP's successfully gapped: 13
Length of query: 156
Length of database: 1,040,966,779
Length adjustment: 117
Effective length of query: 39
Effective length of database: 666,065,434
Effective search space: 25976551926
Effective search space used: 25976551926
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: 0.74  gvh: 0.44  alm: 0.61  top: 0.53  tms: 0.00  mit: 0.52  mip: 0.06
 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 

	 92.0 %: mitochondrial
	  8.0 %: nuclear

>> prediction for Contig-U06822-1 is mit
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