Arabidopsis thaliana gene AT1G57860, encoding 60S ribosomal protein L21.
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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, 3.1 times the average gene in this release. The sequence of this gene is defined by 114 GenBank accessions from 110 cDNA clones, some from ovule (seen 33 times), aerial (27), mixture of silique and flower (7), root (4), flower, leaf and root (3), see description (3), cell suspension culture (2) and 4 other tissues. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 2 distinct gt-ag introns. Transcription produces 3 different mRNAs, 2 alternatively spliced variants and 1 unspliced form.
Function: There is one article specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in pathway (Ribosome) and a process (translation). Proteins are expected to have molecular function (structural constituent of ribosome) and to localize in various compartments (cytoplasm, ribosome, intracellular).
Please see the Arabidopsis TAIR site TAIR:AT1G57860 for in depth functional annotation of this gene.
Protein coding potential: The 2 spliced and the unspliced mRNAs putatively encode good proteins, altogether 3 different isoforms (3 complete), some containing Ribosomal protein L21e domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 1, links to other databases and other names
Map: This gene AT1G57860 maps on chromosome 1. In AceView, it covers 1.05 kb, from 21434531 to 21433483 (NCBI 7_1, April 2007), on the reverse strand.
Links to: manual annotations from TAIR:AT1G57860, KEGG_03010, the SNP view, gene overviews from Entrez Gene 842161, expression data from UniGene At.21612, At.48314.
Other names: The gene is also known as AT1G57860, F12K22.19, LOC842161 or bludar, bleedar. It has been described as 60S ribosomal protein L21.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene LOC653156 (e=10-21).
The closest mouse genes, according to BlastP, are the AceView genes LOC545423 (e=2 10-21), Rpl21 (e=2 10-21), LOC676253 (e=2 10-21), LOC675278 (e=2 10-21), EG637748 (e=3 10-21), LOC637900 (e=4 10-21), EG433125 (e=5 10-21), EG668319 (e=6 10-21), EG665821 (e=2 10-20), EG666340 (e=2 10-20), EG666977 (e=2 10-20), LOC432801 (e=2 10-20), EG545226 (e=3 10-20), LOC545572 (e=4 10-20), LOC667919 (e=7 10-20), LOC667528 (e=10-19), EG627939 (e=2 10-19), LOC666619 (e=5 10-19), LOC667287 (e=5 10-19), EG665251 (e=2 10-18), LOC620771 (e=6 10-18).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene rpl-21 (e=3 10-19), 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 AT1G57860 5' 3' encoded on minus strand of chromosome 1 from 21,434,531 to 21,433,483 a [NM] b c-u 100 200bp 0 276 bp exon 276 bp exon 299 bp [gt-ag] intron 40 GenBank accessions 394 bp exon 40 accessions, NM_104579 some from ovule (seen 7 times) mixture of silique and flower (5) flower, leaf and root (3) root (3), aerial (2) 394 bp exon 275 bp exon 275 bp exon 253 bp [gt-ag] intron 4 GenBank accessions 520 bp exon 68 accessions, some from ovule (seen 26 times) aerial (25), mixture of silique and flower (2) see description (2), cell suspension culture (once) 520 bp exon 393 bp exon 393 bp exon 1 accession 393 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 670 bp 164 aa 39 bp 136 bp 2kb probably including promoter 969 bp 1kb
bOct08 795 bp 85 aa 38 bp 499 bp 2kb probably including promoter 1048 bp 1kb
cOct08-unspliced 393 bp 80 aa 37 bp 113 bp 2kb probably including promoter 393 bp 1kb

Gene neighbors and Navigator on chromosome 1 back to top
AT1G57620 C R AT1G57630 C AT1G57650 C AT1G57660 C AT1G57700 C P AT1G57720 C R P AT1G57760 C R AT1G57765 C AT1G57770 C AT1G57780 C AT1G57830 C C AT1G57850 C AT1G57906 C C AT1G58055 C AT1G58070 C AT1G58090 C AT1G58120 C R AT1G58150 AT1G58130 C C R C R C AT1G57670 C R AT1G57680 C AT1G57690 P AT1G57710 C AT1G57730 C P CYP96A15/MAH1 C AT1G57775 C R AT1G57777 C AT1G57790 C VIM5 D C R P ORTH2/VIM1 C R P AT1G57860 C R AT1G57870 C R P ATPUP17 C R AT1G57980 C P ATPUP18 C R P AT1G58007 C C R AT1G58025 C R P CAT2.1 C P AT1G58037 C AT1G58050 C AT1G58060 C R P ATATP-PRT1 C P AT1G58100 C R AT1G58110 10 20kb 0 AT1G57620, 31 accessions AT1G57630, 2 accessions AT1G57650, 1 accession AT1G57660, 178 accessions 2 variants AT1G57700, 3 accessions AT1G57720, 494 accessions 2 variants AT1G57760, 41 accessions AT1G57765, 27 accessions AT1G57770, 21 accessions AT1G57780, 1 accession AT1G57830, 1 accession derdu, 8 accessions AT1G57850, 1 accession AT1G57906, 1 accession blerdar, 50 accessions AT1G58055, 18 accessions AT1G58070, 10 accessions AT1G58090, 6 accessions AT1G58120, 29 accessions blodar, 1 accession peyfee, 5 accessions blawdar, 28 accessions porfee, 1 accession blordar, 4 accessions AT1G58130, 1 accession AT1G57600, 10 accessions AT1G57610, 19 accessions 3 variants bludar, 13 accessions AT1G57670, 1 accession AT1G57680, 89 accessions 2 variants AT1G57690, 1 accession AT1G57710, 1 accession AT1G57730, 1 accession CYP96A15/MAH1, 133 accessions 2 variants AT1G57775, 26 accessions AT1G57777, 39 accessions AT1G57790, 10 accessions VIM5, 2 accessions ORTH2/VIM1, 32 accessions 2 variants AT1G57860, 110 accessions 3 variants AT1G57870, 39 accessions 3 variants ATPUP17, 13 accessions 3 variants AT1G57980, 15 accessions ATPUP18, 83 accessions AT1G58007, 62 accessions 5 variants bleydar, 45 accessions AT1G58025, 13 accessions 2 variants CAT2.1, 117 accessions 2 variants AT1G58037, 64 accessions 2 variants AT1G58050, 1 accession AT1G58060, 29 accessions ATATP-PRT1, 87 accessions 2 variants AT1G58100, 83 accessions 2 variants AT1G58110, 28 accessions 2 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1 article in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-u 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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