SLC49A4 solute carrier family 49 member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC49A4provided by HGNC
Official Full Name: solute carrier family 49 member 4provided by HGNC
Primary source: HGNC:HGNC:16628
See related: Ensembl:ENSG00000138463 MIM:602773; AllianceGenome:HGNC:16628
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: RCC4; DIRC2
Summary: This gene encodes a membrane-bound protein from the major facilitator superfamily of transporters. Disruption of this gene by translocation has been associated with haplo-insufficiency and renal cell carcinomas. Alternatively spliced transcript variants have been described, but their biological validity has not yet been determined. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in skin (RPKM 3.9), placenta (RPKM 3.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q21.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (122795069..122881139)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (125514258..125600338)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (122513916..122599986)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Disrupted in renal carcinoma 2 (DIRC2/SLC49A4) is an H[+]-driven lysosomal pyridoxine exporter.
Title: Disrupted in renal carcinoma 2 (DIRC2/SLC49A4) is an H(+)-driven lysosomal pyridoxine exporter.
Data strongly support the idea that DIRC2 is an electrogenic lysosomal metabolite transporter which is subjected to and presumably modulated by limited proteolytic processing.
Title: Disrupted in renal carcinoma 2 (DIRC2), a novel transporter of the lysosomal membrane, is proteolytically processed by cathepsin L.
Gene disruption may result in haplo-insufficiency and, through this mechanism, in the onset of tumor growth.
Title: Disruption of a novel MFS transporter gene, DIRC2, by a familial renal cell carcinoma-associated t(2;3)(q35;q21).

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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

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

DIRC2__4741 (e-PCR)
- UniSTS:462868

D3S2898E (e-PCR)
- UniSTS:150886

STS-N25987 (e-PCR)
- UniSTS:72577

D3S4220 (e-PCR)
- UniSTS:27023

RH12232 (e-PCR)
- UniSTS:9882

G16567 (e-PCR)
- UniSTS:76003

WI-20374 (e-PCR)
- UniSTS:73464

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables transmembrane transporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in pyridoxine transport	IDA Inferred from Direct Assay more info	PubMed
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: solute carrier family 49 member 4

Names: disrupted in renal cancer protein 2; disrupted in renal carcinoma 2; renal cell carcinoma 4

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.

Genomic

NG_023324.2 RefSeqGene

Range

5002..91072

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_032839.3 → NP_116228.1 solute carrier family 49 member 4

See identical proteins and their annotated locations for NP_116228.1

Status: REVIEWED

Source sequence(s)

AC048348, AC078794

Consensus CDS

CCDS3018.1

UniProtKB/Swiss-Prot

A8K561, Q8NBX9, Q96SL1

Related

ENSP00000261038.5, ENST00000261038.6

Conserved Domains (2) summary

cd06174
Location:66 → 449

MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

pfam07690
Location:69 → 425

MFS_1; Major Facilitator Superfamily