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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U01624-1
Contig ID Contig-U01624-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01624-1 (Contig-U01624-1Q) /CSM_Contig/Contig-U01624-1Q.Seq.d
CAGTGAAAAACAAGTTTCATTACAACCAAGAACTTCTTCATCACTCTCAA
ATTCACCTTCACCAACTCCAACTATTAATTCAACTCAAACTACTCCAACA
ACTTCTCCTGAAATCGCTTGGATAATATCTTCACCAAAATCATTATCTTT
AACAAATTTAAAATCAAATCAAACTCAAACTCAAAATCAAAATCAAATCC
AAAATCAAAATAATCAAAATAATCAAAATAATAATAATAATAATAATAAT
AATAATAATAATAATAATAATAAAATTAATAATTTAATTATATCATCATC
ATCCTTGAATTTCAATTACATATTGGAAGGGAGTCAATGGACCACGAAGG
ATTTTTTCGTCACCGTCAAGTAAGTATCATTCTGATGATATGCCATCATC
CCCACTTTCAAACTCATCACCGTCAATTAATAACGCTCCAGTAAATACTA
GCCAAGACTCAAACTTTAATTTCTCCGCGCTTACAGACACTTTCCAACTT
TTCATTAACTCAACACCCTGTATCAATCCACTTCCCGAATTCTTTAAAAT
CAAGTGGAAATAATATAAATATTACATACATTAATTATAATAATAATAAT
AATAATATAAAAAATAATATAAATAATAATAATAATAATAGTATAAATAA
TAATTATAATAATTATAATA----------TTAAATTATAATTATAATAA
TTATAATATAAAAAATAATGAAAAAAGCGAAAATAATAATGAAAAAATTA
ATCAAATGAAATCAATTTTAAATTGTACACTTTAAAAATATTTATTCAAA
ATTTCACATTCAAGTGTGTATTACCAATTTTTTTTTTTTTTTTTTTAAAT
TCAAAGAGAGAAGTTAAGAAAGAAAGAAAGAAAAAAGTTAAAAACTGGAA
AAAAAAAAAAAAAAAAAAAAAAAAACAGGA
Gap gap included
Contig length 920
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 3
Number of EST 5
Link to clone list U01624
List of clone(s) 

est1=SSL757Z,-50,671
est2=SSL757F,1,256
est3=SSC883F,67,600
est4=SSG842Z,672,921
est5=SSC883Z,679,922
Translated Amino Acid sequence 
q*ktsfittknffitlkftftnsny*fnsnysnnfs*nrldniftkiiifnkfkiksnsn
sksksnpksk*sk*sk***************n**fnyiiiilefqlhigresmdhegffr
hrqvsiilmichhphfqthhrqlitlq*ILAKTQTLISPRLQTLSNFSLTQHPVSIHFPN
SLKSSGNNINITYINYNNNNNNIKNNINNNNNNSINNNYNNYN---

---LNYNYNNYNIKNNEKSENNNEKINQMKSILNCTL*kylfkishssvyyqffffff*i
qreklrkkerkklktgkkkkkkkknr
Translated Amino Acid sequence (All Frames) 
Frame A:
q*ktsfittknffitlkftftnsny*fnsnysnnfs*nrldniftkiiifnkfkiksnsn
sksksnpksk*sk*sk***************n**fnyiiiilefqlhigresmdhegffr
hrqvsiilmichhphfqthhrqlitlq*ILAKTQTLISPRLQTLSNFSLTQHPVSIHFPN
SLKSSGNNINITYINYNNNNNNIKNNINNNNNNSINNNYNNYN---

---LNYNYNNYNIKNNEKSENNNEKINQMKSILNCTL*kylfkishssvyyqffffff*i
qreklrkkerkklktgkkkkkkkknr

Frame B:
sekqvslqprtssslsnspsptptinstqttpttspeiawiisspkslsltnlksnqtqt
qnqnqiqnqnnqnnqnnnnnnnnnnnnnnnkinnliisssslnfnyilegsqwttkdffv
tvk*vsf**yaiiptfklitvn**rssky*prlkl*flrayrhfptfh*lntlyqstsri
l*nqveii*ilhtliiiiiiii*kii*iiiiiiv*iiiiiiii---

---*iiiiiiii*kimkkakiimkklik*nqf*ivhfkniyskfhiqvcitnffffffkf
kers*erkkeks*klekkkkkkkktg

Frame C:
vknkfhynqellhhsqihlhqlqlliqlkllqqlllkslg*ylhqnhyl*qi*nqiklkl
kikikskikiikiikiiiiiiiiiiiiiiiklii*lyhhhp*isitywkgvngprrifss
psskyhsddmpssplsnsspsinnapvntsqdsnfnfsaltdtfqlfinstpcinplpef
fkikwk*ykyyih*l******ykk*yk******yk**l**l*---

---kl*l**l*ykk**kkrk***kn*sneinfklytlkifiqnftfkcvlpiffffflns
krevkkerkkkvknwkkkkkkkkkq
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01624-1 (Contig-U01624-1Q)
/CSM_Contig/Contig-U01624-1Q.Seq.d
         (930 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01624-1 (Contig-U01624-1Q) /CSM_Contig/Conti...   533  e-151
Contig-U13507-1 (Contig-U13507-1Q) /CSM_Contig/Conti...    40  0.006
Contig-U10865-1 (Contig-U10865-1Q) /CSM_Contig/Conti...    40  0.006
Contig-U10676-1 (Contig-U10676-1Q) /CSM_Contig/Conti...    40  0.006
Contig-U10056-1 (Contig-U10056-1Q) /CSM_Contig/Conti...    36  0.091
Contig-U08935-1 (Contig-U08935-1Q) /CSM_Contig/Conti...    36  0.091
Contig-U05015-1 (Contig-U05015-1Q) /CSM_Contig/Conti...    36  0.091
Contig-U12079-1 (Contig-U12079-1Q) /CSM_Contig/Conti...    34  0.36
Contig-U11057-1 (Contig-U11057-1Q) /CSM_Contig/Conti...    34  0.36
Contig-U10724-1 (Contig-U10724-1Q) /CSM_Contig/Conti...    34  0.36

>Contig-U01624-1 (Contig-U01624-1Q) /CSM_Contig/Contig-U01624-1Q.Seq.d
          Length = 930

 Score =  533 bits (269), Expect = e-151
 Identities = 269/269 (100%)
 Strand = Plus / Plus

                                                                       
Query: 289 tatatcatcatcatccttgaatttcaattacatattggaagggagtcaatggaccacgaa 348
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 289 tatatcatcatcatccttgaatttcaattacatattggaagggagtcaatggaccacgaa 348

                                                                       
Query: 349 ggattttttcgtcaccgtcaagtaagtatcattctgatgatatgccatcatccccacttt 408
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 349 ggattttttcgtcaccgtcaagtaagtatcattctgatgatatgccatcatccccacttt 408

                                                                       
Query: 409 caaactcatcaccgtcaattaataacgctccagtaaatactagccaagactcaaacttta 468
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 409 caaactcatcaccgtcaattaataacgctccagtaaatactagccaagactcaaacttta 468

                                                                       
Query: 469 atttctccgcgcttacagacactttccaacttttcattaactcaacaccctgtatcaatc 528
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 469 atttctccgcgcttacagacactttccaacttttcattaactcaacaccctgtatcaatc 528

                                        
Query: 529 cacttcccgaattctttaaaatcaagtgg 557
           |||||||||||||||||||||||||||||
Sbjct: 529 cacttcccgaattctttaaaatcaagtgg 557


 Score =  266 bits (134), Expect = 5e-71
 Identities = 134/134 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   cagtgaaaaacaagtttcattacaaccaagaacttcttcatcactctcaaattcaccttc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   cagtgaaaaacaagtttcattacaaccaagaacttcttcatcactctcaaattcaccttc 60

                                                                       
Query: 61  accaactccaactattaattcaactcaaactactccaacaacttctcctgaaatcgcttg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  accaactccaactattaattcaactcaaactactccaacaacttctcctgaaatcgcttg 120

                         
Query: 121 gataatatcttcac 134
           ||||||||||||||
Sbjct: 121 gataatatcttcac 134


 Score =  129 bits (65), Expect = 8e-30
 Identities = 65/65 (100%)
 Strand = Plus / Plus

                                                                       
Query: 763 caattttaaattgtacactttaaaaatatttattcaaaatttcacattcaagtgtgtatt 822
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 763 caattttaaattgtacactttaaaaatatttattcaaaatttcacattcaagtgtgtatt 822

                
Query: 823 accaa 827
           |||||
Sbjct: 823 accaa 827


 Score = 38.2 bits (19), Expect = 0.023
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 847 aaattcaaagagagaagtt 865
           |||||||||||||||||||
Sbjct: 847 aaattcaaagagagaagtt 865


>Contig-U13507-1 (Contig-U13507-1Q) /CSM_Contig/Contig-U13507-1Q.Seq.d
          Length = 688

 Score = 40.1 bits (20), Expect = 0.006
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                       
Query: 57  cttcaccaactccaactattaattcaac 84
           |||||||| ||||||||||||| |||||
Sbjct: 521 cttcaccatctccaactattaaatcaac 548


>Contig-U10865-1 (Contig-U10865-1Q) /CSM_Contig/Contig-U10865-1Q.Seq.d
          Length = 5215

 Score = 40.1 bits (20), Expect = 0.006
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                        
Query: 57   cttcaccaactccaactattaattcaac 84
            |||||||| ||||||||||||| |||||
Sbjct: 4006 cttcaccatctccaactattaaatcaac 4033


  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: 10,915
Number of Sequences: 8361
Number of extensions: 10915
Number of successful extensions: 984
Number of sequences better than 10.0: 89
length of query: 930
length of database: 7,895,291
effective HSP length: 16
effective length of query: 914
effective length of database: 7,761,515
effective search space: 7094024710
effective search space used: 7094024710
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2009. 5. 3
Homology vs DNA 
Query= Contig-U01624-1 (Contig-U01624-1Q) /CSM_Contig/Contig-U01624-1Q.Seq.d
         (930 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

(AC117072) Dictyostelium discoideum chromosome 2 map 3879572...   262   e-143  5
(C93822) Dictyostelium discoideum slug cDNA, clone SSL757.        509   e-140  1
(AU074753) Dictyostelium discoideum slug cDNA, clone SSL757.      266   1e-66  1
(AU071977) Dictyostelium discoideum slug cDNA, clone SSC883.      135   2e-28  2
(CO848070) LM_GM5_005660 Locusta migratoria gregarious phase...    36   0.38   2
(EH721922) CNML8303.b1_M12.ab1 CNM(LMS) spotted knapweed Cen...    46   2.4    1
(C93980) Dictyostelium discoideum slug cDNA, clone SSC883.         46   2.4    1
(C84860) Dictyostelium discoideum slug cDNA, clone SSG842.         46   2.4    1
(AP008009) Lotus japonicus genomic DNA, chromosome 1, clone:...    40   3.0    2
(BJ349997) Dictyostelium discoideum cDNA clone:dda38h12, 3' ...    42   6.5    2
(AC158153) Mus musculus chromosome 5, clone RP23-119B3, comp...    44   9.5    1
(AC102011) Mus musculus chromosome 5, clone RP24-536B19, com...    44   9.5    1
(AM450519) Vitis vinifera contig VV78X277211.16, whole genom...    44   9.5    1
(AC110577) Mus musculus chromosome 5 clone RP23-329N11 map 5...    44   9.5    1
(AC177746) Strongylocentrotus purpuratus clone R3-1008E12, W...    44   9.5    1
(AZ383766) 1M0141J01R Mouse 10kb plasmid UUGC1M library Mus ...    44   9.5    1
(CU571945) Theobroma cacao, mRNA sequence (KZ0AAP13YJ11FM1).       44   9.5    1
(CU546001) Theobroma cacao, mRNA sequence (KZ0AA1YG07).            44   9.5    1
(CU510372) Theobroma cacao, mRNA sequence (KZ0ACM3YD21FM1).        44   9.5    1
(CU479362) Theobroma cacao, mRNA sequence (KZ0AAL2YF08FM1).        44   9.5    1
(BM341201) MEST331-G07.T3 ISUM5-RN Zea mays cDNA clone MEST3...    44   9.5    1
(BM161932) EST564455 PyBS Plasmodium yoelii yoelii cDNA clon...    44   9.5    1
(BM161601) EST564124 PyBS Plasmodium yoelii yoelii cDNA clon...    44   9.5    1

>(AC117072) Dictyostelium discoideum chromosome 2 map 3879572-4071762
            strain AX4, complete sequence.
          Length = 192187

 Score =  262 bits (132), Expect(5) = e-143
 Identities = 132/132 (100%)
 Strand = Plus / Plus


Query: 3    gtgaaaaacaagtttcattacaaccaagaacttcttcatcactctcaaattcaccttcac 62
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6906 gtgaaaaacaagtttcattacaaccaagaacttcttcatcactctcaaattcaccttcac 6965


Query: 63   caactccaactattaattcaactcaaactactccaacaacttctcctgaaatcgcttgga 122
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6966 caactccaactattaattcaactcaaactactccaacaacttctcctgaaatcgcttgga 7025


Query: 123  taatatcttcac 134
            ||||||||||||
Sbjct: 7026 taatatcttcac 7037

 Score =  178 bits (90), Expect(5) = e-143
 Identities = 117/126 (92%)
 Strand = Plus / Plus


Query: 360  tcaccgtcaagtaagtatcattctgatgatatgccatcatccccactttcaaactcatca 419
            ||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||||
Sbjct: 7256 tcaccatcaagtaattatcattctgatgatattccatcatctccactttcaaattcatca 7315


Query: 420  ccgtcaattaataacgctccagtaaatactagccaagactcaaactttaatttctccgcg 479
            || |||||||||||||||||| |||||||||||||||| ||||||||||||||||||||
Sbjct: 7316 ccttcaattaataacgctccattaaatactagccaagattcaaactttaatttctccgca 7375


Query: 480  cttaca 485
            ||||||
Sbjct: 7376 cttaca 7381

 Score =  125 bits (63), Expect(5) = e-143
 Identities = 69/71 (97%)
 Strand = Plus / Plus


Query: 487  acactttccaacttttcattaactcaacaccctgtatcaatccacttcccgaattcttta 546
            ||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||
Sbjct: 7382 acactttccaacttttcattaactcaacaacctgtatcaatccacttcccaaattcttta 7441


Query: 547  aaatcaagtgg 557
            |||||||||||
Sbjct: 7442 aaatcaagtgg 7452

 Score = 46.1 bits (23), Expect(5) = e-143
 Identities = 23/23 (100%)
 Strand = Plus / Plus


Query: 805  cacattcaagtgtgtattaccaa 827
            |||||||||||||||||||||||
Sbjct: 7662 cacattcaagtgtgtattaccaa 7684

 Score = 38.2 bits (19), Expect(5) = e-143
 Identities = 19/19 (100%)
 Strand = Plus / Plus


Query: 293  tcatcatcatccttgaatt 311
            |||||||||||||||||||
Sbjct: 7196 tcatcatcatccttgaatt 7214

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 485,154,846
Number of extensions: 28671707
Number of successful extensions: 1893259
Number of sequences better than 10.0: 23
Length of query: 930
Length of database: 101,790,757,118
Length adjustment: 24
Effective length of query: 906
Effective length of database: 99,340,224,878
Effective search space: 90002243739468
Effective search space used: 90002243739468
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01624-1 (Contig-U01624-1Q) /CSM_Contig/Contig-U01624-1Q.Seq.d
         (930 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC117072_1(AC117072|pid:none) Dictyostelium discoideum chromosom...    50   8e-05

>AC117072_1(AC117072|pid:none) Dictyostelium discoideum chromosome 2
           map 3879572-4071762 strain AX4, complete sequence.
          Length = 587

 Score = 50.4 bits (119), Expect = 8e-05
 Identities = 24/26 (92%), Positives = 24/26 (92%)
 Frame = +1

Query: 481 LQTLSNFSLTQHPVSIHFPNSLKSSG 558
           L TLSNFSLTQ PVSIHFPNSLKSSG
Sbjct: 500 LTTLSNFSLTQQPVSIHFPNSLKSSG 525

 Score = 44.7 bits (104), Expect = 0.005
 Identities = 24/54 (44%), Positives = 26/54 (48%)
 Frame = +3

Query: 357 SSPSSKYHSDDMXXXXXXXXXXXXXXXXXXTSQDSNFNFSALTDTFQLFINSTP 518
           SSPSS YHSDD+                  TSQDSNFNFSALT      +   P
Sbjct: 459 SSPSSNYHSDDIPSSPLSNSSPSINNAPLNTSQDSNFNFSALTTLSNFSLTQQP 512

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: 714,656,080
Number of extensions: 8812666
Number of successful extensions: 19250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 19229
Number of HSP's successfully gapped: 2
Length of query: 310
Length of database: 1,051,180,864
Length adjustment: 128
Effective length of query: 182
Effective length of database: 636,901,312
Effective search space: 115916038784
Effective search space used: 115916038784
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: 32 (16.9 bits)
PSORT 

 psg: 0.67  gvh: 0.39  alm: 0.55  top: 0.53  tms: 0.00  mit: 0.44  mip: 0.03
 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 

	 76.0 %: mitochondrial
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: nuclear
	  4.0 %: peroxisomal

>> prediction for Contig-U01624-1 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) 3
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