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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-U06256-1
Contig ID Contig-U06256-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06256-1 (Contig-U06256-1Q) /CSM_Contig/Contig-U06256-1Q.Seq.d
GAATTATCAACTTTTATGGATTCAAGAAAANCAGTTGGTTTAAANGGTAA
TCCATTATNGAATGAAATGAAATCATTTAAAGTNGACCAAGTTAGCTTTC
ATGGTAATTCATTATTAAAGGATATTTTGAAAATGTTCAAGATGATGTTT
TAAATTGTGATTTTGTTTATGAAGAGATTGAAAAGTATGGTCAAATTGCA
ATTGATCTTTATGAATGGATCGATTCAAACTTCACAATAATATCTGTTAA
ATATAGTGAAGATATTTATGATGAAGAAATGTAATATTAATTAATAAAAA
AAAAAAAGAAATATTAAAAAAAAGAAATATTATTAAAAAAC
Gap no gap
Contig length 341
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 4877835
End point 4878088
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U06256
List of clone(s) 

est1=VSA455Z,1,342
Translated Amino Acid sequence 
iinfygfkkxswfkx*sixe*neii*sxps*lsw*FIIKGYFENVQDDVLNCDFVYEEIE
KYGQIAIDLYEWIDSNFTIISVKYSEDIYDEEM*y*likkkkky*kkeillkn
Translated Amino Acid sequence (All Frames) 
Frame A:
elstfmdsrkxvglxgnplxnemksfkvdqvsfhgnsllkdilkmfkmmf*ivilfmkrl
ksmvklqlifmngsiqtsq*yllnivkifmmkkcnin**kkkrnikkkkyy*k


Frame B:
nyqllwiqexqlv*xvihyxmk*nhlkxtklafmvihy*rif*kcsr*cfkl*fcl*rd*
kvwsncn*sl*mdrfklhnnic*i**ryl**rnvilinkkkkeilkkrniikk


Frame C:
iinfygfkkxswfkx*sixe*neii*sxps*lsw*FIIKGYFENVQDDVLNCDFVYEEIE
KYGQIAIDLYEWIDSNFTIISVKYSEDIYDEEM*y*likkkkky*kkeillkn
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06256-1 (Contig-U06256-1Q)
/CSM_Contig/Contig-U06256-1Q.Seq.d
         (341 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06256-1 (Contig-U06256-1Q) /CSM_Contig/Conti...   561  e-160
Contig-U10354-1 (Contig-U10354-1Q) /CSM_Contig/Conti...    36  0.023
Contig-U14896-1 (Contig-U14896-1Q) /CSM_Contig/Conti...    34  0.092
Contig-U12429-1 (Contig-U12429-1Q) /CSM_Contig/Conti...    34  0.092
Contig-U14770-1 (Contig-U14770-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U14741-1 (Contig-U14741-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U13870-1 (Contig-U13870-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U12693-1 (Contig-U12693-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U12376-1 (Contig-U12376-1Q) /CSM_Contig/Conti...    32  0.37
Contig-U11841-1 (Contig-U11841-1Q) /CSM_Contig/Conti...    32  0.37

>Contig-U06256-1 (Contig-U06256-1Q) /CSM_Contig/Contig-U06256-1Q.Seq.d
          Length = 341

 Score =  561 bits (283), Expect = e-160
 Identities = 295/295 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   gaattatcaacttttatggattcaagaaaancagttggtttaaanggtaatccattatng 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gaattatcaacttttatggattcaagaaaancagttggtttaaanggtaatccattatng 60

                                                                       
Query: 61  aatgaaatgaaatcatttaaagtngaccaagttagctttcatggtaattcattattaaag 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aatgaaatgaaatcatttaaagtngaccaagttagctttcatggtaattcattattaaag 120

                                                                       
Query: 121 gatattttgaaaatgttcaagatgatgttttaaattgtgattttgtttatgaagagattg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 gatattttgaaaatgttcaagatgatgttttaaattgtgattttgtttatgaagagattg 180

                                                                       
Query: 181 aaaagtatggtcaaattgcaattgatctttatgaatggatcgattcaaacttcacaataa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aaaagtatggtcaaattgcaattgatctttatgaatggatcgattcaaacttcacaataa 240

                                                                  
Query: 241 tatctgttaaatatagtgaagatatttatgatgaagaaatgtaatattaattaat 295
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tatctgttaaatatagtgaagatatttatgatgaagaaatgtaatattaattaat 295


>Contig-U10354-1 (Contig-U10354-1Q) /CSM_Contig/Contig-U10354-1Q.Seq.d
          Length = 1222

 Score = 36.2 bits (18), Expect = 0.023
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 246 gttaaatatagtgaagat 263
           ||||||||||||||||||
Sbjct: 602 gttaaatatagtgaagat 619


>Contig-U14896-1 (Contig-U14896-1Q) /CSM_Contig/Contig-U14896-1Q.Seq.d
          Length = 846

 Score = 34.2 bits (17), Expect = 0.092
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 122 atattttgaaaatgttc 138
           |||||||||||||||||
Sbjct: 116 atattttgaaaatgttc 100


  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: 5163
Number of Sequences: 6905
Number of extensions: 5163
Number of successful extensions: 565
Number of sequences better than 10.0: 155
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 2008.11. 7
Homology vs DNA 
Query= Contig-U06256-1 (Contig-U06256-1Q) /CSM_Contig/Contig-U06256-1Q.Seq.d
         (341 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

(AU261488) Dictyostelium discoideum vegetative cDNA clone:VS...   561   e-156  1
(EJ990065) 1093023042115 Global-Ocean-Sampling_GS-30-02-01-1...    58   2e-04  1
(AM596515) Paracentrotus lividus EST, clone MPMGp1174I2462Q,...    54   0.003  1
(AL845319) Mouse DNA sequence from clone RP23-429I7 on chrom...    50   0.046  4
(EA427602) Sequence 77 from patent US 7332281.                     50   0.051  1
(DL007621) NOVEL THERAPEUTIC TARGETS IN CANCER.                    50   0.051  1
(CU570993) Zebrafish DNA sequence from clone DKEYP-88C1 in l...    48   0.20   1
(BX936359) Zebrafish DNA sequence from clone CH211-7C14 in l...    48   0.20   1
(CT573164) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    48   0.20   1
(CT573433) Zebrafish DNA sequence from clone DKEY-245G22 in ...    40   0.35   4
(BZ263926) CH230-326M20.TJ CHORI-230 Segment 2 Rattus norveg...    34   0.35   3
(CR933813) Zebrafish DNA sequence from clone CH73-227I15 in ...    40   0.37   3
(AC122344) Mus musculus BAC clone RP23-364M19 from chromosom...    46   0.79   1
(AC159120) Bos taurus clone CH240-46L8, WORKING DRAFT SEQUEN...    46   0.79   1
(AG564168) Mus musculus molossinus DNA, clone:MSMg01-484H22....    46   0.79   1
(CC478913) CH240_305L21.TARBAC13P2 CHORI-240 Bos taurus geno...    46   0.79   1
(AM574756) Paracentrotus lividus EST, clone MPMGp1173O0913Q,...    46   0.79   1
(AC173859) Bos taurus clone CH240-372F9, WORKING DRAFT SEQUE...    42   1.0    5
(CP000048) Borrelia hermsii DAH, complete genome.                  34   1.2    8
(AX347076) Sequence 2147 from Patent WO0200928.                    38   1.6    2
(AC154884) Mus musculus chromosome 3, clone RP23-145H17, com...    44   1.6    3
(AC168512) Strongylocentrotus purpuratus clone R3-3108M11, W...    42   1.9    2
(CP000730) Staphylococcus aureus subsp. aureus USA300_TCH151...    38   2.2    11
(AM285304) Spiroplasma citri GII3-3X chromosome, contig Cont...    34   2.2    7
(CP000255) Staphylococcus aureus subsp. aureus USA300_FPR375...    38   2.5    10
(AC180151) Strongylocentrotus purpuratus clone R3-4005B02, W...    36   2.9    4
(CU467652) Zebrafish DNA sequence from clone DKEY-256O15 in ...    44   3.1    1
(AB005231) Arabidopsis thaliana genomic DNA, chromosome 5, P...    44   3.1    1
(CR548612) Paramecium tetraurelia macronuclear largest chrom...    44   3.1    1
(AC162411) Bos taurus clone CH240-119H12, WORKING DRAFT SEQU...    44   3.1    1
(AC149977) Strongylocentrotus purpuratus clone R3-32A13, WOR...    44   3.1    1
(AC123287) Rattus norvegicus clone CH230-358C16, *** SEQUENC...    44   3.1    1
(AC107429) Rattus norvegicus clone CH230-206H12, WORKING DRA...    44   3.1    1
(AC184508) Strongylocentrotus purpuratus clone R3-41C11, WOR...    44   3.1    1
(AC181577) Strongylocentrotus purpuratus clone R3-1109H12, W...    44   3.1    1
(AC180592) Strongylocentrotus purpuratus clone R3-3016P15, W...    44   3.1    1
(AC168607) Strongylocentrotus purpuratus clone R3-3046K18, W...    44   3.1    1
(AQ897276) HS_5444_A1_C12_T7A RPCI-11 Human Male BAC Library...    44   3.1    1
(EJ364459) 1092963700399 Global-Ocean-Sampling_GS-28-01-01-1...    44   3.1    1
(EG467240) AYBBE48TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467229) AYBBE48TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467218) AYBBE47TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467207) AYBBE47TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467196) AYBBE46TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467185) AYBBE46TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467163) AYBBE44TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467152) AYBBE44TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467140) AYBBE43TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467118) AYBBE43TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467096) AYBBE42TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467074) AYBBE42TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467063) AYBBE41TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467041) AYBBE41TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG467006) AYBBE40TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466984) AYBBE40TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466795) AYBBE39TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466751) AYBBE39TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466607) AYBBE38TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466551) AYBBE38TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466540) AYBBE37TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466529) AYBBE37TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466518) AYBBE36TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466374) AYBBE36TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466196) AYBBE34TR pooled cDNA populations Arabidopsis tha...    44   3.1    1
(EG466185) AYBBE34TF pooled cDNA populations Arabidopsis tha...    44   3.1    1
(DY275136) IC0AAA38CC12RM2 CitNFL Citrus clementina cDNA 5',...    44   3.1    1
(DR908446) USDA-FP_16574 Citrus sinensis phloem Citrus sinen...    44   3.1    1
(DN958510) USDA-FP/ARO_14340 Star Ruby grapefruit hot water-...    44   3.1    1
(DN622018) UCRCA01_01I13_r Bark of Madame Vinous Sweet Orang...    44   3.1    1
(CX673442) UCRCS10_22F09_g Madame Vinous Sweet Orange Multip...    44   3.1    1
(CX305039) C16018D08SK ExocortL1 Citrus medica cDNA clone C1...    44   3.1    1
(CX304281) C16008G11SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX304223) C16008B10SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303879) C16003H03SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303761) C16002C10SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303739) C16002A09SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303736) C16002A06SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303630) C09003E01SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303578) C09002H08SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX303439) C09001C08SK CTVLeafMc1 Citrus macrophylla cDNA cl...    44   3.1    1
(CX298822) C06015H10SK FlavCurFr1 Citrus clementina x Citrus...    44   3.1    1
(CX288994) C02007G09SK IF1 Citrus clementina cDNA clone C020...    44   3.1    1
(CT769770) Paramecium tetraurelia 5-PRIME EST from clone LK0...    44   3.1    1
(CT753896) Paramecium tetraurelia 5-PRIME EST from clone LK0...    44   3.1    1
(CT739787) Paramecium tetraurelia 5-PRIME EST from clone LK0...    44   3.1    1
(CD575194) UCRPT01_02db06_b1 Poncirus trifoliata CTV-challen...    44   3.1    1
(FD986594) RR4G121TF RR4(PB) Raphanus raphanistrum subsp. la...    44   3.1    1
(EY672628) CS00-C1-102-102-D06-CT.F Sweet orange leaf, infec...    44   3.1    1
(EY669211) CS00-C1-102-073-B11-CT.F Sweet orange leaf, infec...    44   3.1    1
(CP000492) Chlorobium phaeobacteroides DSM 266, complete gen...    44   3.1    1
(AC158578) Mus musculus chromosome 1, clone RP24-370C23, com...    38   3.1    3
(EK098169) 1092962054087 Global-Ocean-Sampling_GS-31-01-01-1...    34   3.2    2
(AC200986) Strongylocentrotus purpuratus clone R3-12B22, WOR...    42   4.5    4
(AE017308) Mycoplasma mobile 163K complete genome.                 32   5.1    9
(AC010380) Homo sapiens chromosome 5 clone CTD-2066C3, compl...    40   5.7    4
(CP000551) Prochlorococcus marinus str. AS9601, complete gen...    40   7.0    11
(BX088713) Zebrafish DNA sequence from clone DKEY-1P9 in lin...    38   7.2    2
(EF533696) Glycine max clone BAC GM_WBb026N19, complete sequ...    34   7.3    4
(ED662972) GM_WBa0087D15.f GM_WBa Glycine max genomic clone ...    34   7.7    2
(AV662356) Bos taurus cDNA clone: E1BR030B06, 5' end, expres...    30   8.0    2

>(AU261488) Dictyostelium discoideum vegetative cDNA clone:VSA455,
           3' end single read.
          Length = 342

 Score =  561 bits (283), Expect = e-156
 Identities = 295/295 (100%)
 Strand = Plus / Plus


Query: 1   gaattatcaacttttatggattcaagaaaancagttggtttaaanggtaatccattatng 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gaattatcaacttttatggattcaagaaaancagttggtttaaanggtaatccattatng 60


Query: 61  aatgaaatgaaatcatttaaagtngaccaagttagctttcatggtaattcattattaaag 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aatgaaatgaaatcatttaaagtngaccaagttagctttcatggtaattcattattaaag 120


Query: 121 gatattttgaaaatgttcaagatgatgttttaaattgtgattttgtttatgaagagattg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 gatattttgaaaatgttcaagatgatgttttaaattgtgattttgtttatgaagagattg 180


Query: 181 aaaagtatggtcaaattgcaattgatctttatgaatggatcgattcaaacttcacaataa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 aaaagtatggtcaaattgcaattgatctttatgaatggatcgattcaaacttcacaataa 240


Query: 241 tatctgttaaatatagtgaagatatttatgatgaagaaatgtaatattaattaat 295
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tatctgttaaatatagtgaagatatttatgatgaagaaatgtaatattaattaat 295

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 385,498,730
Number of extensions: 24479311
Number of successful extensions: 2032242
Number of sequences better than 10.0: 108
Length of query: 341
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 318
Effective length of database: 93,106,754,628
Effective search space: 29607947971704
Effective search space used: 29607947971704
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06256-1 (Contig-U06256-1Q) /CSM_Contig/Contig-U06256-1Q.Seq.d
         (341 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000102_452(CP000102|pid:none) Methanosphaera stadtmanae DSM 30...    32   5.3
CP000685_1582(CP000685|pid:none) Flavobacterium johnsoniae UW101...    32   9.0

>CP000102_452(CP000102|pid:none) Methanosphaera stadtmanae DSM 3091,
           complete genome.
          Length = 255

 Score = 32.3 bits (72), Expect = 5.3
 Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
 Frame = +3

Query: 132 NVQDDVLNCDFVYEEIEKYG-QIAIDLYEWIDSNFTIISVKY 254
           NV++D  + DF+YE + KYG ++   + E   SN+T  SV Y
Sbjct: 144 NVKEDRTDLDFIYEIMIKYGIELTSPIEEIKKSNYTFYSVGY 185

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: 334,189,920
Number of extensions: 4219539
Number of successful extensions: 19950
Number of sequences better than 10.0: 2
Number of HSP's gapped: 19932
Number of HSP's successfully gapped: 2
Length of query: 113
Length of database: 1,040,966,779
Length adjustment: 80
Effective length of query: 33
Effective length of database: 784,623,979
Effective search space: 25892591307
Effective search space used: 25892591307
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: 0.50  gvh: 0.23  alm: 0.49  top: 0.53  tms: 0.00  mit: 0.21  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 %: nuclear
	 24.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06256-1 is nuc
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