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Dicty_cDB
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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-U01319-1
Contig ID Contig-U01319-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01319-1 (Contig-U01319-1Q) /CSM_Contig/Contig-U01319-1Q.Seq.d
AACCACATATATCTCTCCTACATATTCATAAATACATTCACTCATGTATT
AATAATAGTTCAAATTAATCATGAGTGAATCAAATAATAATAATAATAAT
AATGATAATAATAAAGATGAAACCAATAATAATAAAGAAGAGCAAACCCA
AACACAACTACCCGTCTCACACAATCCTACGCACATACAATCACCATTAG
CACAAAAACAAACCATTGAATCGAGTAACAATAATAATCATA
Gap no gap
Contig length 242
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3440271
End point 3440029
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U01319
List of clone(s) 

est1=SLF815F,1,243
Translated Amino Acid sequence 
ttyisptys*ihslmy***FKLIMSESNNNNNNNDNNKDETNNNKEEQTQTQLPVSHNPT
HIQSPLAQKQTIESSNNNNH
Translated Amino Acid sequence (All Frames) 
Frame A:
nhiylsyifintfthvliivqinhe*ik**********r*nq***rranpntttrltqsy
ahtitistktnh*ie*q**s


Frame B:
ttyisptys*ihslmy***FKLIMSESNNNNNNNDNNKDETNNNKEEQTQTQLPVSHNPT
HIQSPLAQKQTIESSNNNNH


Frame C:
phisllhihkyihscinnssn*s*vnqiiiiiimiiikmkpiiikkskpkhnypshtilr
tynhh*hknkplnrvtiiii
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01319-1 (Contig-U01319-1Q)
/CSM_Contig/Contig-U01319-1Q.Seq.d
         (242 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01319-1 (Contig-U01319-1Q) /CSM_Contig/Conti...   254  5e-68
Contig-U05293-1 (Contig-U05293-1Q) /CSM_Contig/Conti...    42  4e-04
Contig-U11140-1 (Contig-U11140-1Q) /CSM_Contig/Conti...    36  0.023
Contig-U12689-1 (Contig-U12689-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U11780-1 (Contig-U11780-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U11353-1 (Contig-U11353-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U10922-1 (Contig-U10922-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U07853-1 (Contig-U07853-1Q) /CSM_Contig/Conti...    34  0.090
Contig-U12874-1 (Contig-U12874-1Q) /CSM_Contig/Conti...    32  0.35
Contig-U12607-1 (Contig-U12607-1Q) /CSM_Contig/Conti...    32  0.35

>Contig-U01319-1 (Contig-U01319-1Q) /CSM_Contig/Contig-U01319-1Q.Seq.d
          Length = 242

 Score =  254 bits (128), Expect = 5e-68
 Identities = 128/128 (100%)
 Strand = Plus / Plus

                                                                       
Query: 115 agatgaaaccaataataataaagaagagcaaacccaaacacaactacccgtctcacacaa 174
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115 agatgaaaccaataataataaagaagagcaaacccaaacacaactacccgtctcacacaa 174

                                                                       
Query: 175 tcctacgcacatacaatcaccattagcacaaaaacaaaccattgaatcgagtaacaataa 234
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 175 tcctacgcacatacaatcaccattagcacaaaaacaaaccattgaatcgagtaacaataa 234

                   
Query: 235 taatcata 242
           ||||||||
Sbjct: 235 taatcata 242


 Score =  163 bits (82), Expect = 1e-40
 Identities = 82/82 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  aaccacatatatctctcctacatattcataaatacattcactcatgtattaataatagtt 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  aaccacatatatctctcctacatattcataaatacattcactcatgtattaataatagtt 60

                                
Query: 61 caaattaatcatgagtgaatca 82
          ||||||||||||||||||||||
Sbjct: 61 caaattaatcatgagtgaatca 82


>Contig-U05293-1 (Contig-U05293-1Q) /CSM_Contig/Contig-U05293-1Q.Seq.d
          Length = 375

 Score = 42.1 bits (21), Expect = 4e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 45  tgtattaataatagttcaaat 65
           |||||||||||||||||||||
Sbjct: 248 tgtattaataatagttcaaat 268


 Score = 28.2 bits (14), Expect = 5.5
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                             
Query: 48  attaataatagttcaaat 65
           |||||||||||| |||||
Sbjct: 188 attaataatagtacaaat 205


>Contig-U11140-1 (Contig-U11140-1Q) /CSM_Contig/Contig-U11140-1Q.Seq.d
          Length = 2231

 Score = 36.2 bits (18), Expect = 0.023
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 205  aaaacaaaccattgaatc 222
            ||||||||||||||||||
Sbjct: 1157 aaaacaaaccattgaatc 1174


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 19,249
Number of Sequences: 8361
Number of extensions: 19249
Number of successful extensions: 4014
Number of sequences better than 10.0: 266
length of query: 242
length of database: 7,895,291
effective HSP length: 15
effective length of query: 227
effective length of database: 7,769,876
effective search space: 1763761852
effective search space used: 1763761852
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. 4.26
Homology vs DNA 
Query= Contig-U01319-1 (Contig-U01319-1Q) /CSM_Contig/Contig-U01319-1Q.Seq.d
         (242 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(AU061769) Dictyostelium discoideum slug cDNA, clone SLF815.      212   2e-73  2
(AC172838) Bos taurus clone CH240-272L18, WORKING DRAFT SEQU...    44   2.3    1
(GC528794) Sequence 2304 from patent US 7411051.                   42   9.1    1
(FB711074) Sequence 7 from Patent WO2007135568.                    42   9.1    1
(FB342951) Sequence 7 from Patent EP1857559.                       42   9.1    1
(EA746055) Sequence 2304 from patent US 7368531.                   42   9.1    1
(EA270965) Sequence 102 from patent US 7247442.                    42   9.1    1
(EA102652) Sequence 35 from patent US 7195870.                     42   9.1    1
(DD287902) LYMPHATIC ENDOTHELIAL GENES.                            42   9.1    1
(CS428630) Sequence 1537 from Patent WO2006100066.                 42   9.1    1
(CS040877) Sequence 1431 from Patent WO2005019258.                 42   9.1    1
(CS031925) Sequence 1431 from Patent WO2005016962.                 42   9.1    1
(BD460304) Diagnosis of Diseases Associated with Cell Cycle.       42   9.1    1
(BD452226) Diagnosis of Diseases Associated with Cell Cycle.       42   9.1    1
(BD205724) 97 human secreted proteins.                             42   9.1    1
(AX323555) Sequence 43 from Patent WO0192565.                      42   9.1    1
(AX277872) Sequence 35 from Patent WO0177375.                      42   9.1    1
(AX251840) Sequence 101 from Patent WO0168911.                     42   9.1    1
(GN002236) Sequence 1431 from Patent EP2014675.                    42   9.1    1
(GM995903) Sequence 43 from Patent EP2014776.                      42   9.1    1
(GM527579) Sequence 478257 from Patent WO2005116250.               42   9.1    1
(GM048329) Sequence 165 from Patent WO2007026255.                  42   9.1    1
(BX647990) Homo sapiens mRNA; cDNA DKFZp686N2252 (from clone...    42   9.1    1
(BC027849) Homo sapiens RAS guanyl releasing protein 3 (calc...    42   9.1    1
(AC020594) Homo sapiens BAC clone RP11-322P19 from 2, comple...    42   9.1    1
(AB020653) Homo sapiens mRNA for KIAA0846 protein, partial cds.    42   9.1    1
(AC151950) Takifugu rubripes, *** SEQUENCING IN PROGRESS ***...    42   9.1    1
(CR857545) Pongo abelii mRNA; cDNA DKFZp469M0328 (from clone...    42   9.1    1
(AZ692856) ENTKL59TF Entamoeba histolytica Sheared DNA Entam...    42   9.1    1
(EK576381) 1095521347009 Global-Ocean-Sampling_GS-32-01-01-1...    42   9.1    1
(DU880364) 273076 Tomato HindIII BAC Library Solanum lycoper...    42   9.1    1
(AV723238) Homo sapiens cDNA clone:HTBAGH01, 5'end, expresse...    42   9.1    1
(AV722984) Homo sapiens cDNA clone:HTBAGF11, 5'end, expresse...    42   9.1    1
(AV722123) Homo sapiens cDNA clone:HTBAFC02, 5'end, expresse...    42   9.1    1
(CD724273) oj32e11.y1 Human lacrimal gland, unamplified: oj ...    42   9.1    1
(CD723380) oj21e02.y1 Human lacrimal gland, unamplified: oj ...    42   9.1    1
(BX114300) RZPD Homo sapiens cDNA clone IMAGp998O03186 = IMA...    42   9.1    1
(BU146124) AGENCOURT_8125828 Lupski_dorsal_root_ganglion Hom...    42   9.1    1
(AI361501) qy48d03.x1 NCI_CGAP_Brn23 Homo sapiens cDNA clone...    42   9.1    1
(AA883328) al45a06.s1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA ...    42   9.1    1
(AA766741) oa39f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone ...    42   9.1    1
(Z46162) H. sapiens partial cDNA sequence; clone c-1hf10.          42   9.1    1

>(AU061769) Dictyostelium discoideum slug cDNA, clone SLF815.
          Length = 243

 Score =  212 bits (107), Expect(2) = 2e-73
 Identities = 107/107 (100%)
 Strand = Plus / Plus


Query: 136 agaagagcaaacccaaacacaactacccgtctcacacaatcctacgcacatacaatcacc 195
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 136 agaagagcaaacccaaacacaactacccgtctcacacaatcctacgcacatacaatcacc 195


Query: 196 attagcacaaaaacaaaccattgaatcgagtaacaataataatcata 242
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 196 attagcacaaaaacaaaccattgaatcgagtaacaataataatcata 242

 Score = 97.6 bits (49), Expect(2) = 2e-73
 Identities = 49/49 (100%)
 Strand = Plus / Plus


Query: 1  aaccacatatatctctcctacatattcataaatacattcactcatgtat 49
          |||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  aaccacatatatctctcctacatattcataaatacattcactcatgtat 49

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 173,684,221
Number of extensions: 11106954
Number of successful extensions: 3005853
Number of sequences better than 10.0: 43
Length of query: 242
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 219
Effective length of database: 99,442,330,388
Effective search space: 21777870354972
Effective search space used: 21777870354972
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.14
Homology vs Protein 
Query= Contig-U01319-1 (Contig-U01319-1Q) /CSM_Contig/Contig-U01319-1Q.Seq.d
         (242 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: 271,738,203
Number of extensions: 3859057
Number of successful extensions: 17079
Number of sequences better than 10.0: 0
Number of HSP's gapped: 17074
Number of HSP's successfully gapped: 0
Length of query: 80
Length of database: 1,051,180,864
Length adjustment: 51
Effective length of query: 29
Effective length of database: 886,116,355
Effective search space: 25697374295
Effective search space used: 25697374295
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: 0.41  gvh: 0.27  alm: 0.66  top: 0.53  tms: 0.00  mit: 0.25  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 

	 44.0 %: nuclear
	 28.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U01319-1 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) 1
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