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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U05935-1
Contig ID Contig-U05935-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U05935-1 (Contig-U05935-1Q) /CSM_Contig/Contig-U05935-1Q.Seq.d
AACAAGAGTGTTACAAAATGCCTCAATACAAAATTAGTTTGGATAATACC
AATGATCCAATAATTACGCCAACAATTACACCANCTCTTCTACATTTCCA
ACAANACACCAACTCGNATACGCCAACAACAACTGCACCAACTNCACCAA
CGCCAACACCAACAC
Gap no gap
Contig length 165
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3693400
End point 3693232
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05935
List of clone(s) 

est1=VFA147Z,1,166
Translated Amino Acid sequence 
QECYKMPQYKISLDNTNDPIITPTITPXLLHFQQXTNSXTPTTTAPTXPTPTPT
Translated Amino Acid sequence (All Frames) 
Frame A:
nksvtkclntklvwiipmiq*lrqqlhxlfyisnxtptrirqqqlhqlhqrqhqh


Frame B:
trvlqnasiqn*fg*yq*snnyannytxsstfptxhqlxyannnctnxtnantn


Frame C:
QECYKMPQYKISLDNTNDPIITPTITPXLLHFQQXTNSXTPTTTAPTXPTPTPT
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05935-1 (Contig-U05935-1Q)
/CSM_Contig/Contig-U05935-1Q.Seq.d
         (165 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05935-1 (Contig-U05935-1Q) /CSM_Contig/Conti...   303  3e-83
Contig-U08617-1 (Contig-U08617-1Q) /CSM_Contig/Conti...    42  2e-04
Contig-U00318-1 (Contig-U00318-1Q) /CSM_Contig/Conti...    40  7e-04
Contig-U13594-1 (Contig-U13594-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U13529-1 (Contig-U13529-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U13393-1 (Contig-U13393-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U13187-1 (Contig-U13187-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U11988-1 (Contig-U11988-1Q) /CSM_Contig/Conti...    34  0.043
Contig-U11843-1 (Contig-U11843-1Q) /CSM_Contig/Conti...    34  0.043

>Contig-U05935-1 (Contig-U05935-1Q) /CSM_Contig/Contig-U05935-1Q.Seq.d
          Length = 165

 Score =  303 bits (153), Expect = 3e-83
 Identities = 165/165 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aacaagagtgttacaaaatgcctcaatacaaaattagtttggataataccaatgatccaa 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aacaagagtgttacaaaatgcctcaatacaaaattagtttggataataccaatgatccaa 60

                                                                       
Query: 61  taattacgccaacaattacaccanctcttctacatttccaacaanacaccaactcgnata 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  taattacgccaacaattacaccanctcttctacatttccaacaanacaccaactcgnata 120

                                                        
Query: 121 cgccaacaacaactgcaccaactncaccaacgccaacaccaacac 165
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 cgccaacaacaactgcaccaactncaccaacgccaacaccaacac 165


>Contig-U08617-1 (Contig-U08617-1Q) /CSM_Contig/Contig-U08617-1Q.Seq.d
          Length = 1214

 Score = 42.1 bits (21), Expect = 2e-04
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                       
Query: 136 caccaactncaccaacgccaacaccaac 163
           |||||||  |||||||||||||||||||
Sbjct: 366 caccaacatcaccaacgccaacaccaac 393


 Score = 40.1 bits (20), Expect = 7e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 145 caccaacgccaacaccaaca 164
           ||||||||||||||||||||
Sbjct: 387 caccaacgccaacaccaaca 406


>Contig-U00318-1 (Contig-U00318-1Q) /CSM_Contig/Contig-U00318-1Q.Seq.d
          Length = 1360

 Score = 40.1 bits (20), Expect = 7e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 146 accaacgccaacaccaacac 165
           ||||||||||||||||||||
Sbjct: 193 accaacgccaacaccaacac 212


 Score = 32.2 bits (16), Expect = 0.17
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 145 caccaacgccaacaccaaca 164
           ||||||| ||||||||||||
Sbjct: 168 caccaacaccaacaccaaca 187


 Score = 28.2 bits (14), Expect = 2.6
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                             
Query: 147 ccaacgccaacaccaaca 164
           ||||| ||||||||||||
Sbjct: 200 ccaacaccaacaccaaca 217


  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: 2030
Number of Sequences: 6905
Number of extensions: 2030
Number of successful extensions: 560
Number of sequences better than 10.0: 71
length of query: 165
length of database: 5,674,871
effective HSP length: 15
effective length of query: 150
effective length of database: 5,571,296
effective search space: 835694400
effective search space used: 835694400
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. 6
Homology vs DNA 
Query= Contig-U05935-1 (Contig-U05935-1Q) /CSM_Contig/Contig-U05935-1Q.Seq.d
         (165 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

(BJ428835) Dictyostelium discoideum cDNA clone:ddv1m11, 3' e...   303   9e-79  1
(AF129455) Simian immunodeficiency virus clone SIV1480-AconV...    48   0.090  1
(CV605371) zcm93d01.y1 F_HC7CDNA Ajellomyces capsulatus cDNA...    38   0.27   2
(EB611083) AGENCOURT_54978418 D. mojavensis EST Drosophila m...    34   0.99   2
(AM470018) Vitis vinifera contig VV78X232854.10, whole genom...    42   1.0    2
(AC153565) Mus musculus 10 BAC RP23-228H2 (Roswell Park Canc...    44   1.4    1
(AC206064) Pongo abelii BAC clone CH276-502K14 from chromoso...    44   1.4    1
(AC205916) Pongo abelii BAC clone CH276-68I15 from chromosom...    44   1.4    1
(AC225853) Colobus guereza clone CH272-432I17, WORKING DRAFT...    44   1.4    1
(AC218065) Macaca fuscata clone CH270-415L7, WORKING DRAFT S...    44   1.4    1
(AC145015) Sus scrofa clone RP44-521I21, WORKING DRAFT SEQUE...    34   2.8    2
(AC139734) Sus scrofa clone RP44-334B19, WORKING DRAFT SEQUE...    34   2.8    2
(CT074933) Sus scrofa genomic clone PigE-120E23, genomic sur...    34   3.7    2
(AC189661) Gallus gallus BAC clone CH261-113D21 from chromos...    42   5.6    1
(BV697756) PZA03156-2490-TIP-184 Zea mays ssp. parviglumis T...    42   5.6    1
(BV697748) PZA03156-2490-P39 Zea mays ssp. mays P39 Zea mays...    42   5.6    1
(BV697741) PZA03156-2490-KUI3 Zea mays ssp. mays KUI3 Zea ma...    42   5.6    1
(BV697738) PZA03156-2490-CML69 Zea mays ssp. mays CML69 Zea ...    42   5.6    1
(AM448531) Vitis vinifera, whole genome shotgun sequence, co...    42   5.6    1
(AC226513) Solanum lycopersicum chromosome 2 clone C02SLe000...    42   5.6    1
(AC148744) Macropus eugenii clone ME_KBa-598C23, WORKING DRA...    42   5.6    1
(AY714860) Uncultured archaeon GZfos34G5 clone GZfos34G5, **...    42   5.6    1
(AC184723) Microcebus murinus clone CH257-449H1, WORKING DRA...    42   5.6    1
(EI813106) POTHI63TF Solanum tuberosum RHPOTKEY BAC ends Sol...    42   5.6    1
(DX406314) GR_Sa0007H24.b1 Gossypium raimondii WGS library G...    42   5.6    1
(DU663768) OG_ABa0072K07.r OG_ABa Oryza granulata genomic cl...    42   5.6    1
(DH478090) Monosiga ovata DNA, fosmid clone: MOF-029C10, gen...    42   5.6    1
(CT497775) A BAC library has been constructed from cultivar ...    42   5.6    1
(CC215939) CH261-35P17_RM1.1 CH261 Gallus gallus genomic clo...    42   5.6    1
(BH740621) cpbav00200 Corynebacterium pseudotuberculosis Bac...    42   5.6    1
(DY979105) CLSS12806.b1_L09.ab1 CLS(LMS) lettuce sativa Lact...    42   5.6    1
(DN983357) SV69C12_SOL17A_086 SV6 Solanum chacoense cDNA, mR...    42   5.6    1
(CO901744) Mddb5018l04.y1 Mddb Malus x domestica cDNA clone ...    42   5.6    1
(CO866388) Mddb5007o07.y1 Mddb Malus x domestica cDNA clone ...    42   5.6    1
(CO866384) Mddb5007m07.y1 Mddb Malus x domestica cDNA clone ...    42   5.6    1
(CO418832) Mdfrt3035j08.y1 Mdfrt Malus x domestica cDNA clon...    42   5.6    1
(CN995110) Mdfw2050o18.y1 Mdfw Malus x domestica cDNA clone ...    42   5.6    1
(CN993830) Mdfw2048n08.y1 Mdfw Malus x domestica cDNA clone ...    42   5.6    1
(CN907892) 030109ABLC001235HT (ABLC) Braeburn cell culture t...    42   5.6    1
(CN870348) 001204AAOA007182HT (AAOA) Royal Gala phloem Malus...    42   5.6    1
(CN864282) 000921AALA006659HT (AALA) Royal Gala 150 DAFB fru...    42   5.6    1
(CN491426) Mdfw2010l04.y1 Mdfw Malus x domestica cDNA clone ...    42   5.6    1
(CN489134) Mdfw2018d01.y1 Mdfw Malus x domestica cDNA clone ...    42   5.6    1
(CK278923) EST725001 potato abiotic stress cDNA library Sola...    42   5.6    1
(CK276546) EST722624 potato abiotic stress cDNA library Sola...    42   5.6    1
(CK256717) EST740354 potato callus cDNA library, normalized ...    42   5.6    1
(CK252285) EST735922 potato callus cDNA library, normalized ...    42   5.6    1
(CK243537) EST727174 potato callus cDNA library, normalized ...    42   5.6    1
(CK243382) EST727019 potato callus cDNA library, normalized ...    42   5.6    1
(CK243381) EST727018 potato callus cDNA library, normalized ...    42   5.6    1
(BQ993070) QGF27I02.yg.ab1 QG_EFGHJ lettuce serriola Lactuca...    42   5.6    1
(BQ982208) QGE15N09.yg.ab1 QG_EFGHJ lettuce serriola Lactuca...    42   5.6    1
(BQ873987) QGI4B16.yg.ab1 QG_ABCDI lettuce salinas Lactuca s...    42   5.6    1
(BM110566) EST558102 potato roots Solanum tuberosum cDNA clo...    42   5.6    1
(BJ927967) Daphnia magna cDNA, clone:IGU001_0028_B05.f, 5' e...    42   5.6    1
(BJ325542) Dictyostelium discoideum cDNA clone:dda1g08, 5' e...    42   5.6    1
(BI931581) EST551482 tomato flower, 8 mm to preanthesis buds...    42   5.6    1
(BI930401) EST550278 tomato flower, 8 mm to preanthesis buds...    42   5.6    1
(BG600810) EST505705 cSTS Solanum tuberosum cDNA clone cSTS3...    42   5.6    1
(FG901948) UCRVU08_CCNS2018_g1 Cowpea IT97K-461-4 Mixed Tiss...    42   5.6    1
(FG901947) UCRVU08_CCNS2018_b1 Cowpea IT97K-461-4 Mixed Tiss...    42   5.6    1
(FG881322) UCRVU07_CCNP14112_g1 Cowpea UCR 779 Mixed Tissue ...    42   5.6    1
(FE706963) Pv048A_M13F_E03.ab1 Phaseolus vulgaris cv Early g...    42   5.6    1
(FE702857) Pv033A_M13F_G12.ab1 Phaseolus vulgaris cv Early g...    42   5.6    1
(EX306526) GQ01302.T3_H03 GQ013 - Elongating ROOTS tips - sa...    42   5.6    1
(EV522205) JB2_47_E05 Castor seed endosperm Ricinus communis...    42   5.6    1
(CP001037) Nostoc punctiforme PCC 73102, complete genome.          42   5.6    1
(AB248056) Bacillus circulans agl gene for alpha-1,3-glucana...    42   5.6    1
(CA146433) SCVPRT2080G12.g RT2 Saccharum officinarum cDNA cl...    34   8.3    2
(AC138718) Mus musculus BAC clone RP23-221F8 from 14, comple...    32   9.8    2
(AC124555) Mus musculus BAC clone RP23-245K17 from chromosom...    32   9.9    2
(AC161084) Bos taurus clone CH240-62E12, WORKING DRAFT SEQUE...    30   9.9    2
(AC116960) Dictyostelium discoideum chromosome 2 map complem...    30   9.9    2

>(BJ428835) Dictyostelium discoideum cDNA clone:ddv1m11, 3' end,
           single read.
          Length = 166

 Score =  303 bits (153), Expect = 9e-79
 Identities = 165/165 (100%)
 Strand = Plus / Minus


Query: 1   aacaagagtgttacaaaatgcctcaatacaaaattagtttggataataccaatgatccaa 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 166 aacaagagtgttacaaaatgcctcaatacaaaattagtttggataataccaatgatccaa 107


Query: 61  taattacgccaacaattacaccanctcttctacatttccaacaanacaccaactcgnata 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 106 taattacgccaacaattacaccanctcttctacatttccaacaanacaccaactcgnata 47


Query: 121 cgccaacaacaactgcaccaactncaccaacgccaacaccaacac 165
           |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 46  cgccaacaacaactgcaccaactncaccaacgccaacaccaacac 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 134,695,066
Number of extensions: 7763667
Number of successful extensions: 1971024
Number of sequences better than 10.0: 73
Length of query: 165
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 143
Effective length of database: 93,199,600,587
Effective search space: 13327542883941
Effective search space used: 13327542883941
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.20
Homology vs Protein 
Query= Contig-U05935-1 (Contig-U05935-1Q) /CSM_Contig/Contig-U05935-1Q.Seq.d
         (165 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 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: 3204285
Number of Hits to DB: 157,419,950
Number of extensions: 1607438
Number of successful extensions: 2017
Number of sequences better than 10.0: 0
Number of HSP's gapped: 2017
Number of HSP's successfully gapped: 0
Length of query: 55
Length of database: 1,040,966,779
Length adjustment: 28
Effective length of query: 27
Effective length of database: 951,246,799
Effective search space: 25683663573
Effective search space used: 25683663573
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: 26 (14.6 bits)
PSORT 

 psg: 0.54  gvh: 0.46  alm: 0.54  top: 0.53  tms: 0.00  mit: 0.20  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 

	 40.0 %: cytoplasmic
	 28.0 %: nuclear
	 24.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U05935-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 1
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) 0
FC-IC (SUB) 0