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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-U14060-1
Contig ID Contig-U14060-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Contig-U14060-1Q.Seq.d
NNNNNNNNNNATAATAATGANAATAATGNNNCTCTTTTNGATGANATTAT
GAAGAATACATATGAATATCCAAGCNTTTAGTAANCNATGGTGGACAGAA
AAAGCATCCATNTTCATAGTCNTNGGTNTNACAGGTNNTTCNTCNCTTCA
TGTAGTTNAANTTNTATTGAAATATTTAATTGGTTATCAAAATCCAGTTA
GTCCATNCCGGGGAGGTTTGGAATTAATTCAAAATGATCCANAATATGTA
ATAGTTTATTTTTTAACAATGTAGACAGTTNNTCCTNTCATTCTCATTTC
ATATGGANCTTTATTTGGAAGACCCTCCCATACTTTATCAAACTCTTTAA
TAGAATGTCAATTTTCTCTCNATTAAAAAGATTATTCTTAANATTTTCAA
AAAAATCTTCAAATAAAAAAGAAGTAATANATTTTTTTTTCTTNTAGCGA
TTTAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAA
TAATAATAATAATAATAATAATAATAATTATTATAATAGATTATACTAGA
TAAAAATAATAAACAAATTTAGT
Gap no gap
Contig length 573
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 3023377
End point 3022814
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U14060
List of clone(s) 

est1=AHG104Z,1,564
Translated Amino Acid sequence 
xxxiimximxlfxmxl*RIHMNIQAFSXXWWTEKASXFIVXGXTGXSSLHVVXXXLKYLI
GYQNPVSPXRGGLELIQNDPXYVIVYFLTM*tvxpxilisygxlfgrpshtlsnsliecq
fslx*kdys*xfqknlqikkk*xiffsxsdliiiiiiiiiiiiiiiiiiiiiiiiiiiid
ytr*k**tnl
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxnnxnnxxlxdximkntyeypsx**xmvdrksihxhsxxxxrxfxxscsxxxieifn
wlskss*sxpgrfginsk*sxicnslffnnvdsxsxhshfiwxfiwktlpyfiklfnrms
ifsxlkrlflxfskkssnkkevixfffx*rfnnnnnnnnnnnnnnnnnnnnnnnnnyynr
ly*ikiinkfs


Frame B:
xxxiimximxlfxmxl*RIHMNIQAFSXXWWTEKASXFIVXGXTGXSSLHVVXXXLKYLI
GYQNPVSPXRGGLELIQNDPXYVIVYFLTM*tvxpxilisygxlfgrpshtlsnsliecq
fslx*kdys*xfqknlqikkk*xiffsxsdliiiiiiiiiiiiiiiiiiiiiiiiiiiid
ytr*k**tnl


Frame C:
xxx***x*xxsfx*xyeeyi*iskxlvxxggqkkhpxs*sxvxqvxxxfm*xxxy*ni*l
vikiqlvhxgevwn*fkmixnm**fif*qcrqxxlsfsfhmxlyledppilyqtl**nvn
flsikkiilxifkkifk*krsnxffflxai*************************ll**i
ildknnkqi*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14060-1 (Contig-U14060-1Q)
/CSM_Contig/Contig-U14060-1Q.Seq.d
         (573 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Conti...   617  e-177
Contig-U09764-1 (Contig-U09764-1Q) /CSM_Contig/Conti...    36  0.040
Contig-U08437-1 (Contig-U08437-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U01630-1 (Contig-U01630-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U14499-1 (Contig-U14499-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U14428-1 (Contig-U14428-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U12056-1 (Contig-U12056-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U11430-1 (Contig-U11430-1Q) /CSM_Contig/Conti...    32  0.62
Contig-U11264-1 (Contig-U11264-1Q) /CSM_Contig/Conti...    32  0.62

>Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Contig-U14060-1Q.Seq.d
          Length = 573

 Score =  617 bits (311), Expect = e-177
 Identities = 412/419 (98%)
 Strand = Plus / Plus

                                                                       
Query: 11  ataataatganaataatgnnnctcttttngatganattatgaagaatacatatgaatatc 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  ataataatganaataatgnnnctcttttngatganattatgaagaatacatatgaatatc 70

                                                                       
Query: 71  caagcntttagtaancnatggtggacagaaaaagcatccatnttcatagtcntnggtntn 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  caagcntttagtaancnatggtggacagaaaaagcatccatnttcatagtcntnggtntn 130

                                                                       
Query: 131 acaggtnnttcntcncttcatgtagttnaanttntattgaaatatttaattggttatcaa 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 131 acaggtnnttcntcncttcatgtagttnaanttntattgaaatatttaattggttatcaa 190

                                                                       
Query: 191 aatccagttagtccatnccggggaggtttggaattaattcaaaatgatccanaatatgta 250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 191 aatccagttagtccatnccggggaggtttggaattaattcaaaatgatccanaatatgta 250

                                                                       
Query: 251 atagtttattttttaacaatgtagacagttnntcctntcattctcatttcatatgganct 310
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 atagtttattttttaacaatgtagacagttnntcctntcattctcatttcatatgganct 310

                                                                       
Query: 311 ttatttggaagaccctcccatactttatcaaactctttaatagaatgtcaattttctctc 370
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 311 ttatttggaagaccctcccatactttatcaaactctttaatagaatgtcaattttctctc 370

                                                                      
Query: 371 nattaaaaagattattcttaanattttcnnnnnnntcttcaaataaaaaagaagtaata 429
           ||||||||||||||||||||||||||||       ||||||||||||||||||||||||
Sbjct: 371 nattaaaaagattattcttaanattttcaaaaaaatcttcaaataaaaaagaagtaata 429


>Contig-U09764-1 (Contig-U09764-1Q) /CSM_Contig/Contig-U09764-1Q.Seq.d
          Length = 1283

 Score = 36.2 bits (18), Expect = 0.040
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 249 taatagtttattttttaa 266
           ||||||||||||||||||
Sbjct: 441 taatagtttattttttaa 458


>Contig-U08437-1 (Contig-U08437-1Q) /CSM_Contig/Contig-U08437-1Q.Seq.d
          Length = 1122

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 408 ttcaaataaaaaagaag 424
           |||||||||||||||||
Sbjct: 934 ttcaaataaaaaagaag 918


  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: 5545
Number of Sequences: 6905
Number of extensions: 5545
Number of successful extensions: 521
Number of sequences better than 10.0: 136
length of query: 573
length of database: 5,674,871
effective HSP length: 16
effective length of query: 557
effective length of database: 5,564,391
effective search space: 3099365787
effective search space used: 3099365787
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 2008.12.17
Homology vs DNA 
Query= Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Contig-U14060-1Q.Seq.d
         (573 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

(BJ358195) Dictyostelium discoideum cDNA clone:dda43g01, 3' ...   597   e-166  1
(AC116330) Dictyostelium discoideum chromosome 2 map 3191214...   353   e-141  3
(FG703394) G1144P324FL12.T0 Anolis carolinensis pooled norma...    46   1.4    1
(FG655505) G1142P325FN20.T0 Anolis carolinensis pooled norma...    46   1.4    1
(FG655409) G1142P325RN20.T0 Anolis carolinensis pooled norma...    46   1.4    1
(EY386854) CAXA6450.fwd CAXA Helobdella robusta Subtracted L...    46   1.4    1
(CU928590) S.lycopersicum DNA sequence *** SEQUENCING IN PRO...    32   2.8    2
(AC123930) Mus musculus BAC clone RP24-478K24 from chromosom...    44   5.4    1
(CU582816) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.4    1
(CC463558) ZMMBBc0347M19r ZMMBBc Zea mays subsp. mays genomi...    44   5.4    1

>(BJ358195) Dictyostelium discoideum cDNA clone:dda43g01, 3' end,
           single read.
          Length = 564

 Score =  597 bits (301), Expect = e-166
 Identities = 388/388 (100%)
 Strand = Plus / Minus


Query: 11  ataataatganaataatgnnnctcttttngatganattatgaagaatacatatgaatatc 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 564 ataataatganaataatgnnnctcttttngatganattatgaagaatacatatgaatatc 505


Query: 71  caagcntttagtaancnatggtggacagaaaaagcatccatnttcatagtcntnggtntn 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 504 caagcntttagtaancnatggtggacagaaaaagcatccatnttcatagtcntnggtntn 445


Query: 131 acaggtnnttcntcncttcatgtagttnaanttntattgaaatatttaattggttatcaa 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 444 acaggtnnttcntcncttcatgtagttnaanttntattgaaatatttaattggttatcaa 385


Query: 191 aatccagttagtccatnccggggaggtttggaattaattcaaaatgatccanaatatgta 250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 384 aatccagttagtccatnccggggaggtttggaattaattcaaaatgatccanaatatgta 325


Query: 251 atagtttattttttaacaatgtagacagttnntcctntcattctcatttcatatgganct 310
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 324 atagtttattttttaacaatgtagacagttnntcctntcattctcatttcatatgganct 265


Query: 311 ttatttggaagaccctcccatactttatcaaactctttaatagaatgtcaattttctctc 370
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 264 ttatttggaagaccctcccatactttatcaaactctttaatagaatgtcaattttctctc 205


Query: 371 nattaaaaagattattcttaanattttc 398
           ||||||||||||||||||||||||||||
Sbjct: 204 nattaaaaagattattcttaanattttc 177

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 352,497,192
Number of extensions: 22119264
Number of successful extensions: 1485699
Number of sequences better than 10.0: 10
Length of query: 573
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 550
Effective length of database: 93,106,754,628
Effective search space: 51208715045400
Effective search space used: 51208715045400
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 9
Homology vs Protein 
Query= Contig-U14060-1 (Contig-U14060-1Q) /CSM_Contig/Contig-U14060-1Q.Seq.d
         (573 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116330_31(AC116330|pid:none) Dictyostelium discoideum chromoso...    95   5e-23

>AC116330_31(AC116330|pid:none) Dictyostelium discoideum chromosome
           2 map 3191214-3323468 strain AX4, complete sequence.
          Length = 637

 Score = 95.1 bits (235), Expect(2) = 5e-23
 Identities = 45/58 (77%), Positives = 46/58 (79%)
 Frame = +2

Query: 77  FSXXWWTEKASXFIVXGXTGXSSLHVVXXXLKYLIGYQNPVSPXRGGLELIQNDPXYV 250
           FS  WWTEKA  FIV G TG SSLHVV   LKYLIGYQNPVSP RGGLELIQNDP Y+
Sbjct: 84  FSKQWWTEKAYIFIVFGITGTSSLHVVKFLLKYLIGYQNPVSPFRGGLELIQNDPKYI 141

 Score = 35.4 bits (80), Expect(2) = 5e-23
 Identities = 15/20 (75%), Positives = 15/20 (75%)
 Frame = +1

Query: 13  NNXNNXXLXDXIMKNTYEYP 72
           NN NN  L D IMKNTYEYP
Sbjct: 63  NNENNKTLFDKIMKNTYEYP 82

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: 509,082,057
Number of extensions: 7346863
Number of successful extensions: 6586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6586
Number of HSP's successfully gapped: 2
Length of query: 191
Length of database: 1,051,180,864
Length adjustment: 121
Effective length of query: 70
Effective length of database: 659,557,225
Effective search space: 46169005750
Effective search space used: 46169005750
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: 0.87  gvh: 0.47  alm: 0.47  top: 0.37  tms: 0.00  mit: 0.34  mip: 0.10
 nuc: 0.00  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 

	 32.0 %: nuclear
	 28.0 %: cytoplasmic
	 24.0 %: mitochondrial
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U14060-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
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