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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-U04424-1
Contig ID Contig-U04424-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04424-1 (Contig-U04424-1Q) /CSM_Contig/Contig-U04424-1Q.Seq.d
CAAAAAAAAAAAATTAAAAAATGATGGTCCCATATAGATTTCTCAATATT
GTCAATGGTCTCATTAAATCTAGCAATGAGGCAGCAATGAAAGACGTTGT
TTATGAATTAGTTGATGATGATGAAAAGGTAGGAGGTTTTAAAATTTATT
TAATTGTAGAATCAACTGCATGGAACAAGGCAATCCGTATTTATAACTCT
GATCATGTTGATTCTGGTTTAGATTATTGTGAGGTTAAAGCAGGTGATTC
AACAGGTAAACCAGCAACCTCTGATCCAAAATACAAAGTAGATTCTGAAA
GAATCAACTGGCCAAAGAATGATGATCCAGTTAGATTATGTTTCATGAAA
CCAGGTGCTTTTGGTGTTTGGACTACTGTTTACGATATTAACATTCCAAA
AGAAGATCGTACCAAATTTGGTGGTAAAGCTCTCTACATTTACTGGAGTA
ATGATGGTACTAAACTCTTCTCTGAACCAGCCAACAGATTAAAGAAGGGA
AAACTTTATTAAACATTTATGTTTTTTCAATTTTGTTAAAAAGTATTTAC
TAAACAATTATTTTTTAAAACTAAAAAAAAAAAAAAAAAAACAAAAA
Gap no gap
Contig length 597
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 1695000
End point 1694403
Strand (PLUS/MINUS) MINUS
Number of clones 5
Number of EST 6
Link to clone list U04424
List of clone(s) 

est1=VSA605E,-8,575
est2=SSM896E,1,581
est3=SSB153F,3,228
est4=VSB689Z,183,575
est5=SSA574Z,193,598
est6=SSB153Z,274,579
Translated Amino Acid sequence 
kkkn*KMMVPYRFLNIVNGLIKSSNEAAMKDVVYELVDDDEKVGGFKIYLIVESTAWNKA
IRIYNSDHVDSGLDYCEVKAGDSTGKPATSDPKYKVDSERINWPKNDDPVRLCFMKPGAF
GVWTTVYDINIPKEDRTKFGGKALYIYWSNDGTKLFSEPANRLKKGKLY*tfmffqfc*k
vftkqlffktkkkkkktk
Translated Amino Acid sequence (All Frames) 
Frame A:
qkkkikk*wshidfsilsmvslnlamrqq*ktlfmn*lmmmkr*evlkfi*l*nqlhgtr
qsvfitlimlilv*iivrlkqviqqvnqqpliqntk*ilkestgqrmmiqldyvs*nqvl
lvfgllftiltfqkkivpnlvvklstftgvmmvlnsslnqptd*rrenfikhlcffnfvk
kyllnnyflklkkkkkkqk


Frame B:
kkkklkndgpi*isqycqwsh*i*q*gsnerrcl*is****kgrrf*nlfncrincmeqg
npyl*l*sc*fwfrll*g*sr*fnr*tsnl*skiqsrf*knqlake**ss*imfhetrcf
wcldyclry*hskrrsyqiww*sslhlle**wy*tll*tsqqikegktllniyvfsillk
siy*tiif*n*kkkkknk


Frame C:
kkkn*KMMVPYRFLNIVNGLIKSSNEAAMKDVVYELVDDDEKVGGFKIYLIVESTAWNKA
IRIYNSDHVDSGLDYCEVKAGDSTGKPATSDPKYKVDSERINWPKNDDPVRLCFMKPGAF
GVWTTVYDINIPKEDRTKFGGKALYIYWSNDGTKLFSEPANRLKKGKLY*tfmffqfc*k
vftkqlffktkkkkkktk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04424-1 (Contig-U04424-1Q)
/CSM_Contig/Contig-U04424-1Q.Seq.d
         (597 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04424-1 (Contig-U04424-1Q) /CSM_Contig/Conti...  1092  0.0
Contig-U08172-1 (Contig-U08172-1Q) /CSM_Contig/Conti...    42  7e-04
Contig-U04256-1 (Contig-U04256-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U12804-1 (Contig-U12804-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U09474-1 (Contig-U09474-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U00078-1 (Contig-U00078-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U13865-1 (Contig-U13865-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U12532-1 (Contig-U12532-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U12521-1 (Contig-U12521-1Q) /CSM_Contig/Conti...    34  0.16
Contig-U09471-1 (Contig-U09471-1Q) /CSM_Contig/Conti...    34  0.16

>Contig-U04424-1 (Contig-U04424-1Q) /CSM_Contig/Contig-U04424-1Q.Seq.d
          Length = 597

 Score = 1092 bits (551), Expect = 0.0
 Identities = 551/551 (100%)
 Strand = Plus / Plus

                                                                       
Query: 22  tgatggtcccatatagatttctcaatattgtcaatggtctcattaaatctagcaatgagg 81
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 22  tgatggtcccatatagatttctcaatattgtcaatggtctcattaaatctagcaatgagg 81

                                                                       
Query: 82  cagcaatgaaagacgttgtttatgaattagttgatgatgatgaaaaggtaggaggtttta 141
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82  cagcaatgaaagacgttgtttatgaattagttgatgatgatgaaaaggtaggaggtttta 141

                                                                       
Query: 142 aaatttatttaattgtagaatcaactgcatggaacaaggcaatccgtatttataactctg 201
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 142 aaatttatttaattgtagaatcaactgcatggaacaaggcaatccgtatttataactctg 201

                                                                       
Query: 202 atcatgttgattctggtttagattattgtgaggttaaagcaggtgattcaacaggtaaac 261
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 202 atcatgttgattctggtttagattattgtgaggttaaagcaggtgattcaacaggtaaac 261

                                                                       
Query: 262 cagcaacctctgatccaaaatacaaagtagattctgaaagaatcaactggccaaagaatg 321
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 262 cagcaacctctgatccaaaatacaaagtagattctgaaagaatcaactggccaaagaatg 321

                                                                       
Query: 322 atgatccagttagattatgtttcatgaaaccaggtgcttttggtgtttggactactgttt 381
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 322 atgatccagttagattatgtttcatgaaaccaggtgcttttggtgtttggactactgttt 381

                                                                       
Query: 382 acgatattaacattccaaaagaagatcgtaccaaatttggtggtaaagctctctacattt 441
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 382 acgatattaacattccaaaagaagatcgtaccaaatttggtggtaaagctctctacattt 441

                                                                       
Query: 442 actggagtaatgatggtactaaactcttctctgaaccagccaacagattaaagaagggaa 501
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 442 actggagtaatgatggtactaaactcttctctgaaccagccaacagattaaagaagggaa 501

                                                                       
Query: 502 aactttattaaacatttatgttttttcaattttgttaaaaagtatttactaaacaattat 561
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 502 aactttattaaacatttatgttttttcaattttgttaaaaagtatttactaaacaattat 561

                      
Query: 562 tttttaaaact 572
           |||||||||||
Sbjct: 562 tttttaaaact 572


>Contig-U08172-1 (Contig-U08172-1Q) /CSM_Contig/Contig-U08172-1Q.Seq.d
          Length = 1818

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                 
Query: 551  taaacaattattttttaaaac 571
            |||||||||||||||||||||
Sbjct: 1195 taaacaattattttttaaaac 1175


>Contig-U04256-1 (Contig-U04256-1Q) /CSM_Contig/Contig-U04256-1Q.Seq.d
          Length = 1075

 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                              
Query: 109 tagttgatgatgatgaaaa 127
           |||||||||||||||||||
Sbjct: 419 tagttgatgatgatgaaaa 401


 Score = 32.2 bits (16), Expect = 0.65
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                           
Query: 109 tagttgatgatgatga 124
           ||||||||||||||||
Sbjct: 623 tagttgatgatgatga 608


  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: 11,098
Number of Sequences: 6905
Number of extensions: 11098
Number of successful extensions: 1503
Number of sequences better than 10.0: 153
length of query: 597
length of database: 5,674,871
effective HSP length: 16
effective length of query: 581
effective length of database: 5,564,391
effective search space: 3232911171
effective search space used: 3232911171
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. 6.20
Homology vs DNA 
Query= Contig-U04424-1 (Contig-U04424-1Q) /CSM_Contig/Contig-U04424-1Q.Seq.d
         (597 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

(AU261598) Dictyostelium discoideum vegetative cDNA clone:VS...   957   0.0    1
(C93267) Dictyostelium discoideum slug cDNA, clone SSM896.        957   0.0    1
(AU262182) Dictyostelium discoideum vegetative cDNA clone:VS...   638   e-179  1
(C83910) Dictyostelium discoideum slug cDNA, clone SSA574.        618   e-173  1
(AU051844) Dictyostelium discoideum slug cDNA, clone SSB153.      418   e-112  1
(AU071292) Dictyostelium discoideum slug cDNA, clone SSB153.      410   e-110  1
(AC092865) Homo sapiens 12 BAC RP11-113C12 (Roswell Park Can...    46   1.5    1
(AC220960) Pongo abelii chromosome 12 clone CH276-152J12, WO...    46   1.5    1
(DR134439) 49259096 Drosophila pseudoobscura embryonic cDNA ...    46   1.5    1
(EH211470) USDA-FP_174259 WHMH (pink hibiscus mealybug) Maco...    34   2.0    2
(EK025650) 1092955365472 Global-Ocean-Sampling_GS-31-01-01-1...    36   2.2    3
(AC201349) Strongylocentrotus purpuratus clone R3-17A17, WOR...    44   4.4    2
(AL627226) Mouse DNA sequence from clone RP23-139P4 on chrom...    44   6.0    1
(AM481234) Vitis vinifera contig VV78X108372.6, whole genome...    44   6.0    1
(AM453292) Vitis vinifera contig VV78X262046.4, whole genome...    44   6.0    1
(AC150869) Bos taurus clone CH240-272F24, WORKING DRAFT SEQU...    44   6.0    1
(AC150586) Bos taurus clone CH240-342D13, WORKING DRAFT SEQU...    44   6.0    1
(AC093355) Mus musculus clone RP23-20D22, WORKING DRAFT SEQU...    44   6.0    1
(CU468093) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   6.0    1
(CU467673) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   6.0    1
(AC179267) Strongylocentrotus purpuratus clone R3-43B1, WORK...    44   6.0    1
(AC176462) Strongylocentrotus purpuratus clone R3-3070B21, W...    44   6.0    1
(AZ177481) SP_0147_A1_F04_SP6E Strongylocentrotus purpuratus...    44   6.0    1
(AM651304) Entamoeba moshkovskii FIC GSS, clone mosh094b11.p1k.    44   6.0    1
(DE077598) Oryzias latipes DNA, clone: ola1-181P20.R, genomi...    44   6.0    1
(CR896838) Sus scrofa BES.                                         44   6.0    1
(EH013586) USDA-FP_186372 Lysiphlebus testaceipes adult whol...    44   6.0    1
(EH013219) USDA-FP_186041 Lysiphlebus testaceipes adult whol...    44   6.0    1
(EH009797) USDA-FP_182959 Lysiphlebus testaceipes adult whol...    44   6.0    1
(EH009724) USDA-FP_182893 Lysiphlebus testaceipes adult whol...    44   6.0    1
(DV610522) EST1213518 Glossina morsitans morsitans Fat body ...    44   6.0    1
(GH171515) Nas124_A10_2005-03-10_080.ab1 Nasturtium 22 days ...    44   6.0    1
(AL355888) Human chromosome 14 DNA sequence BAC R-322L17 of ...    36   9.5    4
(CR716367) Tetraodon nigroviridis full-length cDNA.                38   9.6    2
(CR711201) Tetraodon nigroviridis full-length cDNA.                38   9.6    2
(CR710629) Tetraodon nigroviridis full-length cDNA.                38   9.6    2
(CR707434) Tetraodon nigroviridis full-length cDNA.                38   9.6    2

>(AU261598) Dictyostelium discoideum vegetative cDNA clone:VSA605,
           3' end single read.
          Length = 584

 Score =  957 bits (483), Expect = 0.0
 Identities = 483/483 (100%)
 Strand = Plus / Plus


Query: 22  tgatggtcccatatagatttctcaatattgtcaatggtctcattaaatctagcaatgagg 81
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 31  tgatggtcccatatagatttctcaatattgtcaatggtctcattaaatctagcaatgagg 90


Query: 82  cagcaatgaaagacgttgtttatgaattagttgatgatgatgaaaaggtaggaggtttta 141
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 91  cagcaatgaaagacgttgtttatgaattagttgatgatgatgaaaaggtaggaggtttta 150


Query: 142 aaatttatttaattgtagaatcaactgcatggaacaaggcaatccgtatttataactctg 201
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 151 aaatttatttaattgtagaatcaactgcatggaacaaggcaatccgtatttataactctg 210


Query: 202 atcatgttgattctggtttagattattgtgaggttaaagcaggtgattcaacaggtaaac 261
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 211 atcatgttgattctggtttagattattgtgaggttaaagcaggtgattcaacaggtaaac 270


Query: 262 cagcaacctctgatccaaaatacaaagtagattctgaaagaatcaactggccaaagaatg 321
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 271 cagcaacctctgatccaaaatacaaagtagattctgaaagaatcaactggccaaagaatg 330


Query: 322 atgatccagttagattatgtttcatgaaaccaggtgcttttggtgtttggactactgttt 381
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 331 atgatccagttagattatgtttcatgaaaccaggtgcttttggtgtttggactactgttt 390


Query: 382 acgatattaacattccaaaagaagatcgtaccaaatttggtggtaaagctctctacattt 441
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 391 acgatattaacattccaaaagaagatcgtaccaaatttggtggtaaagctctctacattt 450


Query: 442 actggagtaatgatggtactaaactcttctctgaaccagccaacagattaaagaagggaa 501
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 451 actggagtaatgatggtactaaactcttctctgaaccagccaacagattaaagaagggaa 510


Query: 502 aac 504
           |||
Sbjct: 511 aac 513

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 595,118,792
Number of extensions: 36396711
Number of successful extensions: 3077958
Number of sequences better than 10.0: 37
Length of query: 597
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 574
Effective length of database: 99,442,330,388
Effective search space: 57079897642712
Effective search space used: 57079897642712
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04424-1 (Contig-U04424-1Q) /CSM_Contig/Contig-U04424-1Q.Seq.d
         (597 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CU633751_2(CU633751|pid:none) Cupriavidus taiwanensis str. LMG19...    36   0.93
BT065311_1(BT065311|pid:none) Zea mays full-length cDNA clone ZM...    33   4.6
CP001391_560(CP001391|pid:none) Wolbachia sp. wRi, complete geno...    33   7.9

>CU633751_2(CU633751|pid:none) Cupriavidus taiwanensis str. LMG19424
           plasmid pRALTA, complete genome.
          Length = 996

 Score = 35.8 bits (81), Expect = 0.93
 Identities = 33/133 (24%), Positives = 61/133 (45%), Gaps = 16/133 (12%)
 Frame = +3

Query: 141 KIYLIVESTAWNKAIRIYNSDHVDSGLDYCEVKAG------DSTGKPATSDPKYKV---D 293
           +IY  V + +  + +  Y+++ V  G    + + G      D++G  A  D  Y++   D
Sbjct: 442 EIYAEVAAKSIYQGVLTYSAEQVHDGYFSADRRKGKVVTLLDTSGSTAKDDETYELIMKD 501

Query: 294 SERINWPKNDDPVRLCFMKPGAFGVWTT--VYDINIPKE-----DRTKFGGKALYIYWSN 452
            ER+  P  ++P+R  F        W    V+ I   +E     +R +  G+ L +  +
Sbjct: 502 KERLLDP--EEPLRFIFSHSALKEGWDNPNVFQICTLREMGTENERRQTLGRGLRLPVNK 559

Query: 453 DGTKLFSEPANRL 491
           DG ++F+E  NRL
Sbjct: 560 DGDRIFNEQINRL 572

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: 3268448
Number of Hits to DB: 931,422,156
Number of extensions: 18490907
Number of successful extensions: 52779
Number of sequences better than 10.0: 3
Number of HSP's gapped: 52777
Number of HSP's successfully gapped: 3
Length of query: 199
Length of database: 1,061,185,681
Length adjustment: 122
Effective length of query: 77
Effective length of database: 662,435,025
Effective search space: 51007496925
Effective search space used: 51007496925
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: 30 (16.2 bits)
PSORT 

 psg: 0.82  gvh: 0.30  alm: 0.46  top: 0.53  tms: 0.00  mit: 0.32  mip: 0.03
 nuc: 0.03  erl: 0.00  erm: 0.40  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 

	 48.0 %: nuclear
	 32.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: peroxisomal

>> prediction for Contig-U04424-1 is nuc
VS (DIR, S) 2
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