Aliases for RETREG3 Gene

Aliases for RETREG3 Gene

  • Reticulophagy Regulator Family Member 3 2 3 5
  • Family With Sequence Similarity 134 Member C 2 3
  • Reticulophagy Regulator 3 3 4
  • FAM134C 3 4
  • Family With Sequence Similarity 134, Member C 2
  • Protein FAM134C 3
  • DKFZp686B1036 2
  • FLJ33806 2
  • RETREG3 5

External Ids for RETREG3 Gene

Previous HGNC Symbols for RETREG3 Gene

  • FAM134C

Summaries for RETREG3 Gene

GeneCards Summary for RETREG3 Gene

RETREG3 (Reticulophagy Regulator Family Member 3) is a Protein Coding gene. Diseases associated with RETREG3 include Neuropathy, Hereditary Sensory And Autonomic, Type Iib and Neuropathy, Hereditary Sensory And Autonomic, Type Iia.

UniProtKB/Swiss-Prot Summary for RETREG3 Gene

Gene Wiki entry for RETREG3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RETREG3 Gene

Genomics for RETREG3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RETREG3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RETREG3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RETREG3

Genomic Locations for RETREG3 Gene

Latest Assembly
chr17:42,579,508-42,610,623
(GRCh38/hg38)
Size:
31,116 bases
Orientation:
Minus strand

Previous Assembly
chr17:40,731,526-40,761,445
(GRCh37/hg19 by Entrez Gene)
Size:
29,920 bases
Orientation:
Minus strand

chr17:40,731,531-40,762,641
(GRCh37/hg19 by Ensembl)
Size:
31,111 bases
Orientation:
Minus strand

Genomic View for RETREG3 Gene

Genes around RETREG3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RETREG3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RETREG3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RETREG3 Gene

Proteins for RETREG3 Gene

  • Protein details for RETREG3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86VR2-RETR3_HUMAN
    Recommended name:
    Reticulophagy regulator 3
    Protein Accession:
    Q86VR2
    Secondary Accessions:
    • B3KR75

    Protein attributes for RETREG3 Gene

    Size:
    466 amino acids
    Molecular mass:
    51396 Da
    Quaternary structure:
    • Interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1.

    Alternative splice isoforms for RETREG3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RETREG3 Gene

Post-translational modifications for RETREG3 Gene

  • Ubiquitination at Lys115
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RETREG3 Gene

Domains & Families for RETREG3 Gene

Gene Families for RETREG3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for RETREG3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RETREG3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60504 (B3KR75_HUMAN)
  • Protein FAM134C (F134C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86VR2

UniProtKB/Swiss-Prot:

RETR3_HUMAN :
  • The LIR motif interacts with ATG8 family proteins.
  • Belongs to the RETREG family.
Domain:
  • The LIR motif interacts with ATG8 family proteins.
Family:
  • Belongs to the RETREG family.
genes like me logo Genes that share domains with RETREG3: view

Function for RETREG3 Gene

Molecular function for RETREG3 Gene

UniProtKB/Swiss-Prot Function:
Mediates NRF1-enhanced neurite outgrowth.

Phenotypes From GWAS Catalog for RETREG3 Gene

Gene Ontology (GO) - Molecular Function for RETREG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with RETREG3: view
genes like me logo Genes that share phenotypes with RETREG3: view

Animal Models for RETREG3 Gene

MGI Knock Outs for RETREG3:

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RETREG3 Gene

Localization for RETREG3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RETREG3 Gene

Membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RETREG3 gene
Compartment Confidence
plasma membrane 3
nucleus 2
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear membrane (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RETREG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0032991 protein-containing complex IDA 28246125
genes like me logo Genes that share ontologies with RETREG3: view

Pathways & Interactions for RETREG3 Gene

PathCards logo

SuperPathways for RETREG3 Gene

No Data Available

SIGNOR curated interactions for RETREG3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RETREG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010976 positive regulation of neuron projection development IEA,IMP 23939472
GO:0061709 reticulophagy IEA --
genes like me logo Genes that share ontologies with RETREG3: view

No data available for Pathways by source for RETREG3 Gene

Drugs & Compounds for RETREG3 Gene

No Compound Related Data Available

Transcripts for RETREG3 Gene

mRNA/cDNA for RETREG3 Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for RETREG3 Gene

No ASD Table

Relevant External Links for RETREG3 Gene

GeneLoc Exon Structure for
RETREG3

Expression for RETREG3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RETREG3

Evidence on tissue expression from TISSUES for RETREG3 Gene

  • Nervous system(4.9)
  • Liver(4.3)
No Expression Related Data Available

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RETREG3 Gene

Orthologs for RETREG3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RETREG3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia FAM134C 30 31
  • 99.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia FAM134C 30 31
  • 92.27 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia FAM134C 30 31
  • 91.13 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Fam134c 30
  • 90.49 (n)
Mouse
(Mus musculus)
Mammalia Fam134c 30 31
  • 90.34 (n)
OneToOne
Retreg3 17
Oppossum
(Monodelphis domestica)
Mammalia FAM134C 31
  • 76 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia FAM134C 31
  • 61 (a)
OneToOne
Chicken
(Gallus gallus)
Aves FAM134C 30 31
  • 70.34 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia FAM134C 31
  • 62 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia fam134c 30
  • 66.04 (n)
Str.6330 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.30959 30
Zebrafish
(Danio rerio)
Actinopterygii fam134c 30 31
  • 61.19 (n)
OneToOne
Species where no ortholog for RETREG3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RETREG3 Gene

ENSEMBL:
Gene Tree for RETREG3 (if available)
TreeFam:
Gene Tree for RETREG3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RETREG3: view image

Paralogs for RETREG3 Gene

No data available for Paralogs for RETREG3 Gene

Variants for RETREG3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RETREG3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs148592159 Benign: not provided 42,609,335(-) C/A
NM_178126.4(RETREG3):c.-11G>T
NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RETREG3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RETREG3 Gene

Variant ID Type Subtype PubMed ID
esv33998 OTHER inversion 15654335
nsv1064012 CNV gain 25217958
nsv1113874 CNV deletion 24896259
nsv1146669 OTHER inversion 26484159

Variation tolerance for RETREG3 Gene

Residual Variation Intolerance Score: 27% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.29; 40.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RETREG3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RETREG3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RETREG3 Gene

Disorders for RETREG3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RETREG3 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RETREG3

genes like me logo Genes that share disorders with RETREG3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RETREG3 Gene

Publications for RETREG3 Gene

  1. Regulation of endoplasmic reticulum turnover by selective autophagy. (PMID: 26040720) Khaminets A … Dikic I (Nature 2015) 3 4
  2. Novel genes FAM134C, C3orf10 and ENOX1 are regulated by NRF-1 and differentially regulate neurite outgrowth in neuroblastoma cells and hippocampal neurons. (PMID: 23939472) Wang JL … Huang AM (Gene 2013) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3

Products for RETREG3 Gene

Sources for RETREG3 Gene