Caenorhabditis elegans essential gene haf-4, encoding HAlF transporter, PGP related.
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SUMMARY back to top
Summary
[Wormbase] haf-4 encodes a half-molecular ATP-binding cassette (ABC) transporter; haf-4 activity is required in embryos and adults for formation of birefringent material in gut granules, lysosome-related fat storage organelles.
Wormbase predicts one model, but Caenorhabditis elegans 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 4 spliced variants
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 8.9 times the average gene in this release, from L1 to adult, but not in dauers [Kohara cDNAs and SAGE data]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 2%, L1 or L2 larvae 33%, L3 to adult 64%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 77 cDNA clones and 40 elements defined by RNA-seq, some from mixed (seen 19 times), l1 (17), l2 (15), l4 (9), embryo (once), whole animal (once). We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 13 distinct gt-ag introns. Transcription produces at least 6 different mRNAs, 4 alternatively spliced variants and 2 unspliced forms. Variant c is transpliced to SL1, SL4. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of 2 introns. 340 bp of this gene are antisense to spliced gene 1A970, raising the possibility of regulated alternate expression.
Function: There are 2 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (Embryonic Lethal, SLow growth). Functionally, the gene has been proposed to participate in a process (transport). Proteins are expected to have molecular functions (ATP binding activity, ATPase activity, coupled to transmembrane movement of substances) and to localize in various compartments (cytoplasm, endoplasmic reticulum membrane, plasma membrane, integral to membrane).
Protein coding potential: 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (3 complete), some containing domains ABC transporter, transmembrane region, ABC transporter-like [Pfam], some transmembrane domains [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 3 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This essential gene haf-4 maps on chomosome I at position -19.15 (interpolated). In AceView, it covers 7.56 kb, from 488610 to 496170 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1A969, in Wormbase by its cosmid.number name W04C9.1, in NextDB, the Nematode expression pattern database, as CEYK3317.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene ABCB9 (e= 10-161).
The closest mouse gene, according to BlastP, is the AceView gene Abcb9 (e= 10-163).
The closest A.thaliana genes, according to BlastP, are the AceView genes ATTAP2 (e= 10-107), ATTAP1 (e= 10-102)
          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 haf-4 5' 3' encoded on plus strand of chromosome I from 489,958 to 496,170 a b c d e f 1 2kb 0 503 bp exon 503 bp exon 72 bp uORF 503 bp exon 503 bp exon 994 bp [gt-ag] intron 36 GenBank accessions 106 bp exon 106 bp exon 47 bp [gt-ag] intron 35 GenBank accessions 210 bp exon 210 bp exon 50 bp [gt-ag] intron 34 GenBank accessions 115 bp exon 115 bp exon 111 bp [gt-ag] intron 35 GenBank accessions 325 bp exon 325 bp exon 64 bp [gt-ag] intron 14 GenBank accessions 127 bp exon 127 bp exon 515 bp [gt-ag] intron 15 GenBank accessions 690 bp exon 690 bp exon 703 bp [gt-ag] intron 42 GenBank accessions 84 bp exon 84 bp exon 48 bp [gt-ag] intron 43 GenBank accessions 315 bp exon 315 bp exon 1121 bp [gt-ag] intron 51 GenBank accessions 340 bp exon 340 bp exon 85 accessions, some from l1 (seen 16 times) mixed (16), l2 (14), l4 (8) embryo (once) Validated 3' end, 120 accessions 340 bp exon 151 bp exon 994 bp [gt-ag] intron 36 GenBank accessions 106 bp exon 47 bp [gt-ag] intron 35 GenBank accessions 210 bp exon 50 bp [gt-ag] intron 34 GenBank accessions 551 bp exon 551 bp exon 64 bp [gt-ag] intron 14 GenBank accessions 127 bp exon 515 bp [gt-ag] intron 15 GenBank accessions 690 bp exon 703 bp [gt-ag] intron 42 GenBank accessions 84 bp exon 48 bp [gt-ag] intron 43 GenBank accessions 1759 bp exon 3 accessions, some from mixed (seen 2 times) 1759 bp exon 117 bp exon 117 bp exon 44 bp [gt-ag] intron 4 GenBank accessions 66 bp exon 48 bp [gt-ag] intron 5 GenBank accessions 63 bp exon 755 bp [gt-ag] intron 5 GenBank accessions 207 bp exon 8 accessions, some from l1 (seen once) l2 (once), mixed (once) Transpliced 5' end, 1 accession Validated 3' end, 21 accessions Validated 3' end, 66 accessions 207 bp exon 108 bp exon 710 bp [gt-ag] intron 1 GenBank accession 216 bp exon 18 accessions, some from l4 (seen once) Validated 3' end, 21 accessions Validated 3' end, 66 accessions 216 bp exon 166 bp exon 166 bp exon 1 accession Validated 3' end, 3 accessions 166 bp exon 54 bp exon 54 bp exon 2 accessions Validated 3' end, 21 accessions 54 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 uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 2815 bp 842 aa 186 bp 100 bp 69 bp 2kb possibly including promoter 6468 bp 1kb
b 3678 bp 532 aa 785 bp 1294 bp 2kb possibly including promoter 6099 bp 1kb
c 453 bp 102 aa 9 bp 135 bp 2kb including Promoter 1300 bp 1kb
d 324 bp 59 aa 144 bp 2kb 1034 bp 1kb
e 166 bp 41 aa 38 bp 2kb 166 bp 1kb
f 54 bp 5 aa 35 bp 2kb 54 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
P cutl-13 C 1A963 C R haf-4 D C R P deps-1 D C R P C 1A956 D C P 1A970 C I R P 1A976 C R 1A982 C R P 5kb 0 1A945, 4 accessions, 2 variants cutl-13, 9 accessions 1A963, 0 accession haf-4, 117 accessions 6 variants deps-1, 37 accessions 3 variants 1A956, 9 accessions, 2 variants 1A970, 12 accessions, 2 variants 1A976, 17 accessions, 2 variants 1A982, 0 accession acs-13, 59 accessions 7 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 2 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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