NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U04644-1
Contig ID Contig-U04644-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04644-1 (Contig-U04644-1Q) /CSM_Contig/Contig-U04644-1Q.Seq.d
GATTGGGAAGTCATTGATAAAAGATCTTCTTCTGAAGATAATGAAGAAAA
TGATGAATGGGGCGCTTGGGAATAAGTTTTATGTTGAAAACAAATAACAA
ATAACTAATTAAAAAAATTAAATAAATAATTTTTTTTTTTTTTTATTGTT
AATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gap no gap
Contig length 236
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 1265300
End point 1265064
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U04644
List of clone(s) 

est1=SSC122F,1,237
Translated Amino Acid sequence 
igkslikdlllkimkkmmngalgnkfyvenk*qitn*kn*INNFFFFLLLIKKKKKKKKK
KKKKKKKKKKKKKKKKKK
Translated Amino Acid sequence (All Frames) 
Frame A:
dwevidkrsssedneendewgawe*vlc*kqitnn*lkklnk*fffffivnkkkkkkkkk
kkkkkkkkkkkkkkkkkk


Frame B:
igkslikdlllkimkkmmngalgnkfyvenk*qitn*kn*INNFFFFLLLIKKKKKKKKK
KKKKKKKKKKKKKKKKKK


Frame C:
lgsh**kiff*r**rk**mgrlgisfmlktnnk*likkik*iiffffyc**kkkkkkkkk
kkkkkkkkkkkkkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04644-1 (Contig-U04644-1Q)
/CSM_Contig/Contig-U04644-1Q.Seq.d
         (236 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04644-1 (Contig-U04644-1Q) /CSM_Contig/Conti...   170  4e-43
Contig-U02881-1 (Contig-U02881-1Q) /CSM_Contig/Conti...    36  0.016
Contig-U14140-1 (Contig-U14140-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11875-1 (Contig-U11875-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11309-1 (Contig-U11309-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11288-1 (Contig-U11288-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U08437-1 (Contig-U08437-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U06529-1 (Contig-U06529-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U05046-1 (Contig-U05046-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U04777-1 (Contig-U04777-1Q) /CSM_Contig/Conti...    34  0.063

>Contig-U04644-1 (Contig-U04644-1Q) /CSM_Contig/Contig-U04644-1Q.Seq.d
          Length = 236

 Score =  170 bits (86), Expect = 4e-43
 Identities = 86/86 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  gattgggaagtcattgataaaagatcttcttctgaagataatgaagaaaatgatgaatgg 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  gattgggaagtcattgataaaagatcttcttctgaagataatgaagaaaatgatgaatgg 60

                                    
Query: 61 ggcgcttgggaataagttttatgttg 86
          ||||||||||||||||||||||||||
Sbjct: 61 ggcgcttgggaataagttttatgttg 86


>Contig-U02881-1 (Contig-U02881-1Q) /CSM_Contig/Contig-U02881-1Q.Seq.d
          Length = 1290

 Score = 36.2 bits (18), Expect = 0.016
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 40  aatgaagaaaatgatgaa 57
           ||||||||||||||||||
Sbjct: 377 aatgaagaaaatgatgaa 394


 Score = 30.2 bits (15), Expect = 0.98
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 44  aagaaaatgatgaat 58
           |||||||||||||||
Sbjct: 417 aagaaaatgatgaat 431


 Score = 28.2 bits (14), Expect = 3.9
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 44  aagaaaatgatgaa 57
           ||||||||||||||
Sbjct: 399 aagaaaatgatgaa 412


>Contig-U14140-1 (Contig-U14140-1Q) /CSM_Contig/Contig-U14140-1Q.Seq.d
          Length = 392

 Score = 34.2 bits (17), Expect = 0.063
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 33  tgaagataatgaagaaa 49
           |||||||||||||||||
Sbjct: 112 tgaagataatgaagaaa 128


  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: 1189
Number of Sequences: 6905
Number of extensions: 1189
Number of successful extensions: 435
Number of sequences better than 10.0: 72
length of query: 236
length of database: 5,674,871
effective HSP length: 15
effective length of query: 221
effective length of database: 5,571,296
effective search space: 1231256416
effective search space used: 1231256416
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. 6.28
Homology vs DNA 
Query= Contig-U04644-1 (Contig-U04644-1Q) /CSM_Contig/Contig-U04644-1Q.Seq.d
         (236 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(AU071625) Dictyostelium discoideum slug cDNA, clone SSC122.      170   1e-38  1
(AL035475) Plasmodium falciparum MAL4P2.                           48   0.14   1
(U66525) Dictyostelium discoideum ORFveg114 mRNA, complete cds.    46   0.57   1
(CX533998) s13dNF0NG02MJ008_321759 Methyl Jasmonate-Elicited...    46   0.57   1
(BP185498) Dugesia japonica cDNA, clone: 03583_HH, expressed...    46   0.57   1
(BE325640) NF089D04ST1F1030 Developing stem Medicago truncat...    46   0.57   1
(AC225451) Medicago truncatula clone mth2-154e9, WORKING DRA...    32   1.2    2
(CG948057) MBEKH17TFB mth2 Medicago truncatula genomic clone...    32   1.5    2
(AM477911) Vitis vinifera, whole genome shotgun sequence, co...    44   2.2    1
(AM443606) Vitis vinifera contig VV78X014117.29, whole genom...    44   2.2    1
(AM432528) Vitis vinifera contig VV78X221342.3, whole genome...    44   2.2    1
(AM423490) Vitis vinifera contig VV78X249587.4, whole genome...    44   2.2    1
(DD307196) NUCLEIC ACID AND POLYPEPTIDE SEQUENCES FROM LAWSO...    44   2.2    1
(DD307081) NUCLEIC ACID AND POLYPEPTIDE SEQUENCES FROM LAWSO...    44   2.2    1
(DD299343) NUCLEIC ACID AND POLYPEPTIDE SEQUENCES FROM LAWSO...    44   2.2    1
(CL052691) CH216-76F18_RM1.1 CH216 Xenopus (Silurana) tropic...    44   2.2    1
(EY502549) CBBP6429.rev CBBP Hirudo medicinalis hermaphrodit...    44   2.2    1
(EY484983) CBBP14303.rev CBBP Hirudo medicinalis hermaphrodi...    44   2.2    1
(AM180255) Lawsonia intracellularis PHE/MN1-00 plasmid 3.          44   2.2    1
(BX141528) Danio rerio genomic clone DKEY-95N10, genomic sur...    32   2.7    3
(AC104838) Homo sapiens chromosome 1 clone RP4-671I22, compl...    30   4.3    2
(AC206585) Homo sapiens chromosome UNK clone ABC12-49025400G...    30   4.7    2
(AC209544) Homo sapiens chromosome UNK clone ABC9-43908500B1...    30   4.7    2
(CQ752188) Sequence 38122 from Patent WO02068579.                  30   5.8    2
(CR388187) Zebrafish DNA sequence from clone DKEY-109G19 in ...    42   8.8    1
(BV049902) S212P60195FA7.T0 CZECHII/Ei Mus musculus STS geno...    42   8.8    1
(AC165087) Mus musculus BAC clone RP23-198K7 from chromosome...    42   8.8    1
(CU329671) Schizosaccharomyces pombe chromosome II.                42   8.8    1
(AY063003) Arabidopsis thaliana unknown protein (At3g27640) ...    42   8.8    1
(AY035167) Arabidopsis thaliana unknown protein (At3g27640) ...    42   8.8    1
(AM482762) Vitis vinifera contig VV78X000885.34, whole genom...    42   8.8    1
(AM451364) Vitis vinifera contig VV78X256870.28, whole genom...    42   8.8    1
(AC189313) Brassica rapa subsp. pekinensis clone KBrB034N10,...    42   8.8    1
(AC150372) Medicago truncatula clone mth2-151k24, complete s...    42   8.8    1
(AB018114) Arabidopsis thaliana genomic DNA, chromosome 3, P...    42   8.8    1
(AC116986) Dictyostelium discoideum chromosome 2 map 2234041...    42   8.8    1
(AC151262) Mus musculus chromosome 17 clone RP24-393C12, ***...    42   8.8    1
(AC124082) Mus musculus chromosome 17 clone RP24-393C12 map ...    42   8.8    1
(CU463234) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    42   8.8    1
(AP008001) Lotus japonicus genomic DNA, chromosome 5, clone:...    42   8.8    1
(AP007783) Lotus japonicus genomic DNA, chromosome 3, clone:...    42   8.8    1
(AC180752) Strongylocentrotus purpuratus clone R3-3021P19, W...    42   8.8    1
(ER970365) AF__Bc0039K13r AF__Bc Aquilegia formosa genomic, ...    42   8.8    1
(ED190146) AUAC-aas93f09.b1 Ascaris suum whole genome shotgu...    42   8.8    1
(ED151291) AUAC-aat93c01.g1 Ascaris suum whole genome shotgu...    42   8.8    1
(ED123218) AUAC-aaq82c09.b1 Ascaris suum whole genome shotgu...    42   8.8    1
(ED111659) AUAC-aaz43g03.g1 Ascaris suum whole genome shotgu...    42   8.8    1
(CL466939) SAIL_1263_H12.v1 SAIL Collection Arabidopsis thal...    42   8.8    1
(CL465894) SAIL_1247_F07.v1 SAIL Collection Arabidopsis thal...    42   8.8    1
(BZ771636) mct78g03.b6 HFOSMID004 Homo sapiens genomic, geno...    42   8.8    1
(AV782255) Arabidopsis thaliana cDNA clone:RAFL04-15-K15, 3'...    42   8.8    1
(AU309060) Zinnia elegans cDNA, clone:Z19187.                      42   8.8    1
(DC871054) Samia cynthia ricini cDNA, clone: I10A02NGRL0007_...    42   8.8    1
(CK466011) 937176 MARC 4PIG Sus scrofa cDNA 3', mRNA sequence.     42   8.8    1
(BM165866) EST568389 PyBS Plasmodium yoelii yoelii cDNA clon...    42   8.8    1
(BM165358) EST567881 PyBS Plasmodium yoelii yoelii cDNA clon...    42   8.8    1
(BM160796) EST563319 PyBS Plasmodium yoelii yoelii cDNA clon...    42   8.8    1
(BM159312) EST561835 PyBS Plasmodium yoelii yoelii cDNA clon...    42   8.8    1
(BE437729) SFR006.H06F990625 ITEC SFR Barley Leaf Epidermis ...    42   8.8    1
(ES614855) NGPAJ13TR NGPA Nasonia giraulti cDNA, mRNA sequence.    42   8.8    1
(CP000764) Bacillus cereus subsp. cytotoxis NVH 391-98, comp...    42   8.8    1
(AE008384) Methanosarcina mazei strain Goe1, complete genome.      42   8.8    1

>(AU071625) Dictyostelium discoideum slug cDNA, clone SSC122.
          Length = 237

 Score =  170 bits (86), Expect = 1e-38
 Identities = 86/86 (100%)
 Strand = Plus / Plus


Query: 1  gattgggaagtcattgataaaagatcttcttctgaagataatgaagaaaatgatgaatgg 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  gattgggaagtcattgataaaagatcttcttctgaagataatgaagaaaatgatgaatgg 60


Query: 61 ggcgcttgggaataagttttatgttg 86
          ||||||||||||||||||||||||||
Sbjct: 61 ggcgcttgggaataagttttatgttg 86

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 126,187,305
Number of extensions: 7833412
Number of successful extensions: 2251987
Number of sequences better than 10.0: 63
Length of query: 236
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 213
Effective length of database: 99,442,330,388
Effective search space: 21181216372644
Effective search space used: 21181216372644
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04644-1 (Contig-U04644-1Q) /CSM_Contig/Contig-U04644-1Q.Seq.d
         (236 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: 120,573,143
Number of extensions: 691195
Number of successful extensions: 1038
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1038
Number of HSP's successfully gapped: 0
Length of query: 78
Length of database: 1,061,185,681
Length adjustment: 49
Effective length of query: 29
Effective length of database: 901,031,729
Effective search space: 26129920141
Effective search space used: 26129920141
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: 27 (15.0 bits)
PSORT 

 psg: 1.03  gvh: 0.23  alm: 0.59  top: 1.47  tms: 0.00  mit: 0.36  mip: 0.00
 nuc: 2.86  erl: 0.00  erm: 0.80  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 

	 76.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U04644-1 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