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Table 1 Summary on Arabidopsis phospholipase D genes. All genes from the eukaryotic PC-PLD family identified in the complete Arabidopsis genome sequence are listed. An additional gene, PLDδ2, has been reported in the literature [2], there is, however, no corresponding ORF in the genomic clone allegedly harbouring the gene (AC004708), and the genomic clone itself has been annotated as "spurious" and excluded from the final assemblage of the complete Arabidopsis genome.

From: Molecular diversity of phospholipase D in angiosperms

proposed gene name

original gene namea

genomic locusb

number of coding exons

gene sequencec

cDNA

number of ESTs

references

AtPLDα1

PLDα

At3g15730 / MSJ11.13

3

AB017071, NC_003074

U36381, AF428278d

40

[2], [43]

AtPLDα2

 

At1g52570 / F6D8.21

3

AC008016, NC_003070

-

0

-

AtPLDβ1

PLDβ

At2g42010 / T6D20.10

10e

U90439, NC_003071

U84568

5

[2], [11]

AtPLDβ2

PLDδ1

At4g00240 / F5I10.13

10f

AF195115, AL161471, AF013293, NC_003075

-

0

-

AtPLDγ1

 

At4g11850 / T26M18.60

10

AL161532, AL078606, NC_003075

AF027408

8

[2], 27]

AtPLDγ2

 

At4g11830 / T26M18.40

10 (11)g

AL161532, AL078606, NC_003075

AF138281h

1

[2], [18]

AtPLDγ3

 

At4g11840 / T26M18.50

10

AL161532, AL078606, NC_003075

AF138281h

2

[2], [18]

AtPLDδ

 

At4g35790 / F4B14.60

10i

AL161588, AL031986, NC_003075

AF322228j, AB031047, AF306345, AF274239k, AF424632l

29

[15], [16], [44], Cheuk et al., unpubl.

AtPLDε

PLDalpha

At1g55180 / F7A10.25

4

AC027034, NC_003070

-

1m,

-

AtPLDζ

 

At5g25370 / F18G18.110

4

AC006258n, NC_003076

-

0

-

AtPLDp1

PLDzeta 1

At3g16790 (5' part) At3g16785 (3' part) / MGL6.24 (5' part) MGL6.27 (3' part)

20

AB022217 (5' part) AB028608 (3' part), NC_003074

AF411833

7

Qin and Wang, unpubl.

AtPLDp2

 

At3g05630 / F18C1.10

16°

AC011620, NC_003074

-

3

-

  1. aFor clarity, gene names used in [2] differing from our nomenclature are noted. Inappropriate designation of AtPLDε as "PLDalpha" has been used by AGI annotators. AtPLDp1 was designated by Qin and Wang in the respective GenBank entry. bAGI gene identifier (the number following "At" refers to chromosome)/BAC-specific locus number cGenBank/EMBL/DDBJ accession numbers of genomic clones containing the respective PLD genes; multiple numbers noted for several genes refer to redundant clones or clone assemblages. dA 5' truncated cDNA sequence, the ORF incomplete. eCorrections introduced into the AGI annotation: the 1st exon extended with 765 bp in 5' direction (see the text), the 6th exon shortened of 16 bp at the 3' end (according to the respective cDNA and ESTs). fCorrections introduced into the AGI annotation: the 1st predicted intron included into the ORF and the 5th exon extended with 36 bp at the 3' end to restore conserved regions to restore conserved regions. gAn obscure intron may be spliced off (perhaps alternatively) from the 1st predicted exon (see the text), hThe same cDNA is noted here for both the AtPLDγ2 and AtPLDγ3 genes, because it is chimeric and contains portions from both the genes (see the text). iCorrections introduced into the AGI annotation: the last six predicted exons removed (according to the corresponding cDNAs and ESTs). jThe independently reported AtPLDδ cDNAs perhaps represent two distinct splice variants (details in the text). kA 5' truncated cDNA sequence. lA one-nucleotide deletion at the very 5' end resulting in a rearranged N-terminus of the deduced protein, mAn alleged EST (AV547754) corresponding to the PLDε gene is dubious, as it apparently represents an un-spliced transcript or a contamination of the source cDNA library with a genomic fragment. nThe gene is currently not annotated in the GenBank entry of BAC F18G18 (AC006258), but it has been included into annotation of the whole-chromosome pseudomolecule (NC_003076). oCorrections introduced into AGI annotation: the 8th exon extended with 21 bp at the 5' end to restore a highly conserved region.
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BMC Genomics

ISSN: 1471-2164

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