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MSH5-SAPCD1 MSH5-SAPCD1 readthrough (NMD candidate) [ Homo sapiens (human) ]

Gene ID: 100532732, updated on 8-Nov-2023

Summary

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Official Symbol
MSH5-SAPCD1provided by HGNC
Official Full Name
MSH5-SAPCD1 readthrough (NMD candidate)provided by HGNC
Primary source
HGNC:HGNC:41994
See related
Ensembl:ENSG00000255152 AllianceGenome:HGNC:41994
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MSH5-C6orf26
Summary
This locus represents naturally occurring read-through transcription between the neighboring mutS homolog 5 (MSH5) and chromosome 6 open reading frame 26 (C6orf26) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
Expression
Broad expression in testis (RPKM 7.5), bone marrow (RPKM 7.3) and 24 other tissues See more
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Genomic context

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Location:
6p21.33
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31739948..31764850)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31592972..31617897)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31707725..31732627)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:31701615-31702814 Neighboring gene DDAH family member 2, ADMA-independent Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31704508-31705382 Neighboring gene chloride intracellular channel 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31707224-31707854 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31707855-31708486 Neighboring gene mutS homolog 5 Neighboring gene RNA, U6 small nuclear 850, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31731027-31731582 Neighboring gene SAPCD1 antisense RNA 1 Neighboring gene suppressor APC domain containing 1 Neighboring gene Sharpr-MPRA regulatory regions 3149 and 4553 Neighboring gene von Willebrand factor A domain containing 7 Neighboring gene valyl-tRNA synthetase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:31759127-31759287 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:31759783-31760982 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:31763127-31763981

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of multiple HTF-island associated genes in the human major histocompatibility complex class III region. Sargent CA, et al. EMBO J, 1989 Aug. PMID 2477242, Free PMC Article
  2. Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B). Albertella MR, et al. Genomics, 1996 Sep 1. PMID 8812450
  3. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), et al. Nat Genet, 2008 Feb. PMID 18204446, Free PMC Article
  4. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. Prakash T, et al. PLoS One, 2010 Oct 12. PMID 20967262, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Other Names

  • MSH5-C6orf26 readthrough (non-protein coding)
  • MSH5-SAPCD1 readthrough (non-protein coding)

Clone Names

  • DKFZp434C1615

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_037846.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AJ245661, AL662899
    Related
    ENST00000493662.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    31739948..31764850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    3090764..3097462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3217228..3242108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    2987714..3012624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    3044995..3052474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3081824..3106739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    2995767..3017449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    3039245..3064142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31592972..31617897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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