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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U13210-1
Contig ID Contig-U13210-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13210-1 (Contig-U13210-1Q) /CSM_Contig/Contig-U13210-1Q.Seq.d
AATTATTCTTAATATTATTCCAAAATTAACAATACAAATTTGTTATAGGG
GAAATTGTATTAAATAGTAGTCTCATATTTATTTTTTTATAAATCTAATT
AATTTAAAAAAAAAAAAAAAANTTTTTAANTTTTTAAAAAAAAAAAAAAA
GGNAAAAAAAAA
Gap no gap
Contig length 162
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3999898
End point 4000059
Strand (PLUS/MINUS) PLUS
Number of clones 4
Number of EST 4
Link to clone list U13210
List of clone(s) 

est1=SHA342F,1,115
est2=SHA384F,5,162
est3=SHF436F,14,145
est4=CHK316F,52,162
Translated Amino Acid sequence 
iilniipkltiqicyrgncik**SHIYFFINLINLKKKKKXFXFLKKKKKXKK
Translated Amino Acid sequence (All Frames) 
Frame A:
nys*yyskinntnll*gkly*ivvsylffyksn*fkkkkkxf*xfkkkkkgkkk


Frame B:
iilniipkltiqicyrgncik**SHIYFFINLINLKKKKKXFXFLKKKKKXKK


Frame C:
lflilfqn*qykfvigeivlnsslififl*i*li*kkkkxflxf*kkkkrxkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13210-1 (Contig-U13210-1Q)
/CSM_Contig/Contig-U13210-1Q.Seq.d
         (162 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13210-1 (Contig-U13210-1Q) /CSM_Contig/Conti...   167  4e-42
Contig-U13566-1 (Contig-U13566-1Q) /CSM_Contig/Conti...    32  0.16
Contig-U12920-1 (Contig-U12920-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U12334-1 (Contig-U12334-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U11142-1 (Contig-U11142-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U11083-1 (Contig-U11083-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U10832-1 (Contig-U10832-1Q) /CSM_Contig/Conti...    30  0.65
Contig-U08834-1 (Contig-U08834-1Q) /CSM_Contig/Conti...    30  0.65

>Contig-U13210-1 (Contig-U13210-1Q) /CSM_Contig/Contig-U13210-1Q.Seq.d
          Length = 162

 Score =  167 bits (84), Expect = 4e-42
 Identities = 98/105 (93%)
 Strand = Plus / Plus

                                                                       
Query: 1   aattattcttaatattattccaaaattaacaatacaaatttgttataggggaaattgtat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aattattcttaatattattccaaaattaacaatacaaatttgttataggggaaattgtat 60

                                                        
Query: 61  taaatagtagtctcatatttannnnnnnataaatctaattaattt 105
           |||||||||||||||||||||       |||||||||||||||||
Sbjct: 61  taaatagtagtctcatatttatttttttataaatctaattaattt 105


>Contig-U13566-1 (Contig-U13566-1Q) /CSM_Contig/Contig-U13566-1Q.Seq.d
          Length = 1071

 Score = 32.2 bits (16), Expect = 0.16
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                           
Query: 2   attattcttaatatta 17
           ||||||||||||||||
Sbjct: 902 attattcttaatatta 887


>Contig-U12920-1 (Contig-U12920-1Q) /CSM_Contig/Contig-U12920-1Q.Seq.d
          Length = 1683

 Score = 30.2 bits (15), Expect = 0.65
 Identities = 18/19 (94%)
 Strand = Plus / Plus

                              
Query: 2   attattcttaatattattc 20
           |||||| ||||||||||||
Sbjct: 613 attatttttaatattattc 631


  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: 1704
Number of Sequences: 6905
Number of extensions: 1704
Number of successful extensions: 563
Number of sequences better than 10.0: 124
length of query: 162
length of database: 5,674,871
effective HSP length: 15
effective length of query: 147
effective length of database: 5,571,296
effective search space: 818980512
effective search space used: 818980512
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. 7
Homology vs DNA 
Query= Contig-U13210-1 (Contig-U13210-1Q) /CSM_Contig/Contig-U13210-1Q.Seq.d
         (162 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

(BJ391536) Dictyostelium discoideum cDNA clone:dds24d11, 5' ...   208   4e-50  1
(BJ391692) Dictyostelium discoideum cDNA clone:dds24h21, 5' ...   200   1e-47  1
(BJ394234) Dictyostelium discoideum cDNA clone:dds34h10, 5' ...   182   2e-42  1
(BJ367311) Dictyostelium discoideum cDNA clone:ddc42p03, 5' ...   107   1e-19  1
(AC202226) Acyrthosiphon pisum  BAC VMRC38-10-A4 (Benaroya R...    38   0.022  3
(AG377302) Mus musculus molossinus DNA, clone:MSMg01-185E01....    40   0.070  2
(AX345937) Sequence 1008 from Patent WO0200928.                    46   0.075  2
(DK058292) Oryzias latipes cDNA, clone: olea39i14, 5' end.         36   0.15   2
(AM341032) Oryzias latipes EST, clone FOE002-P00126-DPE-F_I15.     36   0.16   2
(BD061520) Genome DNA of symbiotic bacteria of aphid.              32   0.19   2
(AR409405) Sequence 1 from patent US 6632935.                      32   0.19   2
(BA000003) Buchnera aphidicola str. APS (Acyrthosiphon pisum...    32   0.19   2
(AC115684) Dictyostelium discoideum chromosome 2 map 3108975...    38   0.21   2
(CU138528) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    38   0.24   5
(C90966) Dictyostelium discoideum slug cDNA, clone SSJ362.         38   0.27   2
(AL645844) Mouse DNA sequence from clone RP23-82B4 on chromo...    46   0.35   1
(AY875213) Homalodisca coagulata mitochondrion, complete gen...    46   0.35   1
(EK346098) 1095467523151 Global-Ocean-Sampling_GS-31-01-01-1...    46   0.35   1
(ED496348) ix14a08.g1 Sub-library of four pooled sorghum BAC...    46   0.35   1
(CW390478) fsbb001f076c11k0 Sorghum methylation filtered lib...    46   0.35   1
(CW390477) fsbb001f076c11f0 Sorghum methylation filtered lib...    46   0.35   1
(CL194752) 104_419_10941876_114_32295_040 Sorghum methylatio...    46   0.35   1
(CL178354) 104_386_10894525_116_31912_205 Sorghum methylatio...    46   0.35   1
(EG371061) USDA-FP_170245 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368764) USDA-FP_173246 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368459) USDA-FP_169036 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368411) USDA-FP_168993 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368383) USDA-FP_168968 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368353) USDA-FP_168940 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG368307) USDA-FP_168899 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG367490) USDA-FP_169887 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366696) USDA-FP_169169 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366451) USDA-FP_166681 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366354) USDA-FP_167349 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366316) USDA-FP_167315 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366286) USDA-FP_167288 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(EG366203) USDA-FP_167213 Homalodisca vitripennis (syn. H. c...    46   0.35   1
(DR556272) WS0328.C21_E11 WS-MC-N-A-20 Picea glauca cDNA clo...    46   0.35   1
(DR471881) WS00954.B21_K12 IS-B-N-A-10 Picea engelmannii x P...    46   0.35   1
(DR451089) WS00954.BR_K12 IS-B-N-A-10 Picea engelmannii x Pi...    46   0.35   1
(DN203564) USDA-FP_139589 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN203476) USDA-FP_139501 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN203471) USDA-FP_139496 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN203427) USDA-FP_139452 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN203388) USDA-FP_139413 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN199204) USDA-FP_135918 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN199119) USDA-FP_135833 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN199044) USDA-FP_135758 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN198748) USDA-FP_135462 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN198461) USDA-FP_135175 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN198223) USDA-FP_134937 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN198146) USDA-FP_134860 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN197717) USDA-FP_134431 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN197611) USDA-FP_134325 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN197603) USDA-FP_134317 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN197320) USDA-FP_134034 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN197280) USDA-FP_133994 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN196995) USDA-FP_133709 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN196757) USDA-FP_133471 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN196585) USDA-FP_133296 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(DN196234) USDA-FP_132945 5th Instar Glassy-winged Sharpshoo...    46   0.35   1
(CO644447) USDA-FP_113186 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO644351) USDA-FP_113090 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643960) USDA-FP_112699 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643943) USDA-FP_112682 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643916) USDA-FP_112655 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643886) USDA-FP_112625 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643879) USDA-FP_112618 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643850) USDA-FP_112589 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643844) USDA-FP_112583 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643806) USDA-FP_112545 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643763) USDA-FP_112502 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643590) USDA-FP_112329 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643530) USDA-FP_112269 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643434) USDA-FP_112173 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643432) USDA-FP_112171 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643398) USDA-FP_112137 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643348) USDA-FP_112087 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643306) USDA-FP_112045 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643297) USDA-FP_112036 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643277) USDA-FP_112016 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643250) USDA-FP_111989 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO643178) USDA-FP_111917 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642922) USDA-FP_111661 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642743) USDA-FP_111482 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642725) USDA-FP_111464 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642693) USDA-FP_111432 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642662) USDA-FP_111401 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642645) USDA-FP_111384 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642637) USDA-FP_111376 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642550) USDA-FP_111289 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642513) USDA-FP_111252 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642397) USDA-FP_111136 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642390) USDA-FP_111129 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642373) USDA-FP_111112 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642346) USDA-FP_111085 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642328) USDA-FP_111067 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642289) USDA-FP_111028 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642275) USDA-FP_111014 Adult Glassy-winged Sharpshooter H...    46   0.35   1
(CO642239) USDA-FP_110978 Adult Glassy-winged Sharpshooter H...    46   0.35   1

>(BJ391536) Dictyostelium discoideum cDNA clone:dds24d11, 5' end,
           single read.
          Length = 115

 Score =  208 bits (105), Expect = 4e-50
 Identities = 105/105 (100%)
 Strand = Plus / Plus


Query: 1   aattattcttaatattattccaaaattaacaatacaaatttgttataggggaaattgtat 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aattattcttaatattattccaaaattaacaatacaaatttgttataggggaaattgtat 60


Query: 61  taaatagtagtctcatatttatttttttataaatctaattaattt 105
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  taaatagtagtctcatatttatttttttataaatctaattaattt 105

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 199,373,015
Number of extensions: 16929909
Number of successful extensions: 5516163
Number of sequences better than 10.0: 702
Length of query: 162
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 140
Effective length of database: 93,199,600,587
Effective search space: 13047944082180
Effective search space used: 13047944082180
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13210-1 (Contig-U13210-1Q) /CSM_Contig/Contig-U13210-1Q.Seq.d
         (162 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 159,724,034
Number of extensions: 1787731
Number of successful extensions: 1485
Number of sequences better than 10.0: 0
Number of HSP's gapped: 1485
Number of HSP's successfully gapped: 0
Length of query: 54
Length of database: 1,051,180,864
Length adjustment: 27
Effective length of query: 27
Effective length of database: 963,793,771
Effective search space: 26022431817
Effective search space used: 26022431817
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: 26 (14.6 bits)
PSORT 

 psg: 0.90  gvh: 0.09  alm: 0.59  top: 1.10  tms: 0.00  mit: 0.36  mip: 0.00
 nuc: 0.70  erl: 0.00  erm: 0.60  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 

	 72.0 %: nuclear
	 20.0 %: cytoplasmic
	  8.0 %: mitochondrial

>> prediction for Contig-U13210-1 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) 0
SH (FL, L) 3
SF (FL, S) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0