Arabidopsis thaliana gene AT3G42790, encoding PHD finger family protein.
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SUMMARY back to top
TAIR annotates one representative transcript (NM included in AceView variant.a), but Arabidopsis thaliana cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.7 times the average gene in this release. The sequence of this gene is defined by 135 GenBank accessions from 133 cDNA clones, some from aerial (seen 50 times), ovule (20), flower, leaf and root (11), root (8), see description (6), mixture of silique and flower (4), adult vegetative tissue (2) and 7 other tissues.
Alternative mRNA variants and regulation: The gene contains 4 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. The mRNAs appear to differ by truncation of the 5' end.
Function:. Functionally, the gene has been proposed to participate in a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (DNA binding, protein binding, zinc ion binding).
Please see the Arabidopsis TAIR site TAIR:AT3G42790 for in depth functional annotation of this gene.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), containing Zinc finger, PHD-type domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 3, links to other databases and other names
Map: This gene AT3G42790 maps on chromosome 3. In AceView, it covers 1.86 kb, from 14890769 to 14888909 (NCBI 7_1, April 2007), on the reverse strand.
Links to: manual annotations from TAIR:AT3G42790, the SNP view, gene overviews from Entrez Gene 823316, expression data from UniGene.
Other names: The gene is also known as AT3G42790, LOC823316. It has been described as PHD finger family protein.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes BPTF (e=7 10-06), DIDO1 (e=4 10-05), PHF8 (e=10-04), JHDM1D (e=3 10-04).
The closest mouse genes, according to BlastP, are the AceView genes Bptf (e=10-05), Dido1 (e=2 10-05), Phf8 (e=9 10-05), Jhdm1d (e=3 10-04), 4921501E09Rik (e=4 10-04).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene nurf-1 (e=2 10-05), which may contain interesting functional annotation
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene AT3G42790 5' 3' encoded on minus strand of chromosome 3 from 14,890,769 to 14,888,909 a [NM] b 1kb 0 263 bp exon 263 bp exon 106 bp [gt-ag] intron 35 GenBank accessions 33 bp exon 261 bp [gt-ag] intron 35 GenBank accessions 229 bp exon 77 bp [gt-ag] intron 25 GenBank accessions 130 bp exon 294 bp [gt-ag] intron 37 GenBank accessions 468 bp exon 132 accessions, NM_114147 some from aerial (seen 50 times) ovule (20), flower, leaf and root (10) root (8), see description (6) Validated 3' end, 2 accessions 468 bp exon 271 bp exon 271 bp exon 77 bp [gt-ag] intron 25 GenBank accessions 130 bp exon 294 bp [gt-ag] intron 37 GenBank accessions 324 bp exon 1 accession from flower leaf and root 324 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aOct08 1123 bp 250 aa 163 bp 207 bp 2kb possibly including promoter 1861 bp 1kb
bOct08 725 bp 219 aa 63 bp 2kb 1096 bp 1kb

Gene neighbors and Navigator on chromosome 3 back to top
AT3G42719 C C R R AT3G42740 C AT3G42770 C AT3G42780 C AT3G42786 C AT3G42792 C R AT3G42800 C AT3G42806 C R AT3G42810 C R AT3G42870 C AT3G42880 C AT3G42883 C C C AT3G42720 C AT3G42723 C AT3G42725 C R AT3G42790 C C C AT3G42820 C P AT3G42830 C AT3G42850 C AT3G42860 10 20kb 0 AT3G42719, 15 accessions steebey, 4 accessions keyfy, 8 accessions korfy, 10 accessions AT3G42740, 4 accessions AT3G42770, 1 accession AT3G42780, 1 accession AT3G42786, 1 accession AT3G42792, 1 accession AT3G42800, 8 accessions AT3G42806, 14 accessions 5 variants AT3G42810, 55 accessions 2 variants AT3G42870, 1 accession AT3G42880, 20 accessions kofy, 3 accessions AT3G42728, 1 accession keefy, 1 accession kawfy, 1 accession kerfy, 1 accession koyfy, 1 accession AT3G42883, 1 accession lafy, 1 accession stabey, 6 accessions AT3G42712, 3 accessions karfy, 19 accessions AT3G42720, 40 accessions AT3G42723, 1 accession AT3G42725, 8 accessions AT3G42790, 133 accessions 2 variants sterbey, 6 accessions slardoy, 48 accessions AT3G42820, 49 accessions AT3G42830, 13 accessions AT3G42850, 1 accession AT3G42860, 12 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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