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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-U06412-1
Contig ID Contig-U06412-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U06412-1 (Contig-U06412-1Q) /CSM_Contig/Contig-U06412-1Q.Seq.d
CTATCCAACAAATCGAGAAAAATTAACACACTCTCACATACACACTACAT
ACATAATATTAATTTTAATATTAAGTGTATGTGGTAGTATTTATTACTAT
CACATATTTTTATATATATAAAAAAAAAAAAAATTTTAGTTTTTTAAATA
AATAAAAAAACAAAAAAATTTAAACAA
Gap no gap
Contig length 177
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 177392
End point 177215
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06412
List of clone(s) 

est1=VSB858E,1,178
Translated Amino Acid sequence 
YPTNREKLTHSHIHTTYIILILILSVCGSIYYYHIFLYI*kkkkf*ffk*ikkqknln
Translated Amino Acid sequence (All Frames) 
Frame A:
lsnksrkintlshthyihninfnikcmw*ylllshifiyikkkkilvf*inkktkkfkq


Frame B:
YPTNREKLTHSHIHTTYIILILILSVCGSIYYYHIFLYI*kkkkf*ffk*ikkqknln


Frame C:
iqqiekn*htltytlht*y*f*y*vyvvvfitityfyiykkkknfsflnk*knkki*t
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06412-1 (Contig-U06412-1Q)
/CSM_Contig/Contig-U06412-1Q.Seq.d
         (177 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06412-1 (Contig-U06412-1Q) /CSM_Contig/Conti...   236  6e-63
Contig-U04162-1 (Contig-U04162-1Q) /CSM_Contig/Conti...    38  0.003
Contig-U13006-1 (Contig-U13006-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U11866-1 (Contig-U11866-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U09887-1 (Contig-U09887-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U09112-1 (Contig-U09112-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U08866-1 (Contig-U08866-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U04756-1 (Contig-U04756-1Q) /CSM_Contig/Conti...    36  0.012
Contig-U13433-1 (Contig-U13433-1Q) /CSM_Contig/Conti...    34  0.046
Contig-U11327-1 (Contig-U11327-1Q) /CSM_Contig/Conti...    34  0.046

>Contig-U06412-1 (Contig-U06412-1Q) /CSM_Contig/Contig-U06412-1Q.Seq.d
          Length = 177

 Score =  236 bits (119), Expect = 6e-63
 Identities = 119/119 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   ctatccaacaaatcgagaaaaattaacacactctcacatacacactacatacataatatt 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   ctatccaacaaatcgagaaaaattaacacactctcacatacacactacatacataatatt 60

                                                                      
Query: 61  aattttaatattaagtgtatgtggtagtatttattactatcacatatttttatatatat 119
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  aattttaatattaagtgtatgtggtagtatttattactatcacatatttttatatatat 119


 Score = 40.1 bits (20), Expect = 7e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 134 ttttagttttttaaataaat 153
           ||||||||||||||||||||
Sbjct: 134 ttttagttttttaaataaat 153


>Contig-U04162-1 (Contig-U04162-1Q) /CSM_Contig/Contig-U04162-1Q.Seq.d
          Length = 897

 Score = 38.2 bits (19), Expect = 0.003
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 56  atattaattttaatattaa 74
           |||||||||||||||||||
Sbjct: 804 atattaattttaatattaa 822


>Contig-U13006-1 (Contig-U13006-1Q) /CSM_Contig/Contig-U13006-1Q.Seq.d
          Length = 466

 Score = 36.2 bits (18), Expect = 0.012
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                 
Query: 53  ataatattaattttaatattaa 74
           ||||||||||| ||||||||||
Sbjct: 241 ataatattaatattaatattaa 262


  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: 4940
Number of Sequences: 6905
Number of extensions: 4940
Number of successful extensions: 1840
Number of sequences better than 10.0: 243
length of query: 177
length of database: 5,674,871
effective HSP length: 15
effective length of query: 162
effective length of database: 5,571,296
effective search space: 902549952
effective search space used: 902549952
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. 8
Homology vs DNA 
Query= Contig-U06412-1 (Contig-U06412-1Q) /CSM_Contig/Contig-U06412-1Q.Seq.d
         (177 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

(AU262295) Dictyostelium discoideum vegetative cDNA clone:VS...   109   3e-20  1
(AC151968) Mus musculus BAC clone RP24-247B20 from chromosom...    48   0.098  1
(AC096504) Rattus norvegicus clone CH230-167O14, WORKING DRA...    32   0.80   2
(AC103284) Rattus norvegicus clone CH230-125L23, WORKING DRA...    36   0.80   2
(AC133731) Rattus norvegicus clone CH230-11I6, *** SEQUENCIN...    32   0.80   2
(AC096364) Rattus norvegicus clone CH230-59C15, WORKING DRAF...    32   0.81   2
(AY241275) Engraulis encrasicolus microsatellite Ee17 sequence.    44   1.5    1
(AL365324) Mouse DNA sequence from clone RP23-451H2 on chrom...    44   1.5    1
(AC158769) Mus musculus chromosome 15, clone RP23-128J3, com...    44   1.5    1
(AC126942) Mus musculus BAC clone RP23-174P9 from chromosome...    44   1.5    1
(AC123606) Mus musculus chromosome 15, clone RP24-528D12, co...    44   1.5    1
(AC022675) Mus musculus chromosome 1, clone RP23-59N15, comp...    44   1.5    1
(AM459886) Vitis vinifera contig VV78X011329.13, whole genom...    44   1.5    1
(AC171128) Helobdella robusta clone CH306-1A10, complete seq...    44   1.5    1
(AC091891) Homo sapiens chromosome 5 clone RP11-129I19, comp...    44   1.5    1
(AC091890) Homo sapiens chromosome 5 clone RP11-127J11, comp...    44   1.5    1
(AC026791) Homo sapiens chromosome 5 clone CTD-2265D9, compl...    44   1.5    1
(AC152609) Bos taurus clone CH240-18F10, WORKING DRAFT SEQUE...    44   1.5    1
(AC131398) Rattus norvegicus clone CH230-76F20, *** SEQUENCI...    44   1.5    1
(AC126872) Rattus norvegicus clone CH230-235I11, WORKING DRA...    44   1.5    1
(AC112100) Rattus norvegicus clone CH230-118N18, WORKING DRA...    44   1.5    1
(AC222275) Bos taurus clone CH240-413N14, WORKING DRAFT SEQU...    44   1.5    1
(AC221413) Bos taurus clone CH240-406J6, WORKING DRAFT SEQUE...    44   1.5    1
(AC174896) Bos taurus clone CH240-254K23, WORKING DRAFT SEQU...    44   1.5    1
(AC169252) Bos taurus clone CH240-259E18, WORKING DRAFT SEQU...    44   1.5    1
(AC165759) Bos taurus clone CH240-159M22, WORKING DRAFT SEQU...    44   1.5    1
(DU366598) 1098313092658 CHORI-243 Ovis aries genomic clone ...    44   1.5    1
(DH502284) Monosiga ovata DNA, fosmid clone: MOF-071F07, gen...    44   1.5    1
(DH488777) Monosiga ovata DNA, fosmid clone: MOF-047J16, gen...    44   1.5    1
(DH472382) Monosiga ovata DNA, fosmid clone: MOF-019C19, gen...    44   1.5    1
(DH469523) Monosiga ovata DNA, fosmid clone: MOF-014E18, gen...    44   1.5    1
(DT030102) VVL042D07_681830 CabSau Berry Postveraison Mixed ...    44   1.5    1
(DT029245) VVL032C10_680116 CabSau Berry Postveraison Mixed ...    44   1.5    1
(DN905984) 32277.3 In vitro Root Solanum tuberosum cDNA clon...    44   1.5    1
(AC107631) Mus musculus chromosome 5, clone RP23-5M20, compl...    32   2.9    2
(AC162528) Mus musculus BAC clone RP23-4P1 from chromosome 5...    32   2.9    2
(CU467942) Zebrafish DNA sequence from clone CH211-214N12 in...    42   6.0    1
(CU463021) Zebrafish DNA sequence from clone CH73-273K13 in ...    42   6.0    1
(CR385027) Zebrafish DNA sequence from clone DKEY-13A17 in l...    42   6.0    1
(G83177) S210P6039FF3.T0 BALB/cByJ Mus musculus STS genomic,...    42   6.0    1
(BV332275) S230P6456FG3.T0 Rottweiler Canis familiaris STS g...    42   6.0    1
(BV319378) S236P6162FC11.T0 AlaskanMalamute Canis familiaris...    42   6.0    1
(CT990560) M.spretus DNA sequence from clone XX-CH35_359A6 o...    42   6.0    1
(AL772328) Mouse DNA sequence from clone RP23-270A19 on chro...    42   6.0    1
(AL672288) Mouse DNA sequence from clone RP23-186F4 on chrom...    42   6.0    1
(AL645530) Mouse DNA sequence from clone RP23-92N10 on chrom...    42   6.0    1
(AJ311612) Mus musculus partial gene for NH3-dependent NAD+ ...    42   6.0    1
(AC165252) Mus musculus BAC clone RP23-355O12 from chromosom...    42   6.0    1
(AC165163) Mus musculus BAC clone RP23-146B12 from chromosom...    42   6.0    1
(AC158554) Mus musculus chromosome 15, clone RP23-353O17, co...    42   6.0    1
(AC158299) Mus musculus chromosome 7, clone RP24-271L24, com...    42   6.0    1
(AC154470) Mus musculus BAC clone RP23-193P13 from chromosom...    42   6.0    1
(AC147266) Mus musculus BAC clone RP24-246F6 from 8, complet...    42   6.0    1
(AC147048) Mus musculus BAC clone RP23-91H23 from chromosome...    42   6.0    1
(AC140552) Mus musculus BAC clone RP24-372G15 from 8, comple...    42   6.0    1
(AC132570) Mus musculus BAC clone RP24-531D1 from chromosome...    42   6.0    1
(AC132415) Mus musculus BAC clone RP23-246C16 from chromosom...    42   6.0    1
(AC129606) Mus musculus BAC clone RP23-128L6 from 8, complet...    42   6.0    1
(AC125138) Mus musculus BAC clone RP24-324N8 from chromosome...    42   6.0    1
(AC124760) Mus musculus BAC clone RP23-133I8 from chromosome...    42   6.0    1
(AC123621) Mus musculus chromosome 19, clone RP23-74D13, com...    42   6.0    1
(AC118689) Mus musculus chromosome 10, clone RP23-293N21, co...    42   6.0    1
(AC115945) Mus musculus chromosome 3, clone RP24-555P13, com...    42   6.0    1
(AC099699) Mus musculus chromosome 7, clone RP23-32A8, compl...    42   6.0    1
(AC157646) Medicago truncatula clone mth2-164p8, complete se...    42   6.0    1
(CU041296) Human DNA sequence from clone XX-HCC1937_36P12.         42   6.0    1
(AL592429) Human DNA sequence from clone RP11-12A2 on chromo...    42   6.0    1
(AL592295) Human DNA sequence from clone RP11-122G18 on chro...    42   6.0    1
(AL589740) Human DNA sequence from clone RP11-436D23 on chro...    42   6.0    1
(AC207076) Homo sapiens FOSMID clone ABC9-44043600G17 from c...    42   6.0    1
(AC012454) Homo sapiens BAC clone RP11-439L14 from 2, comple...    42   6.0    1
(AC006571) Homo sapiens, clone hRPK.23_A_1, complete sequence.     42   6.0    1
(AC151271) Mus musculus chromosome 8 clone RP24-257M5, *** S...    42   6.0    1
(AC150933) Bos taurus clone CH240-474P3, WORKING DRAFT SEQUE...    42   6.0    1
(AC141905) Rattus norvegicus clone CH230-505D15, WORKING DRA...    42   6.0    1
(AC139607) Rattus norvegicus clone CH230-389L12, WORKING DRA...    42   6.0    1
(AC137374) Rattus norvegicus clone CH230-unknown, WORKING DR...    42   6.0    1
(AC137216) Rattus norvegicus clone CH230-unknown, *** SEQUEN...    42   6.0    1
(AC137057) Rattus norvegicus strain Brown Norway clone CH230...    42   6.0    1
(AC135589) Rattus norvegicus clone CH230-6F7, WORKING DRAFT ...    42   6.0    1
(AC135541) Rattus norvegicus strain Brown Norway clone CH230...    42   6.0    1
(AC135301) Rattus norvegicus clone CH230-45E14, *** SEQUENCI...    42   6.0    1
(AC134152) Rattus norvegicus clone CH230-11E17, *** SEQUENCI...    42   6.0    1
(AC132790) Rattus norvegicus clone CH230-271O22, WORKING DRA...    42   6.0    1
(AC132531) Rattus norvegicus clone CH230-212C6, *** SEQUENCI...    42   6.0    1
(AC130984) Rattus norvegicus clone CH230-61A18, WORKING DRAF...    42   6.0    1
(AC130945) Rattus norvegicus clone CH230-397N7, WORKING DRAF...    42   6.0    1
(AC130626) Rattus norvegicus clone CH230-144E21, WORKING DRA...    42   6.0    1
(AC130226) Rattus norvegicus clone CH230-24F7, WORKING DRAFT...    42   6.0    1
(AC130224) Rattus norvegicus clone CH230-340K1, *** SEQUENCI...    42   6.0    1
(AC129810) Rattus norvegicus clone CH230-237K21, *** SEQUENC...    42   6.0    1
(AC129409) Rattus norvegicus clone CH230-58G22, *** SEQUENCI...    42   6.0    1
(AC128382) Rattus norvegicus clone CH230-141F13, WORKING DRA...    42   6.0    1
(AC128293) Rattus norvegicus clone CH230-394P9, WORKING DRAF...    42   6.0    1
(AC127401) Rattus norvegicus clone CH230-195E24, WORKING DRA...    42   6.0    1
(AC126714) Rattus norvegicus clone CH230-5J11, WORKING DRAFT...    42   6.0    1
(AC123457) Rattus norvegicus clone CH230-22F7, WORKING DRAFT...    42   6.0    1
(AC123290) Rattus norvegicus clone CH230-375K15, WORKING DRA...    42   6.0    1
(AC121352) Rattus norvegicus chromosome 1 clone RP32-98F22 m...    42   6.0    1
(AC112821) Rattus norvegicus clone CH230-36F6, *** SEQUENCIN...    42   6.0    1

>(AU262295) Dictyostelium discoideum vegetative cDNA clone:VSB858,
          3' end single read.
          Length = 178

 Score =  109 bits (55), Expect = 3e-20
 Identities = 55/55 (100%)
 Strand = Plus / Plus


Query: 1  ctatccaacaaatcgagaaaaattaacacactctcacatacacactacatacata 55
          |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  ctatccaacaaatcgagaaaaattaacacactctcacatacacactacatacata 55

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 60,540,771
Number of extensions: 4376706
Number of successful extensions: 1123754
Number of sequences better than 10.0: 139
Length of query: 177
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 155
Effective length of database: 93,199,600,587
Effective search space: 14445938090985
Effective search space used: 14445938090985
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06412-1 (Contig-U06412-1Q) /CSM_Contig/Contig-U06412-1Q.Seq.d
         (177 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE014187_105(AE014187|pid:none) Plasmodium falciparum 3D7 chromo...    37   0.22

>AE014187_105(AE014187|pid:none) Plasmodium falciparum 3D7 chromosome
            14, complete sequence.  &AE014817_43(AE014817|pid:none)
          Length = 1951

 Score = 37.0 bits (84), Expect = 0.22
 Identities = 16/45 (35%), Positives = 29/45 (64%)
 Frame = +1

Query: 7    NKSRKINTLSHTHYIHNINFNIKCMW*YLLLSHIFIYIKKKKILV 141
            NKS+KIN + H    +N N N+  ++ ++ L++ + +IKK KI +
Sbjct: 1420 NKSKKINYVQHLFVNNNYNNNVNPLFIFMSLTYSYYFIKKDKIYI 1464

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: 134,066,038
Number of extensions: 1563088
Number of successful extensions: 3864
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3864
Number of HSP's successfully gapped: 1
Length of query: 59
Length of database: 1,040,966,779
Length adjustment: 31
Effective length of query: 28
Effective length of database: 941,633,944
Effective search space: 26365750432
Effective search space used: 26365750432
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: 0.98  gvh: 0.67  alm: 17.64  top: 0.33  tms: -0.07  mit: 0.38  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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: 1.00  m3b: 0.00  m_ : 0.00 

	 40.0 %: cytoplasmic
	 28.0 %: mitochondrial
	 16.0 %: nuclear
	  8.0 %: cytoskeletal
	  8.0 %: plasma membrane

>> prediction for Contig-U06412-1 is cyt
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