Rnf13 ring finger protein 13 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rnf13provided by MGI
Official Full Name: ring finger protein 13provided by MGI
Primary source: MGI:MGI:1346341
See related: Ensembl:ENSMUSG00000036503 AllianceGenome:MGI:1346341
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Rzf; 2010001H16Rik
Summary: This gene encodes a member of the PA-TM-RING family of proteins that contain a protease associated (PA) domain and a RING finger domain separated by a transmembrane (TM) domain. The encoded protein is an E3 ubiquitin ligase localized to the endosomal-lysosomal vesicles and inner nuclear membrane. Mice lacking the encoded protein have impaired learning abilities associated with a decreased synaptic vesicle density and dysregulated SNARE complex assembly. Alternative splicing of this gene results in multiple transcript variants. A pseudogene for this gene has been identified on the X chromosome. [provided by RefSeq, Jan 2015]
Expression: Ubiquitous expression in cerebellum adult (RPKM 16.4), bladder adult (RPKM 14.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3; 3 D

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (57643468..57742846)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (57736044..57835425)

Chromosome 3 - NC_000069.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Silencing RNF13 Alleviates Parkinson's Disease - Like Problems in Mouse Models by Regulating the Endoplasmic Reticulum Stress-Mediated IRE1alpha-TRAF2-ASK1-JNK Pathway.
Title: Silencing RNF13 Alleviates Parkinson's Disease - Like Problems in Mouse Models by Regulating the Endoplasmic Reticulum Stress-Mediated IRE1α-TRAF2-ASK1-JNK Pathway.
host RNF13 affects the concentration of GM-CSF in tumor-bearing lungs
Title: Enhanced metastasis in RNF13 knockout mice is mediated by a reduction in GM-CSF levels.
These results indicate that RNF13 deficiency promotes skeletal muscle regeneration via the effects on satellite cell niche mediated by IL-4 and IL-6.
Title: Accelerated regeneration of the skeletal muscle in RNF13-knockout mice is mediated by macrophage-secreted IL-4/IL-6.
RNF13 is involved in the regulation of the SNARE complex, which thereby controls synaptic function.
Title: E3 ubiquitin ligase RNF13 involves spatial learning and assembly of the SNARE complex.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2)
Endonuclease-mediated (2)

General gene information

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Markers

Rnf13 (e-PCR), detects polymorphism
- UniSTS:531262

NoName (e-PCR)
- UniSTS:234691

Homology

Orthologs from Annotation Pipeline: 479 organisms have orthologs with human gene Rnf13
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables JUN kinase binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in organelle localization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of stress-activated protein kinase signaling cascade	ISO Inferred from Sequence Orthology more info
involved_in protein autoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF13

Names: RING-type E3 ubiquitin transferase RNF13

NP_001106884.1

EC 2.3.2.27

NP_001291383.1

EC 2.3.2.27

NP_001291385.1

EC 2.3.2.27

NP_001344009.1

EC 2.3.2.27

NP_036013.1

EC 2.3.2.27

XP_006501521.1

EC 2.3.2.27

XP_030108468.1

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_001113413.3 → NP_001106884.1 E3 ubiquitin-protein ligase RNF13 isoform a precursor

See identical proteins and their annotated locations for NP_001106884.1

Status: REVIEWED

Source sequence(s)

AC165888, AK140682, AK158046

Consensus CDS

CCDS50913.1

UniProtKB/Swiss-Prot

O54965, Q6PEA8

Related

ENSMUSP00000049331.10, ENSMUST00000041826.14

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_001304454.2 → NP_001291383.1 E3 ubiquitin-protein ligase RNF13 isoform c

See identical proteins and their annotated locations for NP_001291383.1

Status: REVIEWED

Source sequence(s)

AC165888, AK036591, AK140682

Consensus CDS

CCDS84623.1

UniProtKB/TrEMBL

Q8CB78

Related

ENSMUSP00000142462.2, ENSMUST00000200497.5

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 ...

pfam17123
Location:240 → 260

zf-RING_11; RING-like zinc finger
NM_001304456.2 → NP_001291385.1 E3 ubiquitin-protein ligase RNF13 isoform d

See identical proteins and their annotated locations for NP_001291385.1

Status: REVIEWED

Source sequence(s)

AC165888, AK082296, AW492990

Consensus CDS

CCDS84622.1

UniProtKB/TrEMBL

A0A8C6IDR7, Q8C4F9

Related

ENSMUSP00000143498.2, ENSMUST00000198214.5

Conserved Domains (1) 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 ...
NM_001357080.1 → NP_001344009.1 E3 ubiquitin-protein ligase RNF13 isoform a precursor

Status: REVIEWED

Source sequence(s)

AC165888

Consensus CDS

CCDS50913.1

UniProtKB/Swiss-Prot

Q6PEA8

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_011883.5 → NP_036013.1 E3 ubiquitin-protein ligase RNF13 isoform b precursor

See identical proteins and their annotated locations for NP_036013.1

Status: REVIEWED

Source sequence(s)

AC165888, AK139447

Consensus CDS

CCDS79910.1

UniProtKB/Swiss-Prot

O54965

UniProtKB/TrEMBL

Q3UTG4

Related

ENSMUSP00000142335.2, ENSMUST00000199041.2

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 ...

pfam17123
Location:240 → 260

zf-RING_11; RING-like zinc finger

RNA

NR_130743.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC165888, AK050095, AK140682

Related

ENSMUST00000197205.5

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

57643468..57742846

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030252608.2 → XP_030108468.1 E3 ubiquitin-protein ligase RNF13 isoform X1

Conserved Domains (2) summary

cd02123
Location:37 → 153

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 ...

cl17238
Location:211 → 256

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_006501458.5 → XP_006501521.1 E3 ubiquitin-protein ligase RNF13 isoform X1

See identical proteins and their annotated locations for XP_006501521.1

Conserved Domains (2) summary

cd02123
Location:37 → 153

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 ...

cl17238
Location:211 → 256

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