SURF6 surfeit 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SURF6provided by HGNC
Official Full Name: surfeit 6provided by HGNC
Primary source: HGNC:HGNC:11478
See related: Ensembl:ENSG00000148296 MIM:185642; AllianceGenome:HGNC:11478
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RRP14
Summary: This gene encodes a conserved protein that is localized to the nucleolus. The encoded protein may function as a nucleolar-matrix protein with nucleic acid-binding properties. There is a pseudogene for this gene on chromosome Y. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in colon (RPKM 12.0), ovary (RPKM 11.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (133328776..133336188, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (145542703..145550115, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (136195612..136203025, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human nucleolar protein SURF6/RRP14 participates in early steps of pre-rRNA processing.
Title: Human nucleolar protein SURF6/RRP14 participates in early steps of pre-rRNA processing.
A Higher Level of Expression of the Nucleolar Protein SURF6 in Human Normal Activated Lymphocytes and in Lymphocytes of Patients with Lymphoproliferative Disorders.
Title: A Higher Level of Expression of the Nucleolar Protein SURF6 in Human Normal Activated Lymphocytes and in Lymphocytes of Patients with Lymphoproliferative Disorders.
NPM1 and SURF6 form heterotypic liquid-like droplets in the nucleolus.
Title: Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation.
we identified a consistently replicated loci at 9q34.2 (rs633862 near ABO and SURF6, P(meta) = 8.57 x 10(-7)) (P<0.05 in all three stages)
Title: Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women.
the panel of the GST-Surf6-dom protein partners, which were identified by mass-spectrometry, points to putative interactions of human SURF6 with a number of nuclear and nucleolar proteins of other functional groups
Title: [Identification of the protein partners of the human nucleolar protein SURF6 in HeLa cells by GST pull-down assay].

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study on serum alkaline phosphatase levels in a Chinese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Linkage analysis identifies a locus for plasma von Willebrand factor undetected by genome-wide association. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11910 (e-PCR)
- UniSTS:76637

RH48554 (e-PCR)
- UniSTS:47338

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables molecular condensate scaffold activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ribosomal large subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal small subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IDA Inferred from Direct Assay more info
located_in granular component	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: surfeit locus protein 6

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.

mRNA and Protein(s)

NM_001278942.2 → NP_001265871.1 surfeit locus protein 6 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses alternate splice sites at two coding exons, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL772161, BC003001, BI820270, CB158198, CD104374

UniProtKB/Swiss-Prot

O75683
NM_006753.6 → NP_006744.2 surfeit locus protein 6 isoform 1

See identical proteins and their annotated locations for NP_006744.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AL772161, BC003001, CB158198, CD104374

Consensus CDS

CCDS6962.1

UniProtKB/Swiss-Prot

O75683, Q5T8U1, Q9BRK9, Q9BTZ5, Q9UK24

UniProtKB/TrEMBL

B3KNS8

Related

ENSP00000361092.4, ENST00000372022.6

Conserved Domains (1) summary

pfam04935
Location:197 → 318

SURF6; Surfeit locus protein 6

RNA

NR_103874.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site at an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL772161, BC003001, CB158198, CD104374, CN260811