identity to AB001920 Oryza sativa DNA for phospholipase D
LOCUS AQ576571 560 bp DNA GSS 02-JUN-1999
DEFINITION nbxb0089K24f CUGI Rice BAC Library Oryza sativa genomic clone
nbxb0089K24f, genomic survey sequence.
ACCESSION AQ576571
NID g4977056
VERSION AQ576571.1 GI:4977056
KEYWORDS GSS.
SOURCE Oryza sativa.
ORGANISM Oryza sativa
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
euphyllophytes; Spermatophyta; Magnoliophyta; Liliopsida; Poales;
Poaceae; Oryza.
REFERENCE 1 (bases 1 to 560)
AUTHORS Yu,Y., Budiman,M.A., Boyd,C.A., Gaudette,B., Gayle,A.,
Kingsbury,R., Phillips,K., Sasinowski,M., Dean,R.A. and Wing,R.A.
TITLE A BAC End Sequencing Framework to Sequence the Rice Genome
JOURNAL Unpublished (1998)
COMMENT
Contact: Wing RA
Clemson University Genomics Institute
Clemson University
100 Jordan Hall, Clemson, SC 29634, USA
Tel: 864 656 7288
Fax: 864 656 4293
Email: rwing@clemson.edu
Seq primer: TAATACGACTCACTATAGGG
Class: BAC ends
High quality sequence stop: 354.
FEATURES Location/Qualifiers
source 1..560
/organism="Oryza sativa"
/strain="Japonica"
/cultivar="Nipponbare"
/note="Vector: pBeloBAC11; Site_1: HindIII; Site_2:
HindIII; Rice is one of two most popular grains in the
world. Half of the world population especially those
inhabiting highly populated areas of the humid tropics
and subtropics, rely on rice as their primary source of
carbohydrate. Monocotyledonous rice is a diploid plant
(2n=24) with a haploid genome equivalent of 431 Mbp
(Arumuganathan and Earle, 1991). The relatively small
genome of rice, three times larger than that of
Arabidopsis, makes it suitable for genomic studies. In
order to facilitate positional cloning, physical mapping
and genome sequencing of rice, we have constructed a BAC
library from Oryza sativa, Nipponbare variety. The
library contains 36,864 clones with an average insert size
of 128.5 Kb providing 10.9 haploid genome equivalents.
The deep coverage allows the isolation a particular
sequence with a probability of 99.9 %. Two high density
filters, each containing 18,432 clones (doubly spotted),
represent the whole library for colony screening."
/db_xref="taxon:4530"
/clone="nbxb0089K24f"
/clone_lib="CUGI Rice BAC Library"
/tissue_type="Leaf"
/lab_host="E. coli DH10B"
BASE COUNT 176 a 132 c 107 g 145 t
ORIGIN
1 cacatggatc ttgctctcac caacaggctc gcggttatta tcacagatat cgagccatct
61 gtcaatctcc tctccattga gaagctcttg gacaggcagg taagccctcc caatattcgt
121 tgccccaata gggttatcaa tcttgacagt gaagatcaca ttggaagcca tatgagcgca
181 atagatgtgg aacgactcat accagcgagg gttgatgggc tcattggtta tcatcctagt
241 tcgccctaca cgagctttct ccagatcaat ggtagaatac accttggtgg cgcctttgcc
301 gacacccaca gtgtcctcaa tcccctccac aaactgttga catgagctca cgtgttagat
361 caagaacaac aaagaagaag acattgcatt tcaggtgata cagacacaca tagcatacag
421 caatagattt gtagtaggtc agttaataaa taaataaaaa ctctatcaaa tcaagatttt
481 tggtgacaca agcacacatc acacacagag aactctacat ttttagtagg tcagttaata
541 aataaaattt cagtttagct
//
Score E
Sequences producing significant alignments: (bits) Value
sp|Q43007|PLD1_ORYSA PHOSPHOLIPASE D 1 PRECURSOR (PLD 1) (C... 232 2e-60
sp|Q43270|PLD_MAIZE PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 201 4e-51
emb|CAB43063.1| (AJ133001) phospholipase D1 [Craterostigma ... 182 2e-45
emb|CAB43062.1| (AJ133000) phospholipase D2 [Craterostigma ... 176 1e-43
sp|Q41142|PLD_RICCO PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 175 3e-43
gi|1698844 (U72693) phospholipase D [Ricinus communis] 175 3e-43
gi|3639087 (AF090444) phospholipase D2 [Brassica oleracea] ... 174 5e-43
pir||A54850 phospholipase D (EC 3.1.4.4) - castor bean 173 1e-42
sp|P93400|PLD_TOBAC PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 172 2e-42
sp|O04865|PLD_VIGUN PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 166 9e-41
gi|3639089 (AF090445) phospholipase D1 [Brassica oleracea] ... 164 5e-40
sp|O04883|PLD_PIMBR PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 153 1e-36
sp|P93844|PLD2_ORYSA PHOSPHOLIPASE D 2 PRECURSOR (PLD 2) (C... 150 8e-36
sp|Q38882|PLD_ARATH PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLIN... 127 5e-29
emb|CAB44321.1| (AL078606) putative phospholipase D-gamma [... 58 5e-08
emb|CAA21465.1| (AL031986) putative protein [Arabidopsis th... 58 6e-08
gi|1871182 (U90439) phospholipase D isolog [Arabidopsis tha... 55 4e-07
gi|2252846 (AF013293) Similar to phospholipase D [Arabidops... 55 5e-07
gb|AAD43343.1|AF159139_1 (AF159139) phospholipase D [Gossyp... 50 1e-05
gi|1885383 (U84568) phospholipase D [Arabidopsis thaliana] 47 1e-04
gb|AAD38519.1|AF138281_1 (AF138281) phospholipase D-gamma-2... 46 2e-04
sp|P55939|PLD_BRAOL PHOSPHOLIPASE D (PLD) (CHOLINE PHOSPHAT... 45 3e-04
bbs|136678 phospholipase D, PL D, phosphatidylcholine phosp... 45 3e-04
emb|CAB43284.1| (AL050134) hypothetical protein [Homo sapiens] 36 0.23
dbj|BAA34467.1| (AB018290) KIAA0747 protein [Homo sapiens] 36 0.23
gi|4200444 (AF098634) GLUT4 vesicle protein [Mus musculus] 36 0.30
gi|4193489 (AF099138) GLUT4 vesicle protein [Rattus norvegi... 35 0.39
pir||B26696 hypothetical protein 1 (CYb-COII intergenic reg... 33 2.0
emb|CAA58885| (X84077) DNA topoisomerase (ATP-hydrolysing) ... 33 2.0
sp|P48354|GYRA_MYCSM DNA GYRASE SUBUNIT A >gi|1122892|emb|C... 33 2.0
emb|CAA63254| (X92503) gyrA [Mycobacterium smegmatis] 33 2.0
emb|CAA06687| (AJ005702) cinnamyl alcohol dehydrogenase [Ze... 32 3.4
gi|2429470 (AF025462) strong similarity to phospholipase C;... 31 5.8
gi|3329340 (AE001359) 1, 4-alpha-glucan branching enzyme [C... 31 7.6
sp|Q27869|PIMT_DROME PROTEIN-L-ISOASPARTATE(D-ASPARTATE) O-... 31 7.6
emb|CAA76941| (Y17921) UNC-13 protein [Drosophila melanogas... 31 9.9
emb|CAA76942| (Y17922) UNC-13-B protein [Drosophila melanog... 31 9.9
sp|Q43007|PLD1_ORYSA PHOSPHOLIPASE D 1 PRECURSOR (PLD 1) (CHOLINE PHOSPHATASE 1)
(PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D 1)
>gi|1020415|dbj|BAA11136| (D73411) phospholipase D
[Oryza sativa] >gi|1902903|dbj|BAA19467| (AB001920)
phospholipase D [Oryza sativa]
Length = 812
Score = 232 bits (585), Expect = 2e-60
Identities = 110/113 (97%), Positives = 112/113 (98%)
Frame = -3
Query: 339 QQFVEGIEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASN 160
++FVEGIEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASN
Sbjct: 35 RKFVEGIEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASN 94
Query: 159 VIFTVKIDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNREPVGESKIHV 1
VIFTVKIDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNRE VGESKIHV
Sbjct: 95 VIFTVKIDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNRESVGESKIHV 147
sp|Q43270|PLD_MAIZE PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLINE PHOSPHATASE)
(PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D)
>gi|1020409|dbj|BAA11135| (D73410) phospholipase D [Zea
mays]
Length = 812
Score = 201 bits (505), Expect = 4e-51
Identities = 92/113 (81%), Positives = 106/113 (93%)
Frame = -3
Query: 339 QQFVEGIEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASN 160
++ VEGIEDTVGVGKGATK+Y+T+DLEKARVGRTRMI+NEP+NPRWYESFHIYCAHMA++
Sbjct: 35 RKLVEGIEDTVGVGKGATKIYATVDLEKARVGRTRMISNEPVNPRWYESFHIYCAHMAAD 94
Query: 159 VIFTVKIDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNREPVGESKIHV 1
VIFTVKIDN IGA+ IGRAYL VQ+LL GEEID+WL+I D NREPVG+SKIHV
Sbjct: 95 VIFTVKIDNSIGASLIGRAYLAVQDLLGGEEIDKWLEISDENREPVGDSKIHV 147
emb|CAB43063.1| (AJ133001) phospholipase D1 [Craterostigma plantagineum]
Length = 807
Score = 182 bits (457), Expect = 2e-45
Identities = 85/107 (79%), Positives = 98/107 (91%), Gaps = 1/107 (0%)
Frame = -3
Query: 321 IEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASNVIFTVK 142
IE+TVG GKG K+Y++IDLEKARVGRTRMI +EP NPRWYESFHIYCAHMASNVIFTVK
Sbjct: 36 IEETVGFGKGTPKIYASIDLEKARVGRTRMIEHEPNNPRWYESFHIYCAHMASNVIFTVK 95
Query: 141 IDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNREPV-GESKIHV 1
DNPIGAT IGRAY+PVQE+L+GEEIDRW++I DN++ P+ GESKIHV
Sbjct: 96 DDNPIGATLIGRAYIPVQEILDGEEIDRWVEILDNDKNPISGESKIHV 143
emb|CAB43062.1| (AJ133000) phospholipase D2 [Craterostigma plantagineum]
Length = 807
Score = 176 bits (441), Expect = 1e-43
Identities = 79/107 (73%), Positives = 97/107 (89%), Gaps = 1/107 (0%)
Frame = -3
Query: 321 IEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASNVIFTVK 142
IE+ VG GKG K+Y++IDLEKARVGRTRMI +EP NPRWYESFHIYCAH+ASN+IFTVK
Sbjct: 36 IEEKVGFGKGTPKIYASIDLEKARVGRTRMIEHEPTNPRWYESFHIYCAHLASNIIFTVK 95
Query: 141 IDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNREPV-GESKIHV 1
DNPIGAT IGRAY+PV+++L+GEE+DRW+++ DNN+ P+ GESKIHV
Sbjct: 96 DDNPIGATLIGRAYVPVRDVLDGEELDRWVELLDNNKNPIRGESKIHV 143
sp|Q41142|PLD_RICCO PHOSPHOLIPASE D PRECURSOR (PLD) (CHOLINE PHOSPHATASE)
(PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D)
>gi|1438075 (L33686) phospholipase D [Ricinus communis]
Length = 808
Score = 175 bits (438), Expect = 3e-43
Identities = 82/113 (72%), Positives = 98/113 (86%), Gaps = 1/113 (0%)
Frame = -3
Query: 339 QQFVEGIEDTVGVGKGATKVYSTIDLEKARVGRTRMITNEPINPRWYESFHIYCAHMASN 160
++ VE IE+TVG GKG +K+Y+TIDLEKARVGRTR++ NE NPRWYESFH+YCAH ASN
Sbjct: 30 RKLVENIEETVGFGKGVSKLYATIDLEKARVGRTRILENEQSNPRWYESFHVYCAHQASN 89
Query: 159 VIFTVKIDNPIGATNIGRAYLPVQELLNGEEIDRWLDICDNNREPV-GESKIHV 1
VIFTVK DNPIGAT IGRAY+PV+ELL+GEEIDRW++I D ++ PV SKIHV
Sbjct: 90 VIFTVKDDNPIGATLIGRAYVPVEELLDGEEIDRWVEILDEDKNPVHSGSKIHV 143
**********************************************************************
BLASTN 8-27-99:
Score E
Sequences producing significant alignments: (bits) Value
dbj|AB001920|AB001920 Oryza sativa DNA for phospholipase D,... 1094 0.0
dbj|D73411|RICPHD2 Oryza sativa mRNA for phospholipase D, c... 656 0.0
dbj|D73410|MZEPHD1 Zea mays mRNA for phospholipase D, compl... 113 5e-23
emb|AJ133001.1|CPL133001 Craterostigma plantagineum mRNA fo... 62 2e-07
gb|U72693|RCU72693 Ricinus communis phospholipase D gene, c... 54 4e-05
gb|L33686|RCCPLD Ricinus communis phospholipase D mRNA, com... 54 4e-05
emb|Z84822|NTZ84822 Nicotiana tabacum mRNA for phospholipase D 52 1e-04
gb|AC005697|AC005697 Homo sapiens chromosome 17, clone hRPK... 42 0.14
gb|AF113919|AF113919 Brassica oleracea var. capitata phosph... 42 0.14
gb|AF090444|AF090444 Brassica oleracea phospholipase D2 (PL... 42 0.14
gb|AC004104|AC004104 Homo sapiens 12q24 PAC RPCI5-942N13 (R... 42 0.14
gb|U85482|BOU85482 Brassica oleracea var. capitata phosphol... 42 0.14
gb|U53155|CELZC513 Caenorhabditis elegans cosmid ZC513 42 0.14
gb|AC005909|AC005909 Homo sapiens chromosome 18 BAC RPCI11-... 40 0.56
gb|AC002041|HUAC002041 Human Chromosome 16 BAC clone CIT987... 40 0.56
dbj|AB026644.1|AB026644 Arabidopsis thaliana genomic DNA, c... 40 0.56
emb|X91016|CCUA1EX1 C.carpio Cyca-UA1*01 gene (exon 1) 40 0.56
gb|AC007455.7|AC007455 Homo sapiens chromosome 17, clone hR... 40 0.56
emb|AL023578|HS248E1 Human DNA sequence from clone 248E1 on... 40 0.56
emb|AL021961|ATF28A23 Arabidopsis thaliana DNA chromosome 4... 40 0.56
dbj|AB008269.1|AB008269 Arabidopsis thaliana genomic DNA, c... 40 0.56
gb|AC005242|AC005242 Homo sapiens chromosome 17, clone hRPK... 40 0.56
gb|AE001418|AE001418 Plasmodium falciparum chromosome 2, se... 40 0.56
gb|AC006418|ATAC006418 Arabidopsis thaliana chromosome II B... 40 0.56
emb|AL080058.1|HSM800558 Homo sapiens mRNA; cDNA DKFZp564G2... 40 0.56
gb|AF039712|CELF54D7 Caenorhabditis elegans cosmid F54D7 40 0.56
gb|AC005215|AC005215 Homo sapiens chromosome 5, BAC clone 8... 40 0.56
gb|AC005819|ATAC005819 Arabidopsis thaliana chromosome II B... 40 0.56
gb|AC005684|AC005684 Homo sapiens Chromosome 11p14.4 PAC cl... 40 0.56
gb|AC005320|AC005320 Human Chromosome 11p14.3 PAC clone pDJ... 40 0.56
emb|Z77667|CEM04B2 Caenorhabditis elegans cosmid M04B2, com... 38 2.2
gb|AF016431|CELC10B5 Caenorhabditis elegans cosmid C10B5 38 2.2
gb|AC002978|AC002978 Homo sapiens 12q24 PAC P336P3 (Researc... 38 2.2
gb|AC007182.3|AC007182 Homo sapiens chromosome 14 clone BAC... 38 2.2
emb|X73136|PTRBC P.vittata mRNA for rubisco, small subunit 38 2.2
emb|Z36753|CET09A5 Caenorhabditis elegans cosmid T09A5, com... 38 2.2
emb|AJ228560|NCA228560 Neorotalia calcar SSU rRNA gene, iso... 38 2.2
gb|AC006414.6|AC006414 Drosophila melanogaster, chromosome ... 38 2.2
gb|U29380|CELZK546 Caenorhabditis elegans cosmid ZK546 38 2.2
emb|Z80902|HSN80H12 Human DNA sequence from cosmid N80H12 o... 38 2.2
emb|AL020997|HS426I6 Human DNA sequence from PAC 426I6 on c... 38 2.2
emb|Z92849|CEH12D21 Caenorhabditis elegans cosmid H12D21, c... 38 2.2
dbj|AP000381.1|AP000381 Arabidopsis thaliana genomic DNA, c... 38 2.2
emb|AL033388.1|SPBC887 S.pombe chromosome II cosmid c887 38 2.2
gb|AC006406|AC006406 Homo sapiens, clone hRPK.25_A_1, compl... 38 2.2
emb|AL021706|HS717L17 Human DNA sequence from PAC 717L17 on... 38 2.2
gb|AC005922|AC005922 Homo sapiens chromosome 17, clone hRPK... 38 2.2
gb|AC006577.2|F15I1 Sequence of BAC F15I1 from Arabidopsis ... 38 2.2
emb|X77813|PVRBCSG P.vittata rbcS gene 38 2.2
gb|AE000645.1|AE000645 Helicobacter pylori 26695 section 12... 38 2.2
dbj|AP000362.1|AP000362 Homo sapiens genomic DNA, chromosom... 38 2.2
emb|AL032646|CEY54E2A Caenorhabditis elegans cosmid Y54E2A,... 38 2.2
dbj|AB001920|AB001920 Oryza sativa DNA for phospholipase D, complete cds
Length = 5871
Score = 1094 bits (552), Expect = 0.0
Identities = 555/556 (99%)
Strand = Plus / Minus
Query: 1 cacatggatcttgctctcaccaacaggctcgcggttattatcacagatatcgagccatct 60
|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct: 2856 cacatggatcttgctctcaccaacagactcgcggttattatcacagatatcgagccatct 2797
Query: 61 gtcaatctcctctccattgagaagctcttggacaggcaggtaagccctcccaatattcgt 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2796 gtcaatctcctctccattgagaagctcttggacaggcaggtaagccctcccaatattcgt 2737
Query: 121 tgccccaatagggttatcaatcttgacagtgaagatcacattggaagccatatgagcgca 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2736 tgccccaatagggttatcaatcttgacagtgaagatcacattggaagccatatgagcgca 2677
Query: 181 atagatgtggaacgactcataccagcgagggttgatgggctcattggttatcatcctagt 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2676 atagatgtggaacgactcataccagcgagggttgatgggctcattggttatcatcctagt 2617
Query: 241 tcgccctacacgagctttctccagatcaatggtagaatacaccttggtggcgcctttgcc 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2616 tcgccctacacgagctttctccagatcaatggtagaatacaccttggtggcgcctttgcc 2557
Query: 301 gacacccacagtgtcctcaatcccctccacaaactgttgacatgagctcacgtgttagat 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2556 gacacccacagtgtcctcaatcccctccacaaactgttgacatgagctcacgtgttagat 2497
Query: 361 caagaacaacaaagaagaagacattgcatttcaggtgatacagacacacatagcatacag 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2496 caagaacaacaaagaagaagacattgcatttcaggtgatacagacacacatagcatacag 2437
Query: 421 caatagatttgtagtaggtcagttaataaataaataaaaactctatcaaatcaagatttt 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2436 caatagatttgtagtaggtcagttaataaataaataaaaactctatcaaatcaagatttt 2377
Query: 481 tggtgacacaagcacacatcacacacagagaactctacatttttagtaggtcagttaata 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2376 tggtgacacaagcacacatcacacacagagaactctacatttttagtaggtcagttaata 2317
Query: 541 aataaaatttcagttt 556
||||||||||||||||
Sbjct: 2316 aataaaatttcagttt 2301