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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U13501-1
Contig ID Contig-U13501-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13501-1 (Contig-U13501-1Q) /CSM_Contig/Contig-U13501-1Q.Seq.d
ATTTTTGAGTTTCATTCGTTCAAATACAATTATTGGGTAAATTAAAATTC
TAATTGTCTAAATTTATTTATTTTTTTTTCTTTATTTTATTATTGTTTTT
TTAATAAATAATAGTAATAAATAATAATAAATTATTAATAATTAAAAATC
AATTAAAAAAAAAATAAAAATAAAAAATAAAATAGAAAAAAAAAA
Gap no gap
Contig length 195
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 137392
End point 137197
Strand (PLUS/MINUS) MINUS
Number of clones 11
Number of EST 11
Link to clone list U13501
List of clone(s) 

est1=VFI487F,1,108
est2=VHD472F,1,180
est3=VHH783F,14,194
est4=VHD788F,22,196
est5=VHJ287F,22,196
est6=VHJ528F,22,196
est7=VHP209F,22,196
est8=VHC560F,23,196
est9=VHL340F,28,196
est10=VHG377F,44,196
est11=VHA195F,48,196
Translated Amino Acid sequence 
ifefhsfkynywvn*NSNCLNLFIFFSLFYYCFFNK****iiiny**lkin*kknknkk*
nrkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
ifefhsfkynywvn*NSNCLNLFIFFSLFYYCFFNK****iiiny**lkin*kknknkk*
nrkkk


Frame B:
flsfirsntiig*ikiliv*iylffflyfiivflinnsnk***iinn*ksikkkikiknk
iekk


Frame C:
f*vsfvqiqllgklkf*lskfiyffffilllff**iivinnnklliiknqlkkk*k*kik
*kkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13501-1 (Contig-U13501-1Q)
/CSM_Contig/Contig-U13501-1Q.Seq.d
         (195 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13501-1 (Contig-U13501-1Q) /CSM_Contig/Conti...   127  5e-30
Contig-U06500-1 (Contig-U06500-1Q) /CSM_Contig/Conti...    34  0.051
Contig-U13974-1 (Contig-U13974-1Q) /CSM_Contig/Conti...    32  0.20
Contig-U12007-1 (Contig-U12007-1Q) /CSM_Contig/Conti...    30  0.80
Contig-U06239-1 (Contig-U06239-1Q) /CSM_Contig/Conti...    30  0.80
Contig-U14670-1 (Contig-U14670-1Q) /CSM_Contig/Conti...    28  3.2
Contig-U13998-1 (Contig-U13998-1Q) /CSM_Contig/Conti...    28  3.2
Contig-U13989-1 (Contig-U13989-1Q) /CSM_Contig/Conti...    28  3.2
Contig-U13948-1 (Contig-U13948-1Q) /CSM_Contig/Conti...    28  3.2
Contig-U13887-1 (Contig-U13887-1Q) /CSM_Contig/Conti...    28  3.2

>Contig-U13501-1 (Contig-U13501-1Q) /CSM_Contig/Contig-U13501-1Q.Seq.d
          Length = 195

 Score =  127 bits (64), Expect = 5e-30
 Identities = 64/64 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  atttttgagtttcattcgttcaaatacaattattgggtaaattaaaattctaattgtcta 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttttgagtttcattcgttcaaatacaattattgggtaaattaaaattctaattgtcta 60

              
Query: 61 aatt 64
          ||||
Sbjct: 61 aatt 64


>Contig-U06500-1 (Contig-U06500-1Q) /CSM_Contig/Contig-U06500-1Q.Seq.d
          Length = 556

 Score = 34.2 bits (17), Expect = 0.051
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 31  tattgggtaaattaaaa 47
           |||||||||||||||||
Sbjct: 537 tattgggtaaattaaaa 553


>Contig-U13974-1 (Contig-U13974-1Q) /CSM_Contig/Contig-U13974-1Q.Seq.d
          Length = 1782

 Score = 32.2 bits (16), Expect = 0.20
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 21  caaatacaattattgg 36
           ||||||||||||||||
Sbjct: 971 caaatacaattattgg 986


  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: 1389
Number of Sequences: 6905
Number of extensions: 1389
Number of successful extensions: 391
Number of sequences better than 10.0: 42
length of query: 195
length of database: 5,674,871
effective HSP length: 15
effective length of query: 180
effective length of database: 5,571,296
effective search space: 1002833280
effective search space used: 1002833280
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 2008.12.10
Homology vs DNA 
Query= Contig-U13501-1 (Contig-U13501-1Q) /CSM_Contig/Contig-U13501-1Q.Seq.d
         (195 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

(BJ419947) Dictyostelium discoideum cDNA clone:ddv37p18, 5' ...   121   9e-24  1
(BJ414061) Dictyostelium discoideum cDNA clone:ddv17n22, 5' ...   121   9e-24  1
(BJ422712) Dictyostelium discoideum cDNA clone:ddv46f21, 5' ...    96   5e-16  1
(BJ427010) Dictyostelium discoideum cDNA clone:ddv61a04, 5' ...    80   3e-11  1
(BJ423761) Dictyostelium discoideum cDNA clone:ddv50g07, 5' ...    80   3e-11  1
(BJ423644) Dictyostelium discoideum cDNA clone:ddv49m22, 5' ...    80   3e-11  1
(BJ420335) Dictyostelium discoideum cDNA clone:ddv38p21, 5' ...    80   3e-11  1
(BJ419590) Dictyostelium discoideum cDNA clone:ddv36g15, 5' ...    78   1e-10  1
(BJ424753) Dictyostelium discoideum cDNA clone:ddv53p09, 5' ...    68   1e-07  1
(AY054095) Phrynocephalus versicolor isolate 0983 NADH dehyd...    44   1.7    1
(AY054094) Phrynocephalus versicolor isolate 0981 NADH dehyd...    44   1.7    1
(AY054093) Phrynocephalus versicolor isolate 0787 NADH dehyd...    44   1.7    1
(AY054092) Phrynocephalus versicolor isolate 0760 NADH dehyd...    44   1.7    1
(AY054091) Phrynocephalus versicolor isolate 0706 NADH dehyd...    44   1.7    1
(AY054090) Phrynocephalus versicolor isolate 01072 NADH dehy...    44   1.7    1
(AY054061) Phrynocephalus przewalskii isolate RM3939 NADH de...    44   1.7    1
(AY054060) Phrynocephalus przewalskii isolate 0790 NADH dehy...    44   1.7    1
(AY054059) Phrynocephalus przewalskii isolate 0789 NADH dehy...    44   1.7    1
(AY054023) Phrynocephalus frontalis isolate 01248 NADH dehyd...    44   1.7    1
(AY054022) Phrynocephalus frontalis isolate 01258 NADH dehyd...    44   1.7    1
(AY054021) Phrynocephalus frontalis isolate 01337 NADH dehyd...    44   1.7    1
(AL929003) Zebrafish DNA sequence from clone DKEY-235D18 in ...    42   6.7    1
(AC186826) Gallus gallus BAC clone CH261-136P11 from chromos...    42   6.7    1
(AC116210) Rattus norvegicus clone CH230-32M5, *** SEQUENCIN...    42   6.7    1
(AC200959) Strongylocentrotus purpuratus clone R3-1111E4, WO...    42   6.7    1
(AC179773) Strongylocentrotus purpuratus clone R3-1016E11, W...    42   6.7    1
(AC179681) Strongylocentrotus purpuratus clone R3-1021N7, WO...    42   6.7    1
(AC179201) Strongylocentrotus purpuratus clone R3-4019K13, W...    42   6.7    1
(AC178627) Strongylocentrotus purpuratus clone R3-3007O4, WO...    42   6.7    1
(AC178286) Strongylocentrotus purpuratus clone R3-3094G11, W...    42   6.7    1
(AC177376) Strongylocentrotus purpuratus clone R3-52M20, WOR...    42   6.7    1
(AC176775) Strongylocentrotus purpuratus clone R3-3104K12, W...    42   6.7    1
(AC175920) Strongylocentrotus purpuratus clone R3-12L7, WORK...    42   6.7    1
(AC168770) Strongylocentrotus purpuratus clone R3-13P19, WOR...    42   6.7    1
(AC168606) Strongylocentrotus purpuratus clone R3-3046L6, WO...    42   6.7    1
(AC168506) Strongylocentrotus purpuratus clone R3-3117B23, W...    42   6.7    1
(FI070511) CHO_OF7314xc07r1.ab1 CHO_OF7 Nicotiana tabacum ge...    42   6.7    1
(FH986915) CHO_OF6842xc13r1.ab1 CHO_OF6 Nicotiana tabacum ge...    42   6.7    1
(DH652763) Rattus norvegicus DNA, BAC clone: RNB1-196F13, 3'...    42   6.7    1
(ES248112) WS0367.C21_M16 SS-B-N-21 Picea sitchensis cDNA cl...    42   6.7    1
(DR590284) WS00828.B21_C11 WS-X-N-A-9 Picea glauca cDNA clon...    42   6.7    1
(DR563031) WS02626.C21_J23 WS-PP-N-A-12 Picea glauca cDNA cl...    42   6.7    1
(CO255639) WS00825.B21_L03 WS-X-N-A-9 Picea glauca cDNA clon...    42   6.7    1
(CO255637) WS00825.B21_L01 WS-X-N-A-9 Picea glauca cDNA clon...    42   6.7    1
(CO251897) WS00815.B21_C07 WS-X-N-A-9 Picea glauca cDNA clon...    42   6.7    1
(AE014297) Drosophila melanogaster chromosome 3R, complete s...    30   7.8    2

>(BJ419947) Dictyostelium discoideum cDNA clone:ddv37p18, 5' end,
          single read.
          Length = 179

 Score =  121 bits (61), Expect = 9e-24
 Identities = 61/61 (100%)
 Strand = Plus / Plus


Query: 1  atttttgagtttcattcgttcaaatacaattattgggtaaattaaaattctaattgtcta 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  atttttgagtttcattcgttcaaatacaattattgggtaaattaaaattctaattgtcta 60


Query: 61 a 61
          |
Sbjct: 61 a 61

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 77,844,310
Number of extensions: 5261043
Number of successful extensions: 1445860
Number of sequences better than 10.0: 46
Length of query: 195
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 173
Effective length of database: 93,199,600,587
Effective search space: 16123530901551
Effective search space used: 16123530901551
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 7
Homology vs Protein 
Query= Contig-U13501-1 (Contig-U13501-1Q) /CSM_Contig/Contig-U13501-1Q.Seq.d
         (195 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: 52,771,308
Number of extensions: 237017
Number of successful extensions: 222
Number of sequences better than 10.0: 0
Number of HSP's gapped: 222
Number of HSP's successfully gapped: 0
Length of query: 65
Length of database: 1,051,180,864
Length adjustment: 37
Effective length of query: 28
Effective length of database: 931,428,181
Effective search space: 26079989068
Effective search space used: 26079989068
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: 1.00  gvh: 0.42  alm: 0.35  top: 0.53  tms: 0.00  mit: 0.38  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 

	 40.0 %: cytoplasmic
	 28.0 %: mitochondrial
	 24.0 %: nuclear
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane

>> prediction for Contig-U13501-1 is cyt
VS (DIR, S) 0
VH (FL, L) 10
VF (FL, S) 1
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