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Aliases for RETREG1 Gene

Aliases for RETREG1 Gene

  • Reticulophagy Regulator 1 2 3
  • Family With Sequence Similarity 134 Member B 2 3 5
  • FAM134B 3 4 5
  • Family With Sequence Similarity 134, Member B 2
  • Reticulophagy Receptor FAM134B 3
  • Protein FAM134B 3
  • JK-1 3
  • JK1 3

External Ids for RETREG1 Gene

Previous HGNC Symbols for RETREG1 Gene

  • FAM134B

Summaries for RETREG1 Gene

Entrez Gene Summary for RETREG1 Gene

  • 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]

GeneCards Summary for RETREG1 Gene

RETREG1 (Reticulophagy Regulator 1) is a Protein Coding gene. Diseases associated with RETREG1 include Neuropathy, Hereditary Sensory And Autonomic, Type Iib and Neuropathy, Hereditary Sensory And Autonomic, Type Ii. An important paralog of this gene is RETREG3.

UniProtKB/Swiss-Prot for RETREG1 Gene

  • Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RETREG1 Gene

Genomics for RETREG1 Gene

Regulatory Elements for RETREG1 Gene

Enhancers for RETREG1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G016537 1.6 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +77.7 77674 4.0 TBP RAD21 RFX5 YY1 RCOR1 FOS CEBPB NR2F2 MAFF SMARCA4 RETREG1 ZNF622 ENSG00000250415 LOC101929524
GH05G016505 1.4 Ensembl ENCODE dbSUPER 16.3 +108.8 108781 4.6 KLF17 RAD21 RFX5 YY1 ZNF335 RCOR1 ELK4 SMARCC1 NFYA USF2 RETREG1 ZNF622 LOC101929524
GH05G016519 1.1 ENCODE dbSUPER 15.4 +95.8 95825 4.0 HDAC1 SOX13 PKNOX1 TAF1 ETV1 TAL1 MAX CEBPG ZNF644 RAD21 RETREG1 ZNF622 LOC101929524
GH05G016563 0.7 dbSUPER 23.2 +48.5 48455 9.4 PKNOX1 NFIB SIN3A ZNF266 MNT REST ZIC2 ATF2 SREBF1 ZNF121 RETREG1 ENSG00000250415 ZNF622 LOC101929524
GH05G016564 0.7 dbSUPER 23.2 +48.5 48497 9.7 PKNOX1 NFIB SIN3A ZNF266 ZIC2 ZNF121 CTBP1 GATA3 SCRT2 FOS RETREG1 ENSG00000250415 ZNF622 LOC101929524
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RETREG1 on UCSC Golden Path with GeneCards custom track

Promoters for RETREG1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000178576 58 801 ZNF473 SIN3A ZEB1 ZNF335 ZNF121 GLIS2 KLF7 ZNF263 SP3 HCFC1

Genomic Location for RETREG1 Gene

Chromosome:
5
Start:
16,472,816 bp from pter
End:
16,617,058 bp from pter
Size:
144,243 bases
Orientation:
Minus strand

Genomic View for RETREG1 Gene

Genes around RETREG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RETREG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RETREG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RETREG1 Gene

Proteins for RETREG1 Gene

  • Protein details for RETREG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H6L5-F134B_HUMAN
    Recommended name:
    Reticulophagy receptor FAM134B
    Protein Accession:
    Q9H6L5
    Secondary Accessions:
    • Q69YN8
    • Q9H6K6
    • Q9H764
    • Q9NXM8

    Protein attributes for RETREG1 Gene

    Size:
    497 amino acids
    Molecular mass:
    54681 Da
    Quaternary structure:
    • Interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2.
    SequenceCaution:
    • Sequence=AAH30517.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA90982.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15252.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RETREG1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RETREG1 Gene

Post-translational modifications for RETREG1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RETREG1 Gene

No data available for DME Specific Peptides for RETREG1 Gene

Domains & Families for RETREG1 Gene

Protein Domains for RETREG1 Gene

Suggested Antigen Peptide Sequences for RETREG1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H6L5

UniProtKB/Swiss-Prot:

F134B_HUMAN :
  • The LIR motif interacts with ATG8 family proteins and is necessary to target the ER fragments to autophagosomes for subsequent lysosomal degradation.
  • Belongs to the FAM134 family.
Domain:
  • The LIR motif interacts with ATG8 family proteins and is necessary to target the ER fragments to autophagosomes for subsequent lysosomal degradation.
  • The reticulon homology domain provides capacity to bend the membrane and promotes ER scission (PubMed:26040720). This domain does not show relevant similarities with reticulon domains, preventing any domain predictions within the protein sequence.
Family:
  • Belongs to the FAM134 family.
genes like me logo Genes that share domains with RETREG1: view

No data available for Gene Families for RETREG1 Gene

Function for RETREG1 Gene

Molecular function for RETREG1 Gene

UniProtKB/Swiss-Prot Function:
Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).

Gene Ontology (GO) - Molecular Function for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 26040720
genes like me logo Genes that share ontologies with RETREG1: view
genes like me logo Genes that share phenotypes with RETREG1: view

Human Phenotype Ontology for RETREG1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RETREG1 Gene

MGI Knock Outs for RETREG1:

Animal Model Products

miRNA for RETREG1 Gene

miRTarBase miRNAs that target RETREG1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RETREG1 Gene

Localization for RETREG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RETREG1 Gene

Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein. Endoplasmic reticulum 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 RETREG1 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
plasma membrane 3
golgi apparatus 3
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005801 cis-Golgi network IEA,ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RETREG1: view

Pathways & Interactions for RETREG1 Gene

SuperPathways for RETREG1 Gene

No Data Available

Interacting Proteins for RETREG1 Gene

Gene Ontology (GO) - Biological Process for RETREG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0019233 sensory perception of pain IMP 19838196
GO:0043524 negative regulation of neuron apoptotic process IMP 26040720
GO:0061709 reticulophagy IMP 26040720
genes like me logo Genes that share ontologies with RETREG1: view

No data available for Pathways by source and SIGNOR curated interactions for RETREG1 Gene

Transcripts for RETREG1 Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RETREG1 Gene

No ASD Table

Relevant External Links for RETREG1 Gene

GeneLoc Exon Structure for
RETREG1
ECgene alternative splicing isoforms for
RETREG1

Expression for RETREG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RETREG1 Gene:

RETREG1

Evidence on tissue expression from TISSUES for RETREG1 Gene

  • Intestine(4.3)
  • Lung(4.2)
  • Nervous system(3.8)
  • Kidney(2.6)
  • Muscle(2.3)
  • Heart(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RETREG1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • olfactory bulb
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • esophagus
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • stomach
Pelvis:
  • pelvis
  • prostate
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • bone marrow
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with RETREG1: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for RETREG1 Gene

Orthologs for RETREG1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RETREG1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FAM134B 35 34
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FAM134B 35 34
  • 91.52 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FAM134B 35 34
  • 90.17 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Fam134b 34
  • 87.92 (n)
mouse
(Mus musculus)
Mammalia Fam134b 34 16 35
  • 86.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia FAM134B 35
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FAM134B 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100859798 34
  • 75.8 (n)
FAM134B 35
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia FAM134B 35
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia fam134b 34
  • 66.67 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100003524 34
  • 57.61 (n)
BX323064.1 35
  • 41 (a)
OneToOne
Species where no ortholog for RETREG1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 squirt (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 RETREG1 Gene

ENSEMBL:
Gene Tree for RETREG1 (if available)
TreeFam:
Gene Tree for RETREG1 (if available)

Paralogs for RETREG1 Gene

Paralogs for RETREG1 Gene

genes like me logo Genes that share paralogs with RETREG1: view

Variants for RETREG1 Gene

Sequence variations from dbSNP and Humsavar for RETREG1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs137852736 Pathogenic 16,616,953(-) GCGCC(-/TC)CGGAG intron-variant, reference, frameshift-variant
rs137852737 Pathogenic 16,565,788(-) GTGCA(C/T)AGTTG reference, stop-gained
rs137852738 Pathogenic 16,478,032(-) TAAGG(C/T)ATTTT splice-donor-variant
rs137852739 Pathogenic 16,477,736(-) CGTCT(C/G/T)AGAGG reference, missense, stop-gained
rs886037748 Pathogenic 16,478,081(-) AAAAA(-/A)GTCAC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for RETREG1 Gene

Variant ID Type Subtype PubMed ID
dgv935e201 CNV deletion 23290073
esv1003044 CNV insertion 20482838
esv1371607 CNV insertion 17803354
esv1983383 CNV deletion 18987734
esv2664300 CNV deletion 23128226
esv2670384 CNV deletion 23128226
esv2729832 CNV deletion 23290073
esv2729834 CNV deletion 23290073
esv2729835 CNV deletion 23290073
esv2729836 CNV deletion 23290073
esv275370 CNV loss 21479260
esv3565578 CNV deletion 23714750
esv3604132 CNV gain 21293372
esv3604133 CNV loss 21293372
esv3604134 CNV loss 21293372
nsv1073442 CNV deletion 25765185
nsv1073443 CNV deletion 25765185
nsv1114653 CNV deletion 24896259
nsv1114654 CNV deletion 24896259
nsv1142630 CNV deletion 24896259
nsv1144103 CNV deletion 24896259
nsv1152313 CNV insertion 26484159
nsv476191 CNV novel sequence insertion 20440878

Variation tolerance for RETREG1 Gene

Residual Variation Intolerance Score: 40.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RETREG1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RETREG1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RETREG1 Gene

Disorders for RETREG1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RETREG1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory and autonomic, type iib
  • hereditary sensory and autonomic neuropathy type iib
neuropathy, hereditary sensory and autonomic, type ii
  • neuropathy, hereditary sensory and autonomic, type iib
autonomic neuropathy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

F134B_HUMAN
  • Neuropathy, hereditary sensory and autonomic, 2B (HSAN2B) [MIM:613115]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN2B is an autosomal recessive disorder characterized by impairment of pain, temperature and touch sensation. Onset occurs in the first or second decade, with impaired nociception and progressive mutilating ulceration of the hands and feet with osteomyelitis and acroosteolysis. Amputations of the hands and feet are common. Autonomic dysfunction includes hyperhidrosis, urinary incontinence, and slow pupillary light response. {ECO:0000269 PubMed:19838196}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RETREG1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RETREG1
genes like me logo Genes that share disorders with RETREG1: view

No data available for Genatlas for RETREG1 Gene

Publications for RETREG1 Gene

  1. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. (PMID: 19838196) Kurth I. … Huebner C.A. (Nat. Genet. 2009) 2 3 4 64
  2. Regulation of endoplasmic reticulum turnover by selective autophagy. (PMID: 26040720) Khaminets A. … Dikic I. (Nature 2015) 3 4 64
  3. Mutation in FAM134B causing hereditary sensory neuropathy with spasticity in a Turkish family. (PMID: 24327336) Aydinlar E.I. … Parman Y. (Muscle Nerve 2013) 2 3 64
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  5. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta G.D. … Pelletier L. (Cell 2015) 3 64

Products for RETREG1 Gene

Sources for RETREG1 Gene

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