RNF13 ring finger protein 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF13provided by HGNC
Official Full Name: ring finger protein 13provided by HGNC
Primary source: HGNC:HGNC:10057
See related: Ensembl:ENSG00000082996 MIM:609247; AllianceGenome:HGNC:10057
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: RZF; DEE73; EIEE73
Summary: The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 22.1), brain (RPKM 22.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q25.1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (149812688..149962139)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (152563773..152713514)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (149530475..149679926)

Chromosome 3 - NC_000003.12 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?

E3 Ubiquitin Ligase RNF13 Suppresses TLR Lysosomal Degradation by Promoting LAMP-1 Proteasomal Degradation.
Title: E3 Ubiquitin Ligase RNF13 Suppresses TLR Lysosomal Degradation by Promoting LAMP-1 Proteasomal Degradation.
Heterozygous gain of function variants in a critical region of RNF13 cause congenital microcephaly, epileptic encephalopathy, blindness, and failure to thrive.
Title: Heterozygous gain of function variants in a critical region of RNF13 cause congenital microcephaly, epileptic encephalopathy, blindness, and failure to thrive.
MiR-32-3p Regulates Myocardial Injury Induced by Microembolism and Microvascular Obstruction by Targeting RNF13 to Regulate the Stability of Atherosclerotic Plaques.
Title: MiR-32-3p Regulates Myocardial Injury Induced by Microembolism and Microvascular Obstruction by Targeting RNF13 to Regulate the Stability of Atherosclerotic Plaques.
Circular RNA circRNF13 inhibits proliferation and metastasis of nasopharyngeal carcinoma via SUMO2.
Title: Circular RNA circRNF13 inhibits proliferation and metastasis of nasopharyngeal carcinoma via SUMO2.
RNF13 Dileucine Motif Variants L311S and L312P Interfere with Endosomal Localization and AP-3 Complex Association.
Title: RNF13 Dileucine Motif Variants L311S and L312P Interfere with Endosomal Localization and AP-3 Complex Association.
The Regulation of circRNA RNF13/miRNA-1224-5p Axis Promotes the Malignant Evolution in Acute Myeloid Leukemia.
Title: The Regulation of circRNA RNF13/miRNA-1224-5p Axis Promotes the Malignant Evolution in Acute Myeloid Leukemia.
results indicate that the RNF13 variants confer gain of function to the encoded protein and thereby lead to altered signaling of the ER stress response associated with severe neurodegeneration in infancy
Title: Heterozygous RNF13 Gain-of-Function Variants Are Associated with Congenital Microcephaly, Epileptic Encephalopathy, Blindness, and Failure to Thrive.
Protease-activated point mutations are identified in RNF13 and RNF167.
Title: Tumour-associated mutations of PA-TM-RING ubiquitin ligases RNF167/RNF13 identify the PA domain as a determinant for endosomal localization.
RNF13 is a critical mediator for facilitating endoplasmic reticulum stress-induced apoptosis through the activation of the IRE1alpha-TRAF2-JNK signaling pathway.
Title: RNF13, a RING finger protein, mediates endoplasmic reticulum stress-induced apoptosis through the inositol-requiring enzyme (IRE1α)/c-Jun NH2-terminal kinase pathway.
analysis of nuclear targeting of Nuclear targeting of RNF13 endosomal E3 ubiquitin ligase
Title: Nuclear targeting of an endosomal E3 ubiquitin ligase.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Developmental and epileptic encephalopathy, 73 MedGen: C5193065 OMIM: 618379 GeneReviews: Not available	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

SHGC-77433 (e-PCR)
- UniSTS:10772

A008P47 (e-PCR)
- UniSTS:6988

RH25558 (e-PCR)
- UniSTS:90203

A004H09 (e-PCR)
- UniSTS:44127

RNF13_723 (e-PCR)
- UniSTS:277680

SHGC-37453 (e-PCR)
- UniSTS:39913

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables JUN kinase binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in organelle localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of JNK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein autoubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	HDA more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear inner membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF13

Names: RING zinc finger protein; RING-type E3 ubiquitin transferase RNF13

NP_001365214.1

EC 2.3.2.27

NP_001365215.1

EC 2.3.2.27

NP_001365216.1

EC 2.3.2.27

NP_001365217.1

EC 2.3.2.27

NP_001365218.1

EC 2.3.2.27

NP_001365219.1

EC 2.3.2.27

NP_001365220.1

EC 2.3.2.27

NP_009213.1

EC 2.3.2.27

NP_899237.1

EC 2.3.2.27

NP_899239.2

EC 2.3.2.27

XP_011510675.1

EC 2.3.2.27

XP_016861150.1

EC 2.3.2.27

XP_047303335.1

EC 2.3.2.27

XP_047303336.1

EC 2.3.2.27

XP_047303337.1

EC 2.3.2.27

XP_047303338.1

EC 2.3.2.27

XP_054201085.1

EC 2.3.2.27

XP_054201086.1

EC 2.3.2.27

XP_054201087.1

EC 2.3.2.27

XP_054201088.1

EC 2.3.2.27

XP_054201089.1

EC 2.3.2.27

XP_054201090.1

EC 2.3.2.27

XP_054201091.1

EC 2.3.2.27

XP_054201092.1

EC 2.3.2.27

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_001378285.1 → NP_001365214.1 E3 ubiquitin-protein ligase RNF13 isoform 1 precursor

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS3146.1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9

Conserved Domains (2) summary

cd02123
Location:23 → 180

PA_C_RZF_like; PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo ...

cd16797
Location:238 → 283

RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
NM_001378286.1 → NP_001365215.1 E3 ubiquitin-protein ligase RNF13 isoform 1 precursor

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS3146.1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9

Conserved Domains (2) summary

cd02123
Location:23 → 180

PA_C_RZF_like; PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo ...

cd16797
Location:238 → 283

RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
NM_001378287.1 → NP_001365216.1 E3 ubiquitin-protein ligase RNF13 isoform 3

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS87154.1

UniProtKB/TrEMBL

C9IY58

Conserved Domains (3) summary

cd00162
Location:121 → 162

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

cl28883
Location:21 → 61

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:119 → 164

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001378288.1 → NP_001365217.1 E3 ubiquitin-protein ligase RNF13 isoform 3

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS87154.1

UniProtKB/TrEMBL

C9IY58

Conserved Domains (3) summary

cd00162
Location:121 → 162

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

cl28883
Location:21 → 61

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:119 → 164

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001378289.1 → NP_001365218.1 E3 ubiquitin-protein ligase RNF13 isoform 3

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS87154.1

UniProtKB/TrEMBL

C9IY58

Conserved Domains (3) summary

cd00162
Location:121 → 162

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

cl28883
Location:21 → 61

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:119 → 164

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001378290.1 → NP_001365219.1 E3 ubiquitin-protein ligase RNF13 isoform 3

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

Consensus CDS

CCDS87154.1

UniProtKB/TrEMBL

C9IY58

Related

ENSP00000355268.6, ENST00000361785.10

Conserved Domains (3) summary

cd00162
Location:121 → 162

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

cl28883
Location:21 → 61

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:119 → 164

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_001378291.1 → NP_001365220.1 E3 ubiquitin-protein ligase RNF13 isoform 4

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

UniProtKB/TrEMBL

C9IY58

Conserved Domains (2) summary

cl28883
Location:1 → 49

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:107 → 152

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_007282.4 → NP_009213.1 E3 ubiquitin-protein ligase RNF13 isoform 1 precursor

See identical proteins and their annotated locations for NP_009213.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 4 encode the same protein.

Source sequence(s)

AC117395, BC009803, CB109037, DA031838

Consensus CDS

CCDS3146.1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9

Related

ENSP00000341361.3, ENST00000344229.7

Conserved Domains (2) summary

cd02123
Location:23 → 180

PA_C_RZF_like; PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo ...

cd16797
Location:238 → 283

RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
NM_183381.3 → NP_899237.1 E3 ubiquitin-protein ligase RNF13 isoform 1 precursor

See identical proteins and their annotated locations for NP_899237.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an exon in the 5' UTR compared to variant 1. Both variants 1 and 4 encode the same protein.

Source sequence(s)

AC117395, AK090638

Consensus CDS

CCDS3146.1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9

Related

ENSP00000376628.3, ENST00000392894.8

Conserved Domains (2) summary

cd02123
Location:23 → 180

PA_C_RZF_like; PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo ...

cd16797
Location:238 → 283

RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
NM_183383.2 → NP_899239.2 E3 ubiquitin-protein ligase RNF13 isoform 3

Status: REVIEWED

Source sequence(s)

AC117395, AK090638, AK090771, CB109037, DA031838

Consensus CDS

CCDS87154.1

UniProtKB/TrEMBL

C9IY58

Related

ENSP00000420667.1, ENST00000491086.5

Conserved Domains (3) summary

cd00162
Location:121 → 162

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

cl28883
Location:21 → 61

PA; Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At ...

cl17238
Location:119 → 164

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RNA

NR_165474.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC069216, AC117395

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

149812688..149962139

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047447380.1 → XP_047303336.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_011512373.3 → XP_011510675.1 E3 ubiquitin-protein ligase RNF13 isoform X1

See identical proteins and their annotated locations for XP_011510675.1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9

Conserved Domains (2) summary

cd02123
Location:23 → 180

PA_C_RZF_like; PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo ...

cd16797
Location:238 → 283

RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
XM_047447379.1 → XP_047303335.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_047447381.1 → XP_047303337.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_047447382.1 → XP_047303338.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_017005661.3 → XP_016861150.1 E3 ubiquitin-protein ligase RNF13 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

152563773..152713514

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054345114.1 → XP_054201089.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345110.1 → XP_054201085.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345112.1 → XP_054201087.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345116.1 → XP_054201091.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345111.1 → XP_054201086.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345115.1 → XP_054201090.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345113.1 → XP_054201088.1 E3 ubiquitin-protein ligase RNF13 isoform X1

UniProtKB/Swiss-Prot

A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
XM_054345117.1 → XP_054201092.1 E3 ubiquitin-protein ligase RNF13 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_183382.1: Suppressed sequence

Description

NM_183382.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_183384.2: Suppressed sequence

Description

NM_183384.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.