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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-U14414-1
Contig ID Contig-U14414-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14414-1 (Contig-U14414-1Q) /CSM_Contig/Contig-U14414-1Q.Seq.d
ATTTTTATTGAAAATTTAACTATACAAACACCATAGTGGCATACTACGGT
TTCTTTCATTGTATAATAAAACACAACTTCATTCAAAACACATTAATAAA
AAAAATAAAATAAAAAATTGACATAATAGTAAAGAACATATAAGTAATAC
TATTAAACATATAAATAATAAAAATAAAACACTACAAAAAAGAAAAAATA
AAAAAAAATAAAAAAAAATAAAAATAAAATTAATAAAAAAAAAA
Gap no gap
Contig length 244
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 2427125
End point 2427368
Strand (PLUS/MINUS) PLUS
Number of clones 3
Number of EST 6
Link to clone list U14414
List of clone(s) 

est1=CHN455F,1,244
est2=CHN455Z,1,178
est3=CHN866F,3,244
est4=CHN866Z,3,228
est5=SHC343F,3,244
est6=SHC343Z,3,232
Translated Amino Acid sequence 
fllki*LYKHHSGILRFLSLYNKTQLHSKHINKKNKIKN*hnskehisntikhinnknkt
lqkrknkkk*kkikiklikkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ifienltiqtp*whttvsfiv**nttsfkth**kk*nkklt***rtyk*yy*tyk**k*n
ttkkkk*kkikknknkinkkk


Frame B:
fllki*LYKHHSGILRFLSLYNKTQLHSKHINKKNKIKN*hnskehisntikhinnknkt
lqkrknkkk*kkikiklikkk


Frame C:
fy*kfnytntivayygffhciikhnfiqntlikkik*kidiivkni*villni*iikikh
ykkekikknkkk*k*n**kk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14414-1 (Contig-U14414-1Q)
/CSM_Contig/Contig-U14414-1Q.Seq.d
         (244 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14414-1 (Contig-U14414-1Q) /CSM_Contig/Conti...   192  1e-49
Contig-U14772-1 (Contig-U14772-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U14400-1 (Contig-U14400-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U13310-1 (Contig-U13310-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U12546-1 (Contig-U12546-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U12091-1 (Contig-U12091-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U12070-1 (Contig-U12070-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U11389-1 (Contig-U11389-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U10054-1 (Contig-U10054-1Q) /CSM_Contig/Conti...    30  1.0
Contig-U06086-1 (Contig-U06086-1Q) /CSM_Contig/Conti...    30  1.0

>Contig-U14414-1 (Contig-U14414-1Q) /CSM_Contig/Contig-U14414-1Q.Seq.d
          Length = 244

 Score =  192 bits (97), Expect = 1e-49
 Identities = 97/97 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  atttttattgaaaatttaactatacaaacaccatagtggcatactacggtttctttcatt 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttttattgaaaatttaactatacaaacaccatagtggcatactacggtttctttcatt 60

                                               
Query: 61 gtataataaaacacaacttcattcaaaacacattaat 97
          |||||||||||||||||||||||||||||||||||||
Sbjct: 61 gtataataaaacacaacttcattcaaaacacattaat 97


>Contig-U14772-1 (Contig-U14772-1Q) /CSM_Contig/Contig-U14772-1Q.Seq.d
          Length = 665

 Score = 30.2 bits (15), Expect = 1.0
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 5   ttattgaaaatttaa 19
           |||||||||||||||
Sbjct: 183 ttattgaaaatttaa 197


>Contig-U14400-1 (Contig-U14400-1Q) /CSM_Contig/Contig-U14400-1Q.Seq.d
          Length = 1939

 Score = 30.2 bits (15), Expect = 1.0
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                          
Query: 11  aaaatttaactatac 25
           |||||||||||||||
Sbjct: 667 aaaatttaactatac 653


  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: 1221
Number of Sequences: 6905
Number of extensions: 1221
Number of successful extensions: 401
Number of sequences better than 10.0: 45
length of query: 244
length of database: 5,674,871
effective HSP length: 15
effective length of query: 229
effective length of database: 5,571,296
effective search space: 1275826784
effective search space used: 1275826784
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 2008.12.21
Homology vs DNA 
Query= Contig-U14414-1 (Contig-U14414-1Q) /CSM_Contig/Contig-U14414-1Q.Seq.d
         (244 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

(BJ368947) Dictyostelium discoideum cDNA clone:ddc48n14, 5' ...   192   4e-45  1
(BJ404368) Dictyostelium discoideum cDNA clone:dds28f11, 3' ...   186   2e-43  1
(BJ392615) Dictyostelium discoideum cDNA clone:dds28f11, 5' ...   186   2e-43  1
(BJ384458) Dictyostelium discoideum cDNA clone:ddc49d18, 3' ...   186   2e-43  1
(BJ369155) Dictyostelium discoideum cDNA clone:ddc49d18, 5' ...   186   2e-43  1
(BJ384225) Dictyostelium discoideum cDNA clone:ddc48n14, 3' ...   180   1e-41  1
(AM679018) Entamoeba terrapinae GSS, clone terra167e06.q1k.        42   1.4    2
(BX276090) Zebrafish DNA sequence from clone RP71-39F17 in l...    44   2.2    1
(AC116319) Mus musculus BAC clone RP23-265J2 from chromosome...    44   2.2    1
(AC146564) Medicago truncatula chromosome 8 clone mth2-67l12...    44   2.2    1
(AC137510) Medicago truncatula clone mth2-8m7, complete sequ...    44   2.2    1
(AR584244) Sequence 1 from patent US 6797466.                      44   2.2    1
(AR271569) Sequence 1 from patent US 6503729.                      44   2.2    1
(CT943660) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    44   2.2    1
(AC222340) Bos taurus clone CH240-415G5, WORKING DRAFT SEQUE...    44   2.2    1
(L77117) Methanocaldococcus jannaschii DSM 2661, complete ge...    44   2.2    1
(AC223511) Bos taurus clone CH240-467I14, WORKING DRAFT SEQU...    30   4.1    2
(DU532397) 1098890473232 CHORI-243 Ovis aries genomic clone ...    30   5.6    2
(AC139675) Mus musculus chromosome 3, clone RP23-328D16, com...    38   5.7    3
(AC136702) Mus musculus chromosome 3, clone RP23-24N12, comp...    38   6.0    3
(AC198791) Pongo abelii BAC clone CH276-239N18 from chromoso...    42   8.6    1
(AC170767) Rhesus Macaque  BAC CH250-103N10 () complete sequ...    42   8.6    1
(AC169801) Rhesus Macaque  BAC CH250-205G14 (Children's Hosp...    42   8.6    1
(AC146830) Papio anubis clone RP41-378A10, WORKING DRAFT SEQ...    42   8.6    1
(AC226460) Chlorocebus aethiops clone CH252-293L15, WORKING ...    42   8.6    1
(AC214317) Chlorocebus aethiops clone CH252-13P24, WORKING D...    42   8.6    1
(AC198824) Nomascus leucogenys leucogenys clone CH271-298A2,...    42   8.6    1
(AC196341) Colobus guereza clone CH272-13K4, WORKING DRAFT S...    42   8.6    1
(AC194502) Colobus guereza clone CH272-170A15, WORKING DRAFT...    42   8.6    1
(AC170766) Macaca mulatta clone CH250-253A7, WORKING DRAFT S...    42   8.6    1
(AC170420) Macaca mulatta clone CH250-258E2, WORKING DRAFT S...    42   8.6    1
(AC170201) Macaca mulatta clone CH250-192I12, WORKING DRAFT ...    42   8.6    1
(BH154226) ENTTL58TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(BH148605) ENTPN57TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ691229) ENTJJ41TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ679088) ENTMG60TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ674166) ENTME73TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ673080) ENTHE31TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ551297) ENTDE25TF Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ544039) ENTGI69TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(AZ538812) ENTGQ12TR Entamoeba histolytica Sheared DNA Entam...    42   8.6    1
(ER608493) 1093016291134 Global-Ocean-Sampling_GS-36-01-01-2...    42   8.6    1
(DE584611) Bombyx mori genomic DNA, Fosmid clone:GBMFno235_o...    42   8.6    1
(EB469664) AGENCOURT_73501428 NICHD_XGC_sple_PHA Xenopus lae...    42   8.6    1
(CF365254) 835870 MARC 3PIG Sus scrofa cDNA 3', mRNA sequence.     42   8.6    1
(BG452540) NF106E11LF1F1084 Developing leaf Medicago truncat...    42   8.6    1

>(BJ368947) Dictyostelium discoideum cDNA clone:ddc48n14, 5' end,
          single read.
          Length = 242

 Score =  192 bits (97), Expect = 4e-45
 Identities = 97/97 (100%)
 Strand = Plus / Plus


Query: 1  atttttattgaaaatttaactatacaaacaccatagtggcatactacggtttctttcatt 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttttattgaaaatttaactatacaaacaccatagtggcatactacggtttctttcatt 60


Query: 61 gtataataaaacacaacttcattcaaaacacattaat 97
          |||||||||||||||||||||||||||||||||||||
Sbjct: 61 gtataataaaacacaacttcattcaaaacacattaat 97

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 139,693,965
Number of extensions: 8430226
Number of successful extensions: 2391696
Number of sequences better than 10.0: 47
Length of query: 244
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 221
Effective length of database: 93,106,754,628
Effective search space: 20576592772788
Effective search space used: 20576592772788
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.11
Homology vs Protein 
Query= Contig-U14414-1 (Contig-U14414-1Q) /CSM_Contig/Contig-U14414-1Q.Seq.d
         (244 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: 156,596,622
Number of extensions: 1206068
Number of successful extensions: 2187
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2187
Number of HSP's successfully gapped: 0
Length of query: 81
Length of database: 1,051,180,864
Length adjustment: 51
Effective length of query: 30
Effective length of database: 886,116,355
Effective search space: 26583490650
Effective search space used: 26583490650
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: 0.72  gvh: 0.45  alm: 0.61  top: 0.53  tms: 0.00  mit: 0.42  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.40  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 

	 40.0 %: mitochondrial
	 40.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal

>> prediction for Contig-U14414-1 is mit
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) 1
SF (FL, S) 0
CH (FL, L) 2
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0