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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-U15473-1
Contig ID Contig-U15473-1
Contig update 2004. 6.11
Contig sequence 
>Contig-U15473-1 (Contig-U15473-1Q) /CSM_Contig/Contig-U15473-1Q.Seq.d
CAACTACAACAACACCTATTGAATTCCCAGGTGATGAAAAAGAACAAATG
ATTACAAAAGCATTATTAGNTGGTGATCATAATAGTGCANTTGAATGTNG
TCTTCGTTTAGGTAGATATTCAGATGCATTGATTTTAA
Gap no gap
Contig length 138
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 3834782
End point 3834919
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U15473
List of clone(s) 

est1=VHA577F,1,138
Translated Amino Acid sequence 
TTTTPIEFPGDEKEQMITKALLXGDHNSAXECXLRLGRYSDALIL
Translated Amino Acid sequence (All Frames) 
Frame A:
qlqqhllnsqvmkknk*lqkhy*xviiivxlnvvfv*vdiqmh*f*


Frame B:
nynnty*ipr**krtndyksiixw*s**cx*mxssfr*ifrcidf


Frame C:
TTTTPIEFPGDEKEQMITKALLXGDHNSAXECXLRLGRYSDALIL
own update 2004. 6.23
Homology vs CSM-cDNA 
Query= Contig-U15473-1 (Contig-U15473-1Q)
/CSM_Contig/Contig-U15473-1Q.Seq.d
         (138 letters)

Database: CSM
           8402 sequences; 8,075,542 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U15473-1 (Contig-U15473-1Q) /CSM_Contig/Conti...   256  7e-69
Contig-U16000-1 (Contig-U16000-1Q) /CSM_Contig/Conti...    42  2e-04
Contig-U12174-1 (Contig-U12174-1Q) /CSM_Contig/Conti...    36  0.013
Contig-U13907-1 (Contig-U13907-1Q) /CSM_Contig/Conti...    34  0.050
Contig-U13880-1 (Contig-U13880-1Q) /CSM_Contig/Conti...    34  0.050
Contig-U10672-1 (Contig-U10672-1Q) /CSM_Contig/Conti...    34  0.050
Contig-U15832-1 (Contig-U15832-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U15831-1 (Contig-U15831-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U15639-1 (Contig-U15639-1Q) /CSM_Contig/Conti...    32  0.20

>Contig-U15473-1 (Contig-U15473-1Q) /CSM_Contig/Contig-U15473-1Q.Seq.d
          Length = 138

 Score =  256 bits (129), Expect = 7e-69
 Identities = 138/138 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   caactacaacaacacctattgaattcccaggtgatgaaaaagaacaaatgattacaaaag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caactacaacaacacctattgaattcccaggtgatgaaaaagaacaaatgattacaaaag 60

                                                                       
Query: 61  cattattagntggtgatcataatagtgcanttgaatgtngtcttcgtttaggtagatatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cattattagntggtgatcataatagtgcanttgaatgtngtcttcgtttaggtagatatt 120

                             
Query: 121 cagatgcattgattttaa 138
           ||||||||||||||||||
Sbjct: 121 cagatgcattgattttaa 138


>Contig-U16000-1 (Contig-U16000-1Q) /CSM_Contig/Contig-U16000-1Q.Seq.d
          Length = 1929

 Score = 42.1 bits (21), Expect = 2e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                 
Query: 33   gatgaaaaagaacaaatgatt 53
            |||||||||||||||||||||
Sbjct: 1622 gatgaaaaagaacaaatgatt 1642


>Contig-U12174-1 (Contig-U12174-1Q) /CSM_Contig/Contig-U12174-1Q.Seq.d
          Length = 1800

 Score = 36.2 bits (18), Expect = 0.013
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                
Query: 62  attattagntggtgatcataa 82
           |||||||| ||||||||||||
Sbjct: 874 attattaggtggtgatcataa 894


  Database: CSM
    Posted date:  Jun 21, 2004  1:35 PM
  Number of letters in database: 8,075,542
  Number of sequences in database:  8402
  
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: 2417
Number of Sequences: 8402
Number of extensions: 2417
Number of successful extensions: 1016
Number of sequences better than 10.0: 181
length of query: 138
length of database: 8,075,542
effective HSP length: 15
effective length of query: 123
effective length of database: 7,949,512
effective search space: 977789976
effective search space used: 977789976
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. 1.27
Homology vs DNA 
Query= Contig-U15473-1 (Contig-U15473-1Q) /CSM_Contig/Contig-U15473-1Q.Seq.d
         (138 letters)

Database: ddbj_B
           98,226,423 sequences; 98,766,808,389 total letters

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

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

(BJ418464) Dictyostelium discoideum cDNA clone:ddv32i19, 5' ...   256   2e-64  1
(AB030580) Homo sapiens DNA, breakpoint of inv(11)(q13,q25),...    48   0.076  1
(AC156713) Bos taurus clone CH240-55C17, WORKING DRAFT SEQUE...    44   1.2    1
(AC214010) Macaca mulatta chromosome UNKNOWN clone CH250-72E...    44   1.2    1
(EK080334) 1092961100712 Global-Ocean-Sampling_GS-31-01-01-1...    44   1.2    1
(FC797248) CBGC24679.fwd CBGC Lottia gigantea 15h 18h embryo...    44   1.2    1
(FC797247) CBGC24679.rev CBGC Lottia gigantea 15h 18h embryo...    44   1.2    1
(FC560076) CAWF2681.rev CAWF Lottia gigantea from mantle (H)...    44   1.2    1
(AC119678) Oryza sativa Japonica Group chromosome 11 clone O...    42   3.9    2
(AL626804) Zebrafish DNA sequence from clone RP71-1H10 in li...    36   4.1    2
(AC207021) Pongo abelii BAC clone CH276-258G8 from chromosom...    42   4.7    1
(AP008217) Oryza sativa (japonica cultivar-group) genomic DN...    42   4.7    1
(AC151599) Oryza sativa Japonica Group chromosome 11 clone O...    42   4.7    1
(AC152840) Oryza sativa Japonica Group chromosome 11 clone O...    42   4.7    1
(AC128079) Rattus norvegicus clone CH230-347L4, WORKING DRAF...    42   4.7    1
(AC094156) Rattus norvegicus clone CH230-2M20, *** SEQUENCIN...    42   4.7    1
(AQ556114) HS_5231_B1_C12_SP6E RPCI-11 Human Male BAC Librar...    42   4.7    1
(EE264114) E10_E10gf4o19_pDNRf_505952 Myzus persicae, line G...    42   4.7    1
(EC388064) G04_G04gm1l7_pDNRf_477168 Myzus persicae, line G0...    42   4.7    1
(C25782) Dictyostelium discoideum gamete cDNA, clone FC-BC12.      42   4.7    1
(FF297993) 279319028 Pea aphid whole body normalized full le...    42   4.7    1
(EX653879) 256805676 Pea aphid whole body normalized full le...    42   4.7    1
(EJ023530) 1095454011490 Global-Ocean-Sampling_GS-26-01-01-1...    32   6.8    2
(AC222965) Bos taurus clone CH240-433F14, WORKING DRAFT SEQU...    32   8.2    2
(AC222976) Bos taurus clone CH240-433I3, WORKING DRAFT SEQUE...    32   8.5    2
(AC220440) Bos taurus clone CH240-358F11, WORKING DRAFT SEQU...    32   8.6    2

>(BJ418464) Dictyostelium discoideum cDNA clone:ddv32i19, 5' end,
           single read.
          Length = 138

 Score =  256 bits (129), Expect = 2e-64
 Identities = 138/138 (100%)
 Strand = Plus / Plus


Query: 1   caactacaacaacacctattgaattcccaggtgatgaaaaagaacaaatgattacaaaag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   caactacaacaacacctattgaattcccaggtgatgaaaaagaacaaatgattacaaaag 60


Query: 61  cattattagntggtgatcataatagtgcanttgaatgtngtcttcgtttaggtagatatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cattattagntggtgatcataatagtgcanttgaatgtngtcttcgtttaggtagatatt 120


Query: 121 cagatgcattgattttaa 138
           ||||||||||||||||||
Sbjct: 121 cagatgcattgattttaa 138

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 98226423
Number of Hits to DB: 140,905,366
Number of extensions: 8438869
Number of successful extensions: 2329194
Number of sequences better than 10.0: 26
Length of query: 138
Length of database: 98,766,808,389
Length adjustment: 22
Effective length of query: 116
Effective length of database: 96,605,827,083
Effective search space: 11206275941628
Effective search space used: 11206275941628
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.16
Homology vs Protein 
Query= Contig-U15473-1 (Contig-U15473-1Q) /CSM_Contig/Contig-U15473-1Q.Seq.d
         (138 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q55CT5) RecName: Full=Protein transport protein SEC31;                87   2e-16
(Q3TZ89) RecName: Full=Protein transport protein Sec31B; AltName...    32   5.2

>(Q55CT5) RecName: Full=Protein transport protein SEC31;
          Length = 1355

 Score = 87.0 bits (214), Expect = 2e-16
 Identities = 42/45 (93%), Positives = 42/45 (93%)
 Frame = +3

Query: 3   TTTTPIEFPGDEKEQMITKALLXGDHNSAXECXLRLGRYSDALIL 137
           TTTTPIEFPGDEKEQMITKALL GDHNSA EC LRLGRYSDALIL
Sbjct: 623 TTTTPIEFPGDEKEQMITKALLVGDHNSAVECCLRLGRYSDALIL 667

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: 183,457,312
Number of extensions: 2648213
Number of successful extensions: 2508
Number of sequences better than 10.0: 2
Number of HSP's gapped: 2508
Number of HSP's successfully gapped: 2
Length of query: 46
Length of database: 1,051,180,864
Length adjustment: 20
Effective length of query: 26
Effective length of database: 986,449,684
Effective search space: 25647691784
Effective search space used: 25647691784
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: 25 (14.2 bits)
PSORT 

 psg: 0.75  gvh: 0.39  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.20  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 

	 36.0 %: cytoplasmic
	 36.0 %: nuclear
	 12.0 %: mitochondrial
	  8.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U15473-1 is cyt
VS (DIR, S) 0
VH (FL, L) 1
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