RETREG1 reticulophagy regulator 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RETREG1provided by HGNC
Official Full Name: reticulophagy regulator 1provided by HGNC
Primary source: HGNC:HGNC:25964
See related: Ensembl:ENSG00000154153 MIM:613114; Vega:OTTHUMG00000161788
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: JK1; JK-1; FAM134B
Summary: The protein encoded by this gene is a cis-Golgi transmembrane protein that may be necessary for the long-term survival of nociceptive and autonomic ganglion neurons. Mutations in this gene are a cause of hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), and this gene may also play a role in susceptibility to vascular dementia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
Expression: Broad expression in heart (RPKM 29.0), brain (RPKM 19.9) and 20 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 5p15.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	5	NC_000005.10 (16473038..16617096, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (16472922..16617167, complement)

Chromosome 5 - NC_000005.10 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 Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

FAM134B promoter methylation plays a key role in regulating FAM134B expression in vitro and in vivo, which in turn contributes to the prediction of the biological aggressiveness of colorectal adenocarcinomas.
Title: Promoter hypermethylation inactivate tumor suppressor FAM134B and is associated with poor prognosis in colorectal cancer.
These findings imply that mutation might be the major driving source of FAM134B genetic modulation in oesophageal squamous cell carcinoma.
Title: Identification of Novel FAM134B (JK1) Mutations in Oesophageal Squamous Cell Carcinoma.
NS3-mediated cleavage of FAM134B blocks the formation of endoplasmic reticulum and viral protein-enriched autophagosomes.
Title: Dengue and Zika viruses subvert reticulophagy by NS2B3-mediated cleavage of FAM134B.
miR-186-5p expression promotes colorectal cancer pathogenesis by regulating tumour suppressor FAM134B
Title: MicroRNA-186-5p overexpression modulates colon cancer growth by repressing the expression of the FAM134B tumour inhibitor.
FAM134B protein was noted in both cytoplasm and nuclei of colon cancer cells. In cancer cells derived from stage IV colon cancer, FAM134B expression was remarkably reduced when compared to non-cancer colon cells and cancer cells derived from stage II colon cancer. FAM134B knockdown significantly (P < 0.05) increased the proliferation of colon cancer cells following lentiviral transfection.
Title: Stage dependent expression and tumor suppressive function of FAM134B (JK1) in colon cancer.
FAM134B mutation is common in colorectal cancer. The association of the mutation of this gene with adverse clinical and pathological parameters is congruent with the tumour suppressive properties of the gene
Title: Novel FAM134B mutations and their clinicopathological significance in colorectal cancer.
selective endoplasmic reticulum (ER)-phagy via FAM134 proteins is indispensable for mammalian cell homeostasis and controls ER morphology and turnover in mice and humans
Title: Regulation of endoplasmic reticulum turnover by selective autophagy.
The changes in JK1 DNA copy number associated with progression of colorectal neoplasms.A decrease in JK-1 copy number was correlated with a shorter disease-free survival time.
Title: JK1 (FAM134B) gene and colorectal cancer: a pilot study on the gene copy number alterations and correlations with clinicopathological parameters.
FAM134B represses cell migration in colon cancer.FAM134B has functional role in the pathogenesis of colon cancer.
Title: JK1 (FAM134B) represses cell migration in colon cancer: a functional study of a novel gene.
Low FAM134B expression is associated with colorectal cancer.
Title: The roles of JK-1 (FAM134B) expressions in colorectal cancer.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

Associated conditions

Description	Tests
Hereditary sensory and autonomic neuropathy type IIA MedGen: C2752089 OMIM: 201300 GeneReviews: Hereditary Sensory and Autonomic Neuropathy Type II	Compare labs
Hereditary sensory and autonomic neuropathy type IIB MedGen: C2751092 OMIM: 613115 GeneReviews: Hereditary Sensory and Autonomic Neuropathy Type II	Compare labs

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

RH47732 (e-PCR)
- UniSTS:35905

D5S2685 (e-PCR)
- UniSTS:44107

SHGC-85175 (e-PCR)
- UniSTS:104021

D5S2532 (e-PCR)
- UniSTS:12380

STS-N47332 (e-PCR)
- UniSTS:21861

SHGC-77754 (e-PCR)
- UniSTS:95942

Homology

Homologs of the RETREG1 gene: The RETREG1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 248 organisms have orthologs with human gene RETREG1
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
reticulophagy	IMP Inferred from Mutant Phenotype more info	PubMed
sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
cis-Golgi network	ISS Inferred from Sequence or Structural Similarity more info
endoplasmic reticulum	IDA Inferred from Direct Assay more info
integral component of endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
nuclear body	IDA Inferred from Direct Assay more info
nucleolus	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: reticulophagy regulator 1

Names: family with sequence similarity 134 member B; protein FAM134B; reticulophagy receptor 1; reticulophagy receptor FAM134B

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_016644.2 RefSeqGene

Range

4952..148972

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_363

mRNA and Protein(s)

NM_001034850.2 → NP_001030022.1 reticulophagy regulator 1 isoform 1

See identical proteins and their annotated locations for NP_001030022.1

Status: REVIEWED

Description

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

Source sequence(s)

AI261750, AK025808, AL832438, BG722905, CR994722, DA136983

Consensus CDS

CCDS43304.1

UniProtKB/Swiss-Prot

Q9H6L5

Related

ENSP00000304642.9, OTTHUMP00000220738, ENST00000306320.9, OTTHUMT00000366090

Conserved Domains (2) summary

pfam02453
Location:85 → 233

Reticulon; Reticulon

cl21460
Location:323 → 415

HAD_like; Haloacid Dehalogenase-like Hydrolases
NM_019000.4 → NP_061873.2 reticulophagy regulator 1 isoform 2

See identical proteins and their annotated locations for NP_061873.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC022113, AI261750, AK024920, AL832438

Consensus CDS

CCDS43305.1

UniProtKB/Swiss-Prot

Q9H6L5

Related

ENSP00000382691.2, OTTHUMP00000220739, ENST00000399793.6, OTTHUMT00000366092

Conserved Domains (1) summary

cl21460
Location:182 → 274

HAD_like; Haloacid Dehalogenase-like Hydrolases

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...

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

Reference GRCh38.p12 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p12 Primary Assembly

Range

16473038..16617096 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514053.3 → XP_011512355.1 reticulophagy regulator 1 isoform X1
XM_011514055.3 → XP_011512357.1 reticulophagy regulator 1 isoform X3

Conserved Domains (1) summary

cl21460
Location:190 → 282

HAD_like; Haloacid Dehalogenase-like Hydrolases
XM_024446118.1 → XP_024301886.1 reticulophagy regulator 1 isoform X4

Conserved Domains (1) summary

cl21460
Location:148 → 240

HAD_like; Haloacid Dehalogenase-like Hydrolases
XM_011514054.2 → XP_011512356.1 reticulophagy regulator 1 isoform X2
XM_024446117.1 → XP_024301885.1 reticulophagy regulator 1 isoform X4

Conserved Domains (1) summary

cl21460
Location:148 → 240

HAD_like; Haloacid Dehalogenase-like Hydrolases