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Dicty_cDB
Contig List | Clone List | cDNA Library List
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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-U04334-1
Contig ID Contig-U04334-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04334-1 (Contig-U04334-1Q) /CSM_Contig/Contig-U04334-1Q.Seq.d
CAAAAAAAAAAAAGTAAAACAATAAATTATATAAAAAAAATAAAAAAAAT
GTCAATCATTAATACTATTTCAAAATTAAGTTTATCAAATTCATTAAAAT
CAAATATCACAATCGGGAATTTAAATGGTACAACTGTAAATAACTATACT
CACAACGAAACAAGTAGTAAATTCACAGAATTTTTTTACAAAATCATATA
ACAAAACAAAAGATGGTTTTGAAAAGTTAAAGAATTAAATAAAAAAAAAA
GAAAAAAAGACTATATAATTTCTTCATTTTGTAAACTATATTCAATATAT
TTTGTTTTTTCTGATAATAAATTTAAAAAAAGATTTTCATTCTAATTTCA
AACAATATCAATAAAATGTTATATAATTACTATTAAAATGAAAAAAAAA
Gap no gap
Contig length 399
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 3746420
End point 3746021
Strand (PLUS/MINUS) MINUS
Number of clones 3
Number of EST 3
Link to clone list U04334
List of clone(s) 

est1=SSA210F,1,105
est2=SSB524E,1,391
est3=SSE780E,3,400
Translated Amino Acid sequence 
QKKKSKTINYIKKIKKMSIINTISKLSLSNSLKSNITIGNLNGTTVNNYTHNETSSKFTE
FFYKII*qnkrwf*kvkelnkkkrkkdyiissfcklysiyfvfsdnkfkkrfsf*fqtis
ikcyiitikmkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
QKKKSKTINYIKKIKKMSIINTISKLSLSNSLKSNITIGNLNGTTVNNYTHNETSSKFTE
FFYKII*qnkrwf*kvkelnkkkrkkdyiissfcklysiyfvfsdnkfkkrfsf*fqtis
ikcyiitikmkkk


Frame B:
kkkkvkq*ii*kk*kkcqslilfqn*vyqih*nqisqsgi*mvql*itilttkqvvnsqn
fftksynktkdgfeklkn*ikkkekkti*flhfvnyiqyilffliinlkkdfhsnfkqyq
*nvi*lllk*kk


Frame C:
kkkk*nnklykknkknvnh*yyfkikfikfikikyhnrefkwynck*lysqrnk**ihri
flqnhitkqkmvlks*rik*kkkkkrlynffil*tifnifcff***i*kkifilisnnin
kmlynyy*nekk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04334-1 (Contig-U04334-1Q)
/CSM_Contig/Contig-U04334-1Q.Seq.d
         (399 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04334-1 (Contig-U04334-1Q) /CSM_Contig/Conti...   337  5e-93
Contig-U12524-1 (Contig-U12524-1Q) /CSM_Contig/Conti...    38  0.007
Contig-U06369-1 (Contig-U06369-1Q) /CSM_Contig/Conti...    36  0.027
Contig-U13050-1 (Contig-U13050-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U11657-1 (Contig-U11657-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U11444-1 (Contig-U11444-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U05881-1 (Contig-U05881-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U05415-1 (Contig-U05415-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U05113-1 (Contig-U05113-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U14470-1 (Contig-U14470-1Q) /CSM_Contig/Conti...    32  0.43

>Contig-U04334-1 (Contig-U04334-1Q) /CSM_Contig/Contig-U04334-1Q.Seq.d
          Length = 399

 Score =  337 bits (170), Expect = 5e-93
 Identities = 184/191 (96%)
 Strand = Plus / Plus

                                                                       
Query: 50  tgtcaatcattaatactatttcaaaattaagtttatcaaattcattaaaatcaaatatca 109
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 50  tgtcaatcattaatactatttcaaaattaagtttatcaaattcattaaaatcaaatatca 109

                                                                       
Query: 110 caatcgggaatttaaatggtacaactgtaaataactatactcacaacgaaacaagtagta 169
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 110 caatcgggaatttaaatggtacaactgtaaataactatactcacaacgaaacaagtagta 169

                                                                       
Query: 170 aattcacagaannnnnnnacaaaatcatataacaaaacaaaagatggttttgaaaagtta 229
           |||||||||||       ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 170 aattcacagaatttttttacaaaatcatataacaaaacaaaagatggttttgaaaagtta 229

                      
Query: 230 aagaattaaat 240
           |||||||||||
Sbjct: 230 aagaattaaat 240


 Score =  220 bits (111), Expect = 9e-58
 Identities = 125/132 (94%)
 Strand = Plus / Plus

                                                                       
Query: 259 gactatataatttcttcattttgtaaactatattcaatatattttgttttttctgataat 318
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 259 gactatataatttcttcattttgtaaactatattcaatatattttgttttttctgataat 318

                                                                       
Query: 319 aaatttnnnnnnngattttcattctaatttcaaacaatatcaataaaatgttatataatt 378
           ||||||       |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 319 aaatttaaaaaaagattttcattctaatttcaaacaatatcaataaaatgttatataatt 378

                       
Query: 379 actattaaaatg 390
           ||||||||||||
Sbjct: 379 actattaaaatg 390


>Contig-U12524-1 (Contig-U12524-1Q) /CSM_Contig/Contig-U12524-1Q.Seq.d
          Length = 1393

 Score = 38.2 bits (19), Expect = 0.007
 Identities = 25/27 (92%)
 Strand = Plus / Minus

                                       
Query: 291  ttcaatatattttgttttttctgataa 317
            ||||||| |||||| ||||||||||||
Sbjct: 1037 ttcaatagattttgatttttctgataa 1011


>Contig-U06369-1 (Contig-U06369-1Q) /CSM_Contig/Contig-U06369-1Q.Seq.d
          Length = 563

 Score = 36.2 bits (18), Expect = 0.027
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                             
Query: 222 aaaagttaaagaattaaa 239
           ||||||||||||||||||
Sbjct: 316 aaaagttaaagaattaaa 333


  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: 7640
Number of Sequences: 6905
Number of extensions: 7640
Number of successful extensions: 876
Number of sequences better than 10.0: 278
length of query: 399
length of database: 5,674,871
effective HSP length: 16
effective length of query: 383
effective length of database: 5,564,391
effective search space: 2131161753
effective search space used: 2131161753
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. 6.16
Homology vs DNA 
Query= Contig-U04334-1 (Contig-U04334-1Q) /CSM_Contig/Contig-U04334-1Q.Seq.d
         (399 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

(AU037140) Dictyostelium discoideum slug cDNA, clone SSB524.      260   e-125  3
(C92573) Dictyostelium discoideum slug cDNA, clone SSE780.        260   e-125  3
(AU075086) Dictyostelium discoideum slug cDNA, clone SSA210.      111   2e-20  1
(ER442497) 1092963818584 Global-Ocean-Sampling_GS-35-01-01-1...    52   0.016  1
(AC234784) Solanum tuberosum chromosome 6 clone RHPOTKEY179H...    42   0.17   5
(AP009731) Lotus japonicus genomic DNA, chromosome 1, clone:...    38   0.17   5
(DC218865) Plasmodium berghei strain ANKA cDNA clone:MZ00015...    38   0.25   3
(AC185017) Bos taurus clone CH240-275N4, WORKING DRAFT SEQUE...    48   0.25   1
(ER587036) 1093015883141 Global-Ocean-Sampling_GS-36-01-01-2...    48   0.25   1
(EJ618135) 1092963038696 Global-Ocean-Sampling_GS-29-01-01-1...    48   0.25   1
(EJ612140) 1092962052544 Global-Ocean-Sampling_GS-29-01-01-1...    48   0.25   1
(AC178804) Strongylocentrotus purpuratus clone R3-22F23, WOR...    40   0.26   3
(AC005507) Plasmodium falciparum chromosome 12 clone PFYACB8...    36   0.39   6
(AC214320) Pteropus vampyrus clone CH279-117B12, WORKING DRA...    40   0.76   5
(AC160012) Medicago truncatula chromosome 2 clone mth2-168l8...    38   0.88   4
(AE014830) Plasmodium falciparum 3D7 chromosome 10 section 2...    46   1.0    1
(AC222790) Bos taurus clone CH240-438G9, WORKING DRAFT SEQUE...    46   1.0    1
(AC169424) Bos taurus clone CH240-203M15, WORKING DRAFT SEQU...    46   1.0    1
(EJ295618) 1095388034362 Global-Ocean-Sampling_GS-27-01-01-1...    46   1.0    1
(BZ441442) BONJU01TR BO_1.6_2_KB_tot Brassica oleracea genom...    46   1.0    1
(EL503179) F10_PFLAB1-M-PLATE10B.AB1 Blood stage Plasmodium ...    46   1.0    1
(CA854774) PfESToac13e11.y1 Plasmodium falciparum 3D7 gameto...    46   1.0    1
(AR475454) Sequence 3 from patent US 6692948.                      42   1.1    2
(AR411949) Sequence 3 from patent US 6638745.                      42   1.1    2
(ED234102) AUAC-aas55c02.g1 Ascaris suum whole genome shotgu...    36   1.2    2
(AP001461) Homo sapiens genomic DNA, chromosome 18q22 clone:...    34   1.3    5
(BQ434849) AGENCOURT_7826562 NIH_MGC_67 Homo sapiens cDNA cl...    38   1.3    2
(BX537104) Zebrafish DNA sequence from clone DKEY-80G18 in l...    42   1.9    4
(AC010483) Homo sapiens chromosome 5 clone CTD-2321L15, comp...    36   2.0    3
(BX004776) Zebrafish DNA sequence from clone CH211-137A8 in ...    42   2.0    3
(AC189604) Brassica rapa subsp. pekinensis clone KBrH015E17,...    34   2.1    2
(AC004813) Homo sapiens clone 277F10, complete sequence.           42   2.2    2
(BD460506) Diagnosis of Diseases Associated with Cell Cycle.       44   2.3    2
(BD452428) Diagnosis of Diseases Associated with Cell Cycle.       44   2.3    2
(AX348821) Sequence 279 from Patent WO0202807.                     44   2.3    2
(AX344426) Sequence 273 from Patent WO0200926.                     44   2.3    2
(AX252042) Sequence 303 from Patent WO0168911.                     44   2.3    2
(AC178362) Strongylocentrotus purpuratus clone R3-3106G20, W...    36   2.9    4
(EC820711) SME00005719 esmbsro2 Sawyeria marylandensis cDNA,...    36   3.1    2
(CP000395) Borrelia afzelii PKo, complete genome.                  34   3.1    8
(EJ100276) 1095467039310 Global-Ocean-Sampling_GS-26-01-01-1...    30   3.2    3
(AR721111) Sequence 3 from patent US 6946276.                      42   3.3    2
(AR453416) Sequence 3 from patent US 6680188.                      42   3.3    2
(AR253938) Sequence 3 from patent US 6479269.                      42   3.3    2
(AL929204) Zebrafish DNA sequence from clone CH211-138E4.          34   3.5    4
(AC160642) Gallus gallus BAC clone CH261-121M12 from chromos...    44   4.0    1
(CU682339) Mouse DNA sequence from clone RP23-353M1 on chrom...    44   4.0    1
(DJ402719) Methods and nucleic acids for analyses of colo re...    44   4.0    1
(DJ402603) Methods and nucleic acids for analyses of colo re...    44   4.0    1
(AL590142) Human DNA sequence from clone RP13-232D5 on chrom...    44   4.0    1
(AC011305) Homo sapiens BAC clone RP11-390E9 from Y, complet...    44   4.0    1
(AC149695) Bos taurus clone CH240-410D11, WORKING DRAFT SEQU...    44   4.0    1
(AC115227) Rattus norvegicus clone CH230-43L8, *** SEQUENCIN...    44   4.0    1
(CU856422) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.0    1
(CU407283) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   4.0    1
(AC204022) Zea mays chromosome 1 clone CH201-528G6; ZMMBBc05...    44   4.0    1
(ER449526) 1092963843615 Global-Ocean-Sampling_GS-35-01-01-1...    44   4.0    1
(EK437033) 1095521071655 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK409820) 1095505155178 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK369326) 1095469410141 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK363896) 1095469389389 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK345993) 1095467510443 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK340845) 1095467060675 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK111344) 1092963112372 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EK020530) 1092955315817 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(AM624096) Entamoeba dispar GSS, clone dispar106e02.q1k.           44   4.0    1
(EJ712213) 1092956083558 Global-Ocean-Sampling_GS-30-02-01-1...    44   4.0    1
(EJ705742) 1092956052574 Global-Ocean-Sampling_GS-30-02-01-1...    44   4.0    1
(CR837154) GR0AAA71CE08RM1 INRA BAC Bos taurus genomic clone...    44   4.0    1
(CL574376) OB__Ba0021A20.r OB__Ba Oryza brachyantha genomic ...    44   4.0    1
(CC935391) ZMMBBc0549C16f ZMMBBc Zea mays subsp. mays genomi...    44   4.0    1
(BZ525481) OGAGR95TC ZM2_0.7_1.5_KB Zea mays genomic clone Z...    44   4.0    1
(BX220367) Danio rerio genomic clone DKEY-47N11, genomic sur...    44   4.0    1
(AC175078) Bos taurus clone CH240-233H13, WORKING DRAFT SEQU...    36   4.0    4
(AL929357) Plasmodium falciparum strain 3D7, chromosome 9; s...    36   4.1    7
(DJ386650) Diagnosis of Diseases Associated with Metastasis.       40   4.5    2
(AX348716) Sequence 174 from Patent WO0202807.                     40   4.5    2
(AX346129) Sequence 1200 from Patent WO0200928.                    40   4.5    2
(AX281446) Sequence 110 from Patent WO0177376.                     40   4.5    2
(AC152099) Bos taurus clone CH240-2P10, WORKING DRAFT SEQUEN...    36   5.4    4
(EJ795031) 1093017395909 Global-Ocean-Sampling_GS-30-02-01-1...    36   5.5    2
(FB571033) Sequence 36 from Patent WO2007116417.                   40   5.6    2
(FB571031) Sequence 34 from Patent WO2007116417.                   40   5.6    2
(FF574971) TTEF678THB Tetrahymena thermophila conjugation cD...    34   5.7    2
(AL355333) Human DNA sequence from clone RP11-575N15 on chro...    36   6.1    3
(AE014848) Plasmodium falciparum 3D7 chromosome 12, section ...    38   6.7    5
(AC121768) Mus musculus BAC clone RP23-339H16 from 15, compl...    36   7.2    3
(CU633666) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    30   7.2    2
(AC155005) Bos taurus clone CH240-36J15, WORKING DRAFT SEQUE...    36   7.2    3
(AL355979) Human DNA sequence from clone RP11-466G24 on chro...    40   7.9    2
(AC202473) Medicago truncatula clone mth2-152o8, WORKING DRA...    34   8.8    3
(AP010559) Lotus japonicus genomic DNA, clone: LjT15F22, TM2...    34   9.2    4
(AM472037) Vitis vinifera contig VV78X278490.1, whole genome...    32   9.7    2
(AC024006) Homo sapiens chromosome 1 clone RP11-156L20 map 1...    42   9.8    2
(ET102711) QM0AAB21AH07FM1 CCER1 Citrus clementina genomic c...    30   9.9    2
(CE417719) tigr-gss-dog-17000362683022 Dog Library Canis lup...    30   9.9    2

>(AU037140) Dictyostelium discoideum slug cDNA, clone SSB524.
          Length = 391

 Score =  260 bits (131), Expect(3) = e-125
 Identities = 131/131 (100%)
 Strand = Plus / Plus


Query: 50  tgtcaatcattaatactatttcaaaattaagtttatcaaattcattaaaatcaaatatca 109
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 50  tgtcaatcattaatactatttcaaaattaagtttatcaaattcattaaaatcaaatatca 109


Query: 110 caatcgggaatttaaatggtacaactgtaaataactatactcacaacgaaacaagtagta 169
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 110 caatcgggaatttaaatggtacaactgtaaataactatactcacaacgaaacaagtagta 169


Query: 170 aattcacagaa 180
           |||||||||||
Sbjct: 170 aattcacagaa 180

 Score =  131 bits (66), Expect(3) = e-125
 Identities = 66/66 (100%)
 Strand = Plus / Plus


Query: 259 gactatataatttcttcattttgtaaactatattcaatatattttgttttttctgataat 318
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 259 gactatataatttcttcattttgtaaactatattcaatatattttgttttttctgataat 318


Query: 319 aaattt 324
           ||||||
Sbjct: 319 aaattt 324

 Score =  117 bits (59), Expect(3) = e-125
 Identities = 59/59 (100%)
 Strand = Plus / Plus


Query: 332 gattttcattctaatttcaaacaatatcaataaaatgttatataattactattaaaatg 390
           |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 332 gattttcattctaatttcaaacaatatcaataaaatgttatataattactattaaaatg 390

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 419,842,461
Number of extensions: 30404800
Number of successful extensions: 2648061
Number of sequences better than 10.0: 97
Length of query: 399
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 376
Effective length of database: 99,442,330,388
Effective search space: 37390316225888
Effective search space used: 37390316225888
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04334-1 (Contig-U04334-1Q) /CSM_Contig/Contig-U04334-1Q.Seq.d
         (399 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 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: 3268448
Number of Hits to DB: 371,864,805
Number of extensions: 5010334
Number of successful extensions: 8854
Number of sequences better than 10.0: 0
Number of HSP's gapped: 8854
Number of HSP's successfully gapped: 0
Length of query: 133
Length of database: 1,061,185,681
Length adjustment: 98
Effective length of query: 35
Effective length of database: 740,877,777
Effective search space: 25930722195
Effective search space used: 25930722195
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: 0.62  gvh: 0.46  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.40  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 %: mitochondrial
	 28.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: plasma membrane
	  4.0 %: peroxisomal

>> prediction for Contig-U04334-1 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