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SNHG28 small nucleolar RNA host gene 28 [ Homo sapiens (human) ]

Gene ID: 284677, updated on 10-Oct-2023

Summary

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Official Symbol
SNHG28provided by HGNC
Official Full Name
small nucleolar RNA host gene 28provided by HGNC
Primary source
HGNC:HGNC:27647
See related
Ensembl:ENSG00000188004 AllianceGenome:HGNC:27647
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
C1orf204; VSIG8-OT1
Summary
Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in appendix (RPKM 8.6), lymph node (RPKM 7.4) and 23 other tissues See more
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Genomic context

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Location:
1q23.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159834478..159855037, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (158971473..158992042, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (159804268..159824827, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:159751068-159751644 Neighboring gene CRISPRi-validated cis-regulatory element chr1.9322 Neighboring gene dual specificity phosphatase 23 Neighboring gene Sharpr-MPRA regulatory region 9392 Neighboring gene uncharacterized LOC105371464 Neighboring gene Fc receptor like 6 Neighboring gene SLAM family member 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159815652-159816152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159816153-159816653 Neighboring gene small nucleolar RNA SNORD64 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1455 Neighboring gene uncharacterized LOC107985216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159830948-159831862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159831863-159832775 Neighboring gene V-set and immunoglobulin domain containing 8 Neighboring gene Sharpr-MPRA regulatory region 5062 Neighboring gene cilia and flagella associated protein 45 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:159859176-159860375 Neighboring gene uncharacterized LOC124904434 Neighboring gene microRNA 4259

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. Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. Mero IL, et al. PLoS One, 2013. PMID 23472185, Free PMC Article
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Hillier LW, et al. Nature, 2005 Apr 7. PMID 15815621
  3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

See all (6) citations in PubMed

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
Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
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

  • VSIG8 overlapping transcript 1

Clone Names

  • FLJ20442, FLJ39187

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 

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_147122.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL080176, AL590560, DA364631
    Related
    ENST00000676197.1

  2. NR_147123.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL080176, AL590560, DA288133

  3. NR_147124.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL080176, AL590560, BI753917
    Related
    ENST00000491974.2

  4. NR_147125.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL080176, AL537381, AL590560
    Related
    ENST00000674760.1

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    159834478..159855037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    158971473..158992042 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001134233.1: Suppressed sequence

    Description
    NM_001134233.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0DPA3.1 GenPept UniProtKB/Swiss-Prot:P0DPA3

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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