Caenorhabditis elegans essential gene bli-4, encoding kex-2 Proprotein Convertase, subtilisin-like endoprotease, BLIstered cuticle, LEThal let-77.
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SUMMARY back to top
Summary
[Wormbase] bli-4 encodes a variety of related subtilases (serine endoproteases of the KEX2/subtilisin class), with shared N-termini but varying C-termini, that are collectively required both for larval viability and for stable adhesion of the adult cuticle.
Wormbase predicts 6 models, 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 17 spliced variants.

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, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 12%, L1 or L2 larvae 10%, L3 to adult 77%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 57 cDNA clones and 60 elements defined by RNA-seq, some from mixed (seen 19 times), embryo (8), l4 (6), l1 (4), l2 (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 36 distinct gt-ag introns. Transcription produces at least 18 different mRNAs, 17 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1, d to SL1. There are 5 probable alternative promotors, 8 non overlapping alternative last exons and 18 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 11 cassette exons, overlapping exons with different boundaries. 549 bp of this gene are antisense to spliced gene mut-2, raising the possibility of regulated alternate expression.
Function: There are 11 articles specifically referring to this gene in PubMed. In addition we point below to 42 abstracts. This essential gene is associated to a phenotype (BLIstered cuticle, DumPY : shorter than wild-type, LEThal, MoLT defect, embryonic and early larval arrest). Functionally, the gene has been proposed to participate in processes (cuticle formation, cuticle structure, proteolysis and peptidolysis). Proteins are expected to have molecular function (serine-type endopeptidase activity) and to localize in various compartments (extracellular space, membrane). These proteins appear to interact with another protein (CDF-3). The gene interacts with 3 other genes (BLI-1, DPY-9, DPY-18).
Protein coding potential: 14 spliced mRNAs putatively encode good proteins, altogether 14 different isoforms (5 complete, 7 COOH complete, 2 partial), some containing domains Peptidase S8 and S53, subtilisin, kexin, sedolisin, Proprotein convertase, P, ubiquitin interacting motif [Pfam], a coiled coil stretch [Psort2]; 2 of the 5 complete proteins appear to be secreted. The remaining 4 mRNA variants (3 spliced, 1 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 bli-4 maps on chomosome I at position +0.99 (interpolated). In AceView, it covers 15.59 kb, from 6341311 to 6356899 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known kpc-4, let-77, in Wormgenes/AceView by its positional name 1G931, in Wormbase by its cosmid.number name K04F10.4, in NextDB, the Nematode expression pattern database, as CEYK849.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes FURIN (e= 10-134), PCSK6 (e= 10-130), PCSK1 (e= 10-129), PCSK5 (e= 10-126), PCSK4 (e= 10-122).
The closest mouse genes, according to BlastP, are the AceView genes Furin (e= 10-137), Pcsk6 (e= 10-130), Pcsk1 (e= 10-128), Pcsk5 (e= 10-125).
The closest A.thaliana gene, according to BlastP, is the AceView gene ATS1P\/ATSBT6.1\/S1P (e=0.049)
          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 bli-4 5' 3' encoded on plus strand of chromosome I from 6,341,344 to 6,356,752 a b c o d r j e f g h l i k m n p q 5kb 0 130 bp exon 48 bp [gt-ag] intron 16 GenBank accessions 109 bp exon 109 bp exon 44 bp [gt-ag] intron 23 GenBank accessions 288 bp exon 107 bp [gt-ag] intron 25 GenBank accessions 144 bp exon 60 bp [gt-ag] intron 25 GenBank accessions 206 bp exon 55 bp [gt-ag] intron 15 GenBank accessions 318 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 131 bp exon 8415 bp [gt-ag] intron 8 GenBank accessions 73 bp exon 855 bp [gt-ag] intron 8 GenBank accessions 179 bp exon 51 bp [gt-ag] intron 13 GenBank accessions 109 bp exon 620 bp [gt-ag] intron 16 GenBank accessions 228 bp exon 53 bp [gt-ag] intron 26 GenBank accessions 154 bp exon 50 bp [gt-ag] intron 27 GenBank accessions 554 bp exon 47 accessions, some from mixed (seen 12 times) embryo (7), l1 (3), l4 (2) Transpliced 5' end, 4 accessions Validated 3' end, 4 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 84 accessions 554 bp exon 81 bp exon 44 bp [gt-ag] intron 23 GenBank accessions 288 bp exon 107 bp [gt-ag] intron 25 GenBank accessions 144 bp exon 60 bp [gt-ag] intron 25 GenBank accessions 206 bp exon 55 bp [gt-ag] intron 15 GenBank accessions 318 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 131 bp exon 8415 bp [gt-ag] intron 8 GenBank accessions 73 bp exon 855 bp [gt-ag] intron 8 GenBank accessions 179 bp exon 51 bp [gt-ag] intron 13 GenBank accessions 109 bp exon 42 bp [gt-ag] intron 2 GenBank accessions 422 bp exon 2 accessions Validated 3' end, 4 accessions 422 bp exon 52 bp exon 870 bp [gt-ag] intron 5 GenBank accessions 130 bp exon 48 bp [gt-ag] intron 16 GenBank accessions 109 bp exon 109 bp exon 44 bp [gt-ag] intron 23 GenBank accessions 288 bp exon 107 bp [gt-ag] intron 25 GenBank accessions 144 bp exon 60 bp [gt-ag] intron 25 GenBank accessions 206 bp exon 55 bp [gt-ag] intron 15 GenBank accessions 318 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 131 bp exon 7803 bp [gt-ag] intron 5 GenBank accessions 685 bp exon 12 accessions, some from mixed (seen 4 times) Validated 3' end, 91 accessions 685 bp exon 149 bp exon 149 bp exon 55 bp [gt-ag] intron 1 GenBank accession 554 bp exon 24 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 84 accessions 554 bp exon 130 bp exon 48 bp [gt-ag] intron 16 GenBank accessions 109 bp exon 109 bp exon 44 bp [gt-ag] intron 23 GenBank accessions 288 bp exon 107 bp [gt-ag] intron 25 GenBank accessions 144 bp exon 60 bp [gt-ag] intron 25 GenBank accessions 206 bp exon 55 bp [gt-ag] intron 15 GenBank accessions 318 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 131 bp exon 2735 bp [gt-ag] intron 8 GenBank accessions 195 bp exon 7 accessions, some from l4 (seen 3 times) mixed (2) Transpliced 5' end, 2 accessions Validated 3' end, 2 accessions Validated 3' end, 19 accessions 195 bp exon 77 bp exon 77 bp exon 1 accession Validated 3' end, 9 accessions 77 bp exon 109 bp exon 437 bp [gt-ag] intron 1 GenBank accession 27 bp exon 156 bp [gt-ag] intron 1 GenBank accession 219 bp exon 2 accessions 219 bp exon 84 bp exon 48 bp [gt-ag] intron 16 GenBank accessions 109 bp exon 109 bp exon 44 bp [gt-ag] intron 23 GenBank accessions 288 bp exon 107 bp [gt-ag] intron 25 GenBank accessions 144 bp exon 60 bp [gt-ag] intron 25 GenBank accessions 206 bp exon 55 bp [gt-ag] intron 15 GenBank accessions 318 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 755 bp exon 3 accessions, some from embryo (seen once) l2 (once), mixed (once) Validated 3' end, 2 accessions 755 bp exon 244 bp exon 244 bp exon 45 bp [gt-ag] intron 15 GenBank accessions 81 bp exon 109 bp [gt-ag] intron 13 GenBank accessions 177 bp exon 51 bp [gt-ag] intron 15 GenBank accessions 228 bp exon 46 bp [gt-ag] intron 16 GenBank accessions 110 bp exon 52 bp [gt-ag] intron 15 GenBank accessions 207 bp exon 580 bp [gt-ag] intron 18 GenBank accessions 131 bp exon 8415 bp [gt-ag] intron 8 GenBank accessions 73 bp exon 855 bp [gt-ag] intron 8 GenBank accessions 186 bp exon 44 bp [gt-ag] intron 1 GenBank accession 109 bp exon 109 bp exon 620 bp [gt-ag] intron 16 GenBank accessions 228 bp exon 53 bp [gt-ag] intron 26 GenBank accessions 154 bp exon 50 bp [gt-ag] intron 27 GenBank accessions 1 accession from l1 Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 84 accessions 333 bp exon 34 bp exon 73 bp [gt-ag] intron 1 GenBank accession 131 bp exon 2735 bp [gt-ag] intron 8 GenBank accessions 4906 bp exon 4906 bp exon 7 accessions Validated 3' end, 19 accessions 4906 bp exon 109 bp exon 63 bp [gt-ag] intron 1 GenBank accession 99 bp exon 99 bp exon 2803 bp [gt-ag] intron 1 GenBank accession 74 bp exon 4351 bp [gt-ag] intron 1 GenBank accession 3290 bp exon 3 accessions 3290 bp exon 222 bp exon 222 bp exon 90 bp [gt-ag] intron 1 GenBank accession 66 bp exon 1 accession 66 bp exon 74 bp exon 74 bp exon 74 bp exon 3020 bp [gt-ag] intron 1 GenBank accession 4621 bp exon 4621 bp exon 1 accession 4621 bp exon 74 bp exon 74 bp exon 1416 bp [gt-ag] intron 1 GenBank accession 245 bp exon 1 accession 245 bp exon 74 bp exon 74 bp exon 967 bp [gt-ag] intron 1 GenBank accession 694 bp exon 1 accession 694 bp exon 74 bp exon 74 bp exon 4037 bp [gt-ag] intron 1 GenBank accession 3604 bp exon 1 accession 3604 bp exon 74 bp exon 74 bp exon 9343 bp [gt-ag] intron 1 GenBank accession 178 bp exon 1 accession 178 bp exon 74 bp exon 74 bp exon 8446 bp [gt-ag] intron 1 GenBank accession 42 bp exon 1 accession 42 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 3426 bp 942 aa 158 bp 439 bp 2kb including Promoter 14667 bp 1kb
b 2754 bp 827 aa 270 bp 2kb 13266 bp 1kb
c 2866 bp 730 aa 210 bp 463 bp 2kb possibly including promoter 12736 bp 1kb
d 2324 bp 670 aa 158 bp 153 bp 2kb including Promoter 6256 bp 1kb
e 2707 bp 666 aa 112 bp 594 bp 2kb possibly including promoter 3904 bp 1kb
f 2261 bp 480 aa 816 bp 2kb 13181 bp 1kb
g 5071 bp 145 aa 282 bp 4351 bp 105 bp 2kb 7879 bp 1kb
h 3572 bp 44 aa 195 bp 3242 bp 2kb possibly including promoter 10789 bp 1kb
i 4695 bp 113 aa 4351 bp 2kb probably including promoter 7715 bp 1kb
j 355 bp 118 aa 2kb 948 bp 1kb
k 319 bp 102 aa 8 bp 2kb probably including promoter 1735 bp 1kb
l 288 bp 95 aa 2kb 378 bp 1kb
m 768 bp 91 aa 490 bp 2kb probably including promoter 1735 bp 1kb
n 3678 bp 83 aa 3424 bp 2kb probably including promoter 7715 bp 1kb
o 703 bp 56 aa 530 bp 2kb 758 bp 1kb
p 252 bp 40 aa 127 bp 2kb probably including promoter 9595 bp 1kb
q 116 bp 31 aa 6 bp 14 bp 2kb probably including promoter 8562 bp 1kb
r 77 bp 19 aa 15 bp 2kb 77 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1G905 D P bli-4 D C I R P 1G935 D C R P 1G937 C I R P 1G939 C R 1G943 C 1G945 C R P 1G924 D C I R P mut-2 5kb 0 1G905, 26 accessions, 2 variants bli-4, 117 accessions 18 variants 1G935, 32 accessions, 3 variants 1G937, 10 accessions, 3 variants 1G939, 21 accessions, 3 variants 1G943, 25 accessions, 2 variants 1G945, 30 accessions, 2 variants gld-2, 94 accessions, 10 variants 1G903, 3 accessions 1G924, 0 accession mut-2, 15 accessions, 4 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 11 articles in PubMed.
In addition we found 42 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q, .r Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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