Caenorhabditis elegans essential gene him-1, encoding structural Maintenance of Chromosomes, High Incidence of Males.
SUMMARY back to top
[Wormbase] him-1 encodes a homolog of the conserved eukaryotic protein, SMC1, a member of the SMC (structural maintenance of chromosomes) superfamily that is required for embryonic viability, germline mitosis, chromosome pairing, and the segregation of mitotic chromosomes; HIM-1 can interact with SMC-3 and is required for DPY-28 localization to meiotic chromosomes; associates with the chromatin of transition-zone nuclei.
Wormbase predicts 2 models from 2 genes

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 4.0 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 4%, L1 or L2 larvae 45%, L3 to adult 51%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 35 cDNA clones and 18 elements defined by RNA-seq, some from l1 (seen 11 times), l2 (8), mixed (6), l4 (3), embryo (once). We annotate structural defects or features in 12 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 3 different mRNAs, 2 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL2, SL3, SL4, SL7, SL6, c to SL1. There are 2 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 3' end.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 16 abstracts. This essential gene is associated to a phenotype (High Incidence of Males, increased X chromosome loss, shared oogenic and spermatogenic protein copurified with chromatin). Proteins are expected to have molecular functions (ATP binding activity, protein binding activity) and to localize in chromosome.
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), some containing domains SMCs flexible hinge, RecF/RecN/SMC protein, N-terminal [Pfam], a coiled coil stretch [Psort2]. The remaining mRNA variant (unspliced; partial) appears not to encode a good protein.

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 him-1 maps on chomosome I at position -0.57 (interpolated). In AceView, it covers 6.12 kb, from 4957668 to 4951547 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known smc-1, in Wormgenes/AceView by its positional name 1F522, in Wormbase by its cosmid.number name F28B3.7, in NextDB, the Nematode expression pattern database, as CEYK2184.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes SMC1A, SMC1B.
The closest mouse gene, according to BlastP, is the AceView gene Smc1b (e=2 10-48).
The closest A.thaliana genes, according to BlastP, are the AceView genes TTN8andAT3G54680, SMC_N.0
          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 him-1 5' 3' encoded on minus strand of chromosome I from 4,957,668 to 4,951,547 a c b 1 2kb 0 229 bp exon 229 bp exon 49 bp [gt-ag] intron 11 GenBank accessions 582 bp exon 249 bp [gt-ag] intron 9 GenBank accessions 909 bp exon 52 bp [gt-ag] intron 7 GenBank accessions 350 bp exon 57 bp [gt-ag] intron 8 GenBank accessions 220 bp exon 187 bp [gt-ag] intron 7 GenBank accessions 282 bp exon 97 bp [gt-ag] intron 12 GenBank accessions 349 bp exon 135 bp [gt-ag] intron 6 GenBank accessions 122 bp exon 281 bp [gt-ag] intron 5 GenBank accessions 207 bp exon 697 bp [gt-ag] intron 18 GenBank accessions 324 bp exon 258 bp [gt-ag] intron 23 GenBank accessions 482 bp exon 51 accessions, some from l1 (seen 11 times) l2 (8), mixed (6), l4 (3) embryo (once) Transpliced 5' end, 10 accessions Validated 3' end, 94 accessions 482 bp exon 207 bp exon 207 bp exon 1 accession Transpliced 5' end, 1 accession 207 bp exon 343 bp exon 194 bp [gt-ag] intron 1 GenBank accession 62 bp exon 1 accession 62 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.
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
Downstream sequence
a 4056 bp 1262 aa 7 bp 260 bp 2kb including Promoter 6118 bp 1kb
b 405 bp 133 aa 3 bp 2kb 599 bp 1kb
c 207 bp 28 aa 122 bp 2kb including Promoter 207 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1F517 C R 1F529 C 1F531 C I P snf-1 1F507 C 1F518 C 1F520 D C P him-1 C I P app-1 C 1F536 5kb 0 acl-11, 16 accessions 3 variants 1F517, 64 accessions, 8 variants 1F529, 19 accessions, 3 variants 1F531, 7 accessions snf-1, 25 accessions, 2 variants 1F507, 0 accession 1F539, 2 accessions 1F526, 6 accessions, 2 variants 1F518, 36 accessions, 4 variants 1F520, 0 accession him-1, 53 accessions, 3 variants app-1, 101 accessions 3 variants 1F536, 7 accessions 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 5 articles in PubMed.
In addition we found 16 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c 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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