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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-U05153-1
Contig ID Contig-U05153-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U05153-1 (Contig-U05153-1Q) /CSM_Contig/Contig-U05153-1Q.Seq.d
GAAAATTTATATTTCTTTTTCAGGTCATAGAAATTATGAAACCCAACAAA
ATTAAATTACAATAAATCATTTTATTCAACAAGTGATGAAATTAGATTAA
AAACCAAAGTACCAATCTTTAGACAATGATGAAAATGCCGACCATTTATC
AATTGGTAAACTTAGAGAATCTGAACACTCTGTAGCATTAGTAAACTTGG
AATTCATTAAAATTGATTCAATTGTAAATTTAACAGCTGAAGAATTAAAT
NGATTAGTAGTTATTCCAAAAACTGAAAAAATTTCACCAGAAAATAGAAT
CGAAAAACTTGAAAATGATATGAAACAAATTAAAGAACAATTAGATAGAT
TATTACCAAAATCACATAATACTGCTTTATAAGATTTTTAATTATTTTTT
TCCAGTTTTTTTTTTTTAAAATGGAAATAAAAAATAATAAAAATTAATAA
TAAATTAATAATTTATTTTATAATTAATAAACAAATTATAATTATAAATA
AAAACGCAAATATACAAATAAACAAATAAATAAAAAAATAATAATTGATA
AATATGTAGTACAG
Gap no gap
Contig length 564
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 7308956
End point 7308384
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 2
Link to clone list U05153
List of clone(s) 

est1=SSF678E,1,562
est2=SSM674Z,261,565
Translated Amino Acid sequence 
kiyisfsghrnyetqqn*itinhfiqqvmkld*KPKYQSLDNDENADHLSIGKLRESEHS
VALVNLEFIKIDSIVNLTAEELNXLVVIPKTEKISPENRIEKLENDMKQIKEQLDRLLPK
SHNTAL*df*lffssffflkwk*kiikinnkliiyfiinkqiiiinknaniqink*ikk*
*linm*y
Translated Amino Acid sequence (All Frames) 
Frame A:
enlyfffrs*kl*nptklnynksfystsdeirlktkvpifrq**kcrpfinw*t*ri*tl
csisklgih*n*fnckfns*rikxissyskn*knftrk*nrkt*k*yetn*rtir*iitk
it*ycfirfliiffqffffkmeiknnkn***innlfyn**tnynyk*krkytnkqinkki
iidkyvvq


Frame B:
kiyisfsghrnyetqqn*itinhfiqqvmkld*KPKYQSLDNDENADHLSIGKLRESEHS
VALVNLEFIKIDSIVNLTAEELNXLVVIPKTEKISPENRIEKLENDMKQIKEQLDRLLPK
SHNTAL*df*lffssffflkwk*kiikinnkliiyfiinkqiiiinknaniqink*ikk*
*linm*y


Frame C:
kfiflfqvieimkpnkiklq*iilfnk**n*iknqstnl*tmmkmptiyqlvnlenlntl
*h**twnslkliql*i*qlkn*xd**lfqklkkfhqkiesknlkmi*nklknn*idyyqn
hiillykifnyffpvfff*ngnkk**kliin**fil*linkl*l*iktqiyk*tnk*knn
n**icst
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05153-1 (Contig-U05153-1Q)
/CSM_Contig/Contig-U05153-1Q.Seq.d
         (564 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05153-1 (Contig-U05153-1Q) /CSM_Contig/Conti...   523  e-149
Contig-U04813-1 (Contig-U04813-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U14182-1 (Contig-U14182-1Q) /CSM_Contig/Conti...    38  0.010
Contig-U13722-1 (Contig-U13722-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U07287-1 (Contig-U07287-1Q) /CSM_Contig/Conti...    36  0.039
Contig-U12811-1 (Contig-U12811-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U12223-1 (Contig-U12223-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U05086-1 (Contig-U05086-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U13901-1 (Contig-U13901-1Q) /CSM_Contig/Conti...    32  0.61
Contig-U06609-1 (Contig-U06609-1Q) /CSM_Contig/Conti...    28  9.6

>Contig-U05153-1 (Contig-U05153-1Q) /CSM_Contig/Contig-U05153-1Q.Seq.d
          Length = 564

 Score =  523 bits (264), Expect = e-149
 Identities = 267/267 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gaaaatttatatttctttttcaggtcatagaaattatgaaacccaacaaaattaaattac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gaaaatttatatttctttttcaggtcatagaaattatgaaacccaacaaaattaaattac 60

                                                                       
Query: 61  aataaatcattttattcaacaagtgatgaaattagattaaaaaccaaagtaccaatcttt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aataaatcattttattcaacaagtgatgaaattagattaaaaaccaaagtaccaatcttt 120

                                                                       
Query: 121 agacaatgatgaaaatgccgaccatttatcaattggtaaacttagagaatctgaacactc 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 agacaatgatgaaaatgccgaccatttatcaattggtaaacttagagaatctgaacactc 180

                                                                       
Query: 181 tgtagcattagtaaacttggaattcattaaaattgattcaattgtaaatttaacagctga 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 tgtagcattagtaaacttggaattcattaaaattgattcaattgtaaatttaacagctga 240

                                      
Query: 241 agaattaaatngattagtagttattcc 267
           |||||||||||||||||||||||||||
Sbjct: 241 agaattaaatngattagtagttattcc 267


 Score =  137 bits (69), Expect = 1e-32
 Identities = 69/69 (100%)
 Strand = Plus / Plus

                                                                       
Query: 316 tgatatgaaacaaattaaagaacaattagatagattattaccaaaatcacataatactgc 375
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 316 tgatatgaaacaaattaaagaacaattagatagattattaccaaaatcacataatactgc 375

                    
Query: 376 tttataaga 384
           |||||||||
Sbjct: 376 tttataaga 384


>Contig-U04813-1 (Contig-U04813-1Q) /CSM_Contig/Contig-U04813-1Q.Seq.d
          Length = 591

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                   
Query: 48  aaaattaaattacaataaatcatt 71
           |||||||||||||||| |||||||
Sbjct: 439 aaaattaaattacaatcaatcatt 462


>Contig-U14182-1 (Contig-U14182-1Q) /CSM_Contig/Contig-U14182-1Q.Seq.d
          Length = 1547

 Score = 38.2 bits (19), Expect = 0.010
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 212 attgattcaattgtaaatt 230
           |||||||||||||||||||
Sbjct: 200 attgattcaattgtaaatt 218


  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: 7462
Number of Sequences: 6905
Number of extensions: 7462
Number of successful extensions: 791
Number of sequences better than 10.0: 267
length of query: 564
length of database: 5,674,871
effective HSP length: 16
effective length of query: 548
effective length of database: 5,564,391
effective search space: 3049286268
effective search space used: 3049286268
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. 7.12
Homology vs DNA 
Query= Contig-U05153-1 (Contig-U05153-1Q) /CSM_Contig/Contig-U05153-1Q.Seq.d
         (564 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

(AC115581) Dictyostelium discoideum chromosome 2 map complem...   278   e-147  4
(AU072999) Dictyostelium discoideum slug cDNA, clone SSF678.      250   e-123  2
(C84770) Dictyostelium discoideum slug cDNA, clone SSF678.        278   1e-89  2
(C93140) Dictyostelium discoideum slug cDNA, clone SSM674.         94   7e-15  1
(AC168554) Strongylocentrotus purpuratus clone R3-3091G16, W...    40   0.37   3
(ER492287) 1093015331551 Global-Ocean-Sampling_GS-35-01-01-1...    48   0.37   1
(ER446572) 1092963832820 Global-Ocean-Sampling_GS-35-01-01-1...    48   0.37   1
(AC216660) Solanum lycopersicum chromosome 6 clone C06SLe012...    46   1.5    1
(AC124915) Homo sapiens chromosome 3 clone RP11-717N7, compl...    46   1.5    1
(AC104445) Homo sapiens chromosome 3 clone RP11-444P10, comp...    46   1.5    1
(AC025343) Homo sapiens chromosome 19 clone RP11-330I7 map 1...    46   1.5    1
(EY498542) CBBP4184.fwd CBBP Hirudo medicinalis hermaphrodit...    46   1.5    1
(EY498541) CBBP4184.rev CBBP Hirudo medicinalis hermaphrodit...    46   1.5    1
(EY488990) CBBP16769.rev CBBP Hirudo medicinalis hermaphrodi...    46   1.5    1
(AP008068) Lotus japonicus genomic DNA, chromosome 5, clone:...    40   2.3    4
(AC146590) Medicago truncatula chromosome 8 clone mth2-145p1...    34   3.0    2
(AC202301) Medicago truncatula clone mth2-166m2, complete se...    34   3.0    2
(AC153123) Medicago truncatula clone mte1-72m7, complete seq...    34   3.0    2
(AP009963) Lotus japonicus genomic DNA, chromosome 1, clone:...    32   3.0    2
(AC140858) Homo sapiens chromosome 16 clone RP11-1007N21, WO...    38   4.7    3
(AL928675) Zebrafish DNA sequence from clone DKEY-13B16 in l...    36   5.3    3
(CU571088) Zebrafish DNA sequence from clone DKEY-239H4 in l...    44   5.8    1
(CU463231) Zebrafish DNA sequence from clone CH73-15B2 in li...    44   5.8    1
(CR382299) Zebrafish DNA sequence from clone DKEY-9I13 in li...    44   5.8    1
(BX572076) Zebrafish DNA sequence from clone DKEY-69N5 in li...    44   5.8    1
(AL731819) Mouse DNA sequence from clone RP23-107K16 on chro...    44   5.8    1
(AC154500) Mus musculus BAC clone RP23-207P3 from chromosome...    44   5.8    1
(AC099158) Rattus norvegicus  BAC CH230-49H2 (Children's Hos...    44   5.8    1
(AL133298) Arabidopsis thaliana DNA chromosome 3, BAC clone ...    44   5.8    1
(AC174290) Medicago truncatula clone mth2-52e11, complete se...    44   5.8    1
(AL035593) Human DNA sequence from clone RP1-310J6 on chromo...    44   5.8    1
(AC064878) Homo sapiens chromosome 6 clone RP11-13I13, compl...    44   5.8    1
(AC129770) Rattus norvegicus clone CH230-11N14, *** SEQUENCI...    44   5.8    1
(AC120481) Rattus norvegicus clone CH230-38H9, WORKING DRAFT...    44   5.8    1
(AC117043) Rattus norvegicus clone CH230-26A20, *** SEQUENCI...    44   5.8    1
(AC112064) Rattus norvegicus clone CH230-213F14, *** SEQUENC...    44   5.8    1
(AC110134) Rattus norvegicus clone CH230-45H18, *** SEQUENCI...    44   5.8    1
(AC098262) Rattus norvegicus clone CH230-1K1, *** SEQUENCING...    44   5.8    1
(CU856603) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.8    1
(AP007701) Lotus japonicus genomic DNA, chromosome 5, clone:...    44   5.8    1
(AC231362) Medicago truncatula clone mth2-34c4, WORKING DRAF...    44   5.8    1
(AC202347) Medicago truncatula clone mth2-31l19, WORKING DRA...    44   5.8    1
(AC185367) Otolemur garnettii clone CH256-171D14, WORKING DR...    44   5.8    1
(ET298485) S0232I02_T7 CHORI-214 Salmo salar genomic clone S...    44   5.8    1
(AL975288) Danio rerio genomic clone DKEY-46P24, genomic sur...    44   5.8    1
(CL030941) CH216-31M5_Sp6.1 CH216 Xenopus (Silurana) tropica...    44   5.8    1
(CC191952) CH261-191I13_RM1.1 CH261 Gallus gallus genomic cl...    44   5.8    1
(EG853038) EST_ssal_eve_13926 ssaleve thyroid Salmo salar cD...    44   5.8    1
(DN583995) 93849037 Sea Urchin primary mesenchyme cell cDNA ...    44   5.8    1
(CA049208) ssalksha001095 kidney Salmo salar cDNA, mRNA sequ...    44   5.8    1
(BQ870428) QGD9A11.yg.ab1 QG_ABCDI lettuce salinas Lactuca s...    44   5.8    1
(BQ869591) QGD6K02.yg.ab1 QG_ABCDI lettuce salinas Lactuca s...    44   5.8    1
(EY059065) CATF11397.rev CATF Artemisia annua, Tanzanian, fr...    44   5.8    1
(EL505134) F04_732_302.AB1 Blood stage Plasmodium falciparum...    36   9.2    2

>(AC115581) Dictyostelium discoideum chromosome 2 map
             complement(3527391-3470188) strain AX4, complete sequence.
          Length = 57203

 Score =  278 bits (140), Expect(4) = e-147
 Identities = 142/143 (99%)
 Strand = Plus / Minus


Query: 125   aatgatgaaaatgccgaccatttatcaattggtaaacttagagaatctgaacactctgta 184
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 56068 aatgatgaaaatgccgaccatttatcaattggtaaacttagagaatctgaacactctgta 56009


Query: 185   gcattagtaaacttggaattcattaaaattgattcaattgtaaatttaacagctgaagaa 244
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 56008 gcattagtaaacttggaattcattaaaattgattcaattgtaaatttaacagctgaagaa 55949


Query: 245   ttaaatngattagtagttattcc 267
             |||||| ||||||||||||||||
Sbjct: 55948 ttaaatagattagtagttattcc 55926

 Score =  176 bits (89), Expect(4) = e-147
 Identities = 89/89 (100%)
 Strand = Plus / Minus


Query: 38    gaaacccaacaaaattaaattacaataaatcattttattcaacaagtgatgaaattagat 97
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 56157 gaaacccaacaaaattaaattacaataaatcattttattcaacaagtgatgaaattagat 56098


Query: 98    taaaaaccaaagtaccaatctttagacaa 126
             |||||||||||||||||||||||||||||
Sbjct: 56097 taaaaaccaaagtaccaatctttagacaa 56069

 Score = 93.7 bits (47), Expect(4) = e-147
 Identities = 47/47 (100%)
 Strand = Plus / Minus


Query: 338   caattagatagattattaccaaaatcacataatactgctttataaga 384
             |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55739 caattagatagattattaccaaaatcacataatactgctttataaga 55693

 Score = 75.8 bits (38), Expect(4) = e-147
 Identities = 38/38 (100%)
 Strand = Plus / Minus


Query: 1     gaaaatttatatttctttttcaggtcatagaaattatg 38
             ||||||||||||||||||||||||||||||||||||||
Sbjct: 56765 gaaaatttatatttctttttcaggtcatagaaattatg 56728

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 462,525,726
Number of extensions: 29591805
Number of successful extensions: 2567022
Number of sequences better than 10.0: 56
Length of query: 564
Length of database: 104,622,809,269
Length adjustment: 23
Effective length of query: 541
Effective length of database: 102,190,702,835
Effective search space: 55285170233735
Effective search space used: 55285170233735
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 8. 1
Homology vs Protein 
Query= Contig-U05153-1 (Contig-U05153-1Q) /CSM_Contig/Contig-U05153-1Q.Seq.d
         (564 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC115581_27(AC115581|pid:none) Dictyostelium discoideum chromoso...   162   3e-51
AM910987_178(AM910987|pid:none) Plasmodium knowlesi strain H chr...    39   0.096
CP000743_304(CP000743|pid:none) Methanococcus aeolicus Nankai-3,...    37   0.36
BC152012_1(BC152012|pid:none) Danio rerio similar to GTPase, IMA...    36   0.62
(Q8EVP2) RecName: Full=Ribosomal RNA large subunit methyltransfe...    35   1.4
(O61308) RecName: Full=227 kDa spindle- and centromere-associate...    34   2.4
AM778941_23(AM778941|pid:none) Microcystis aeruginosa PCC 7806 g...    34   2.4
CP000517_1569(CP000517|pid:none) Lactobacillus helveticus DPC 45...    34   3.1
(Q6LFN2) RecName: Full=RING finger protein PFF0165c;  &AL844505_...    33   4.0
FM864216_551(FM864216|pid:none) Mycoplasma conjunctivae HRC/581T...    33   5.3
CP000312_1054(CP000312|pid:none) Clostridium perfringens SM101, ...    33   6.9
Z22176_11(Z22176|pid:none) Caenorhabditis elegans Cosmid ZK1098,...    33   6.9
CP000771_320(CP000771|pid:none) Fervidobacterium nodosum Rt17-B1...    32   9.0
CP000552_1217(CP000552|pid:none) Prochlorococcus marinus str. MI...    32   9.0

>AC115581_27(AC115581|pid:none) Dictyostelium discoideum chromosome
           2 map complement(3527391-3470188) strain AX4, complete
           sequence.
          Length = 133

 Score =  162 bits (410), Expect(2) = 3e-51
 Identities = 83/85 (97%), Positives = 84/85 (98%)
 Frame = +2

Query: 125 NDENADHLSIGKLRESEHSVALVNLEFIKIDSIVNLTAEELNXLVVIPKTEKISPENRIE 304
           NDENADHLSIGKLRESEHSVALVNLEFIKIDSIVNLTAEELN LVVIPKTEKISPENRIE
Sbjct: 49  NDENADHLSIGKLRESEHSVALVNLEFIKIDSIVNLTAEELNRLVVIPKTEKISPENRIE 108

Query: 305 KLENDMKQIKEQLDRLLPKSHNTAL 379
           KLEND+KQIKEQLDRLLPKSHNTAL
Sbjct: 109 KLENDIKQIKEQLDRLLPKSHNTAL 133

 Score = 62.8 bits (151), Expect(2) = 3e-51
 Identities = 29/29 (100%), Positives = 29/29 (100%)
 Frame = +1

Query: 40  NPTKLNYNKSFYSTSDEIRLKTKVPIFRQ 126
           NPTKLNYNKSFYSTSDEIRLKTKVPIFRQ
Sbjct: 20  NPTKLNYNKSFYSTSDEIRLKTKVPIFRQ 48

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: 487,042,817
Number of extensions: 7186511
Number of successful extensions: 23055
Number of sequences better than 10.0: 14
Number of HSP's gapped: 23040
Number of HSP's successfully gapped: 15
Length of query: 188
Length of database: 1,061,185,681
Length adjustment: 121
Effective length of query: 67
Effective length of database: 665,703,473
Effective search space: 44602132691
Effective search space used: 44602132691
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: 0.45  alm: 0.39  top: 0.53  tms: 0.00  mit: 0.20  mip: 0.00
 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 

	 56.0 %: cytoplasmic
	 28.0 %: nuclear
	  8.0 %: cytoskeletal
	  4.0 %: Golgi
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U05153-1 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) 2
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