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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-U07481-1
Contig ID Contig-U07481-1
Contig update 2002. 5. 9
Contig sequence 
>Contig-U07481-1 (Contig-U07481-1Q) /CSM_Contig/Contig-U07481-1Q.Seq.d
NNNNNNNNNNTAATCGCAGGAGCAGGGGNTTTTNTGNATNATTNNNGGAA
TAATAAANAAACATTTCNGTTNNTAGNGCCAGGGNCATTTCANNTTTTTT
NTTNACCATACAAAAAAAAATAATAATTATAATAATAATAATAAAACTTA
CTTGGNNTTNACTTGGAATCNTATTTAATGAGTNCACNATTTTTTCCACT
TTTATCAACACCAGCCCATGCTAAAAAGAATTTTAATTGACAACNGACAC
CTTCATCACATCTCATATCATNGNATTTGGTTGCACATTGATTANCGATA
CAGGAAGCACAATTTTTACAAATTGAAGTATCTCTATCACCATCCCAAAC
TGCATCCACAATGGCACCATTATCAAGTTGGAAAATGATAGTGAAATAGC
TGACAAATGTTCTTG
Gap no gap
Contig length 415
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 2
Number of EST 1
Link to clone list U07481
List of clone(s) 

est1=FC-IC0780Z,1,406
Translated Amino Acid sequence 
xxx*sqeqgxxxxixgiixkhfxx*xqghfxffxxhtkknnnynnnnktylxxtwnxi**
VHXFFHFYQHQPMLKRILIDNXHLHHISYHXIWLHIDXRYRKHNFYKLKYLYHHPKLHPQ
WHHYQVGK***ns*qmfl
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxiagagxfxxxxxnnkxtfxxxxpgxfxxfxxpykkk**l*****nllgxxlesylm
sxxffpllstpahakknfn*qxtpsshlisxxlvah*lxiqeaqflqievslspsqtast
maplsswkmivk*ltnvl


Frame B:
xxx*sqeqgxxxxixgiixkhfxx*xqghfxffxxhtkknnnynnnnktylxxtwnxi**
VHXFFHFYQHQPMLKRILIDNXHLHHISYHXIWLHIDXRYRKHNFYKLKYLYHHPKLHPQ
WHHYQVGK***ns*qmfl


Frame C:
xxxnrrsrgfxxxxxe**xnisvxxarxisxfxxtiqkkiiiiiiiikltwxxlgixfne
xtifstfintspc*kef*lttdtfitshixxfgctlixdtgstiftn*sisitipncihn
gtiiklendseiadkcs
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U07481-1 (Contig-U07481-1Q)
/CSM_Contig/Contig-U07481-1Q.Seq.d
         (415 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U07481-1 (Contig-U07481-1Q) /CSM_Contig/Conti...   478  e-135
Contig-U13902-1 (Contig-U13902-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U12568-1 (Contig-U12568-1Q) /CSM_Contig/Conti...    36  0.029
Contig-U12162-1 (Contig-U12162-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U12295-1 (Contig-U12295-1Q) /CSM_Contig/Conti...    32  0.45
Contig-U11579-1 (Contig-U11579-1Q) /CSM_Contig/Conti...    32  0.45
Contig-U09203-1 (Contig-U09203-1Q) /CSM_Contig/Conti...    32  0.45
Contig-U14498-1 (Contig-U14498-1Q) /CSM_Contig/Conti...    30  1.8
Contig-U13280-1 (Contig-U13280-1Q) /CSM_Contig/Conti...    30  1.8

>Contig-U07481-1 (Contig-U07481-1Q) /CSM_Contig/Contig-U07481-1Q.Seq.d
          Length = 415

 Score =  478 bits (241), Expect = e-135
 Identities = 271/271 (100%)
 Strand = Plus / Plus

                                                                       
Query: 145 aacttacttggnnttnacttggaatcntatttaatgagtncacnattttttccactttta 204
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 145 aacttacttggnnttnacttggaatcntatttaatgagtncacnattttttccactttta 204

                                                                       
Query: 205 tcaacaccagcccatgctaaaaagaattttaattgacaacngacaccttcatcacatctc 264
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205 tcaacaccagcccatgctaaaaagaattttaattgacaacngacaccttcatcacatctc 264

                                                                       
Query: 265 atatcatngnatttggttgcacattgattancgatacaggaagcacaatttttacaaatt 324
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 265 atatcatngnatttggttgcacattgattancgatacaggaagcacaatttttacaaatt 324

                                                                       
Query: 325 gaagtatctctatcaccatcccaaactgcatccacaatggcaccattatcaagttggaaa 384
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 325 gaagtatctctatcaccatcccaaactgcatccacaatggcaccattatcaagttggaaa 384

                                          
Query: 385 atgatagtgaaatagctgacaaatgttcttg 415
           |||||||||||||||||||||||||||||||
Sbjct: 385 atgatagtgaaatagctgacaaatgttcttg 415


 Score = 99.6 bits (50), Expect = 2e-21
 Identities = 101/101 (100%)
 Strand = Plus / Plus

                                                                       
Query: 11  taatcgcaggagcaggggnttttntgnatnattnnnggaataataaanaaacatttcngt 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  taatcgcaggagcaggggnttttntgnatnattnnnggaataataaanaaacatttcngt 70

                                                    
Query: 71  tnntagngccagggncatttcannttttttnttnaccatac 111
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  tnntagngccagggncatttcannttttttnttnaccatac 111


>Contig-U13902-1 (Contig-U13902-1Q) /CSM_Contig/Contig-U13902-1Q.Seq.d
          Length = 2177

 Score = 36.2 bits (18), Expect = 0.029
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                              
Query: 311  aatttttacaaattgaag 328
            ||||||||||||||||||
Sbjct: 2041 aatttttacaaattgaag 2024


>Contig-U12568-1 (Contig-U12568-1Q) /CSM_Contig/Contig-U12568-1Q.Seq.d
          Length = 1697

 Score = 36.2 bits (18), Expect = 0.029
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 218  atgctaaaaagaatttta 235
            ||||||||||||||||||
Sbjct: 1329 atgctaaaaagaatttta 1346


  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: 2309
Number of Sequences: 6905
Number of extensions: 2309
Number of successful extensions: 213
Number of sequences better than 10.0: 65
length of query: 415
length of database: 5,674,871
effective HSP length: 16
effective length of query: 399
effective length of database: 5,564,391
effective search space: 2220192009
effective search space used: 2220192009
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 2008.11.11
Homology vs DNA 
Query= Contig-U07481-1 (Contig-U07481-1Q) /CSM_Contig/Contig-U07481-1Q.Seq.d
         (415 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

(AU271818) Dictyostelium discoideum gamete cDNA clone:FC-IC0...   474   e-153  2
(AC116330) Dictyostelium discoideum chromosome 2 map 3191214...   412   e-111  1
(AC115684) Dictyostelium discoideum chromosome 2 map 3108975...    44   2.5    4
(AC172743) Medicago truncatula chromosome 2 BAC clone mth2-2...    44   3.9    1
(AY392439) Dictyostelium discoideum P-selectin gene, complet...    44   3.9    1
(CU372914) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   3.9    1
(CL329959) CH242_3M1.r CHORI-242 Sus scrofa genomic clone CH...    44   3.9    1
(DR062070) iq08c12.g1 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(CB089273) qs07b05.b1 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX927575) ll03a03.g7 Cycas ovule - normalized (NYBG) Cycas ...    44   3.9    1
(EX920794) lj39e08.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX919947) lj37a07.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX919748) lj34f11.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX919601) lj32h11.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX919321) lj29e12.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(EX918404) lj18h03.g7 Cycas sporophyll (w/o ovule) (NYBG) Cy...    44   3.9    1
(AC161005) Pan troglodytes BAC clone CH251-668M6 from chromo...    34   8.1    4

>(AU271818) Dictyostelium discoideum gamete cDNA clone:FC-IC0780, 3'
           end single read.
          Length = 406

 Score =  474 bits (239), Expect(2) = e-153
 Identities = 269/269 (100%)
 Strand = Plus / Plus


Query: 147 cttacttggnnttnacttggaatcntatttaatgagtncacnattttttccacttttatc 206
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 137 cttacttggnnttnacttggaatcntatttaatgagtncacnattttttccacttttatc 196


Query: 207 aacaccagcccatgctaaaaagaattttaattgacaacngacaccttcatcacatctcat 266
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 197 aacaccagcccatgctaaaaagaattttaattgacaacngacaccttcatcacatctcat 256


Query: 267 atcatngnatttggttgcacattgattancgatacaggaagcacaatttttacaaattga 326
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 257 atcatngnatttggttgcacattgattancgatacaggaagcacaatttttacaaattga 316


Query: 327 agtatctctatcaccatcccaaactgcatccacaatggcaccattatcaagttggaaaat 386
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 317 agtatctctatcaccatcccaaactgcatccacaatggcaccattatcaagttggaaaat 376


Query: 387 gatagtgaaatagctgacaaatgttcttg 415
           |||||||||||||||||||||||||||||
Sbjct: 377 gatagtgaaatagctgacaaatgttcttg 405

 Score = 99.6 bits (50), Expect(2) = e-153
 Identities = 101/101 (100%)
 Strand = Plus / Plus


Query: 11  taatcgcaggagcaggggnttttntgnatnattnnnggaataataaanaaacatttcngt 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   taatcgcaggagcaggggnttttntgnatnattnnnggaataataaanaaacatttcngt 60


Query: 71  tnntagngccagggncatttcannttttttnttnaccatac 111
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tnntagngccagggncatttcannttttttnttnaccatac 101

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 290,345,935
Number of extensions: 16162502
Number of successful extensions: 1159505
Number of sequences better than 10.0: 17
Length of query: 415
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 392
Effective length of database: 93,106,754,628
Effective search space: 36497847814176
Effective search space used: 36497847814176
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.23
Homology vs Protein 
Query= Contig-U07481-1 (Contig-U07481-1Q) /CSM_Contig/Contig-U07481-1Q.Seq.d
         (415 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116330_2(AC116330|pid:none) Dictyostelium discoideum chromosom...   151   6e-36
AC115684_25(AC115684|pid:none) Dictyostelium discoideum chromoso...    80   3e-14
AF514281_1(AF514281|pid:none) Oreochromis aureus vitellogenin re...    34   1.8
AK061238_1(AK061238|pid:none) Oryza sativa Japonica Group cDNA c...    33   3.1
AC145811_6(AC145811|pid:none) Oryza sativa (japonica cultivar-gr...    33   3.1
(P04929) Histidine-rich glycoprotein precursor.  &KGZQHL(A22692)...    33   4.0
AJ879619_2(AJ879619|pid:none) Solea senegalensis mRNA for very l...    32   5.3
AJ879619_1(AJ879619|pid:none) Solea senegalensis mRNA for very l...    32   5.3
(Q8MP30) RecName: Full=Uncharacterized histidine-rich protein DD...    32   6.9
AE014134_613(AE014134|pid:none) Drosophila melanogaster chromoso...    32   8.9

>AC116330_2(AC116330|pid:none) Dictyostelium discoideum chromosome 2
           map 3191214-3323468 strain AX4, complete sequence.
          Length = 311

 Score =  151 bits (382), Expect = 6e-36
 Identities = 70/75 (93%), Positives = 70/75 (93%)
 Frame = -3

Query: 413 RTFVSYFTIIFQLDNGAIVDAVWDGDRDTSICKNCASCIXNQCATKXXDMRCDEGVXCQL 234
           RTFVSYFTIIFQLDNGAIVDAVWDGDRDTSICKNC SCI NQCATK  DMRCDEGV CQL
Sbjct: 193 RTFVSYFTIIFQLDNGAIVDAVWDGDRDTSICKNCDSCIDNQCATKFDDMRCDEGVGCQL 252

Query: 233 KFFLAWAGVDKSGKN 189
           KFFLAWAGVDKSGKN
Sbjct: 253 KFFLAWAGVDKSGKN 267

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: 500,669,507
Number of extensions: 9622371
Number of successful extensions: 16606
Number of sequences better than 10.0: 10
Number of HSP's gapped: 16542
Number of HSP's successfully gapped: 13
Length of query: 138
Length of database: 1,040,966,779
Length adjustment: 102
Effective length of query: 36
Effective length of database: 714,129,709
Effective search space: 25708669524
Effective search space used: 25708669524
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: 29 (15.8 bits)
PSORT 

 psg: 0.83  gvh: 0.31  alm: 0.59  top: 0.53  tms: 0.00  mit: 0.30  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.50  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 

	 52.0 %: nuclear
	 32.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U07481-1 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) 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) 1
FC-IC (SUB) 1