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

Gene ID: 24017, updated on 6-Jun-2024

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
VALIDATED
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
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Genomic context

See Rnf13 in Genome Data Viewer
Location:
3 D; 3 28.04 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 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_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_07737 Neighboring gene ankyrin repeat and ubiquitin domain containing 1 Neighboring gene STARR-seq mESC enhancer starr_07738 Neighboring gene STARR-positive B cell enhancer mm9_chr3:57539802-57540103 Neighboring gene ribosomal protein S11 pseudogene Neighboring gene ribosomal protein L7A pseudogene Neighboring gene ribosomal protein 10 pseudogene Neighboring gene profilin 2 Neighboring gene STARR-seq mESC enhancer starr_07740 Neighboring gene predicted gene, 32753 Neighboring gene predicted gene, 40055 Neighboring gene eukaryotic translation initiation factor 5 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (4)  1 citation

General gene information

Markers

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
 
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 JNK 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
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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

Preferred Names
E3 ubiquitin-protein ligase RNF13
Names
RING-type E3 ubiquitin transferase RNF13
NP_001106884.1
NP_001291383.1
NP_001291385.1
NP_001344009.1
NP_036013.1
XP_006501521.1
XP_030108468.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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)

  1. NM_001113413.4NP_001106884.1  E3 ubiquitin-protein ligase RNF13 isoform a precursor

    See identical proteins and their annotated locations for NP_001106884.1

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Consensus CDS
    CCDS50913.1
    UniProtKB/Swiss-Prot
    O54965, O54966, Q6PEA8
    UniProtKB/TrEMBL
    Q3TJV7
    Related
    ENSMUSP00000049331.10, ENSMUST00000041826.14
    Conserved Domains (2) summary
    cd02123
    Location:23180
    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:238283
    RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
  2. NM_001304454.3NP_001291383.1  E3 ubiquitin-protein ligase RNF13 isoform c

    See identical proteins and their annotated locations for NP_001291383.1

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Consensus CDS
    CCDS84623.1
    UniProtKB/TrEMBL
    Q3TJV7, Q8CB78
    Related
    ENSMUSP00000142462.2, ENSMUST00000200497.5
    Conserved Domains (2) summary
    cd02123
    Location:23180
    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:240260
    zf-RING_11; RING-like zinc finger
  3. NM_001304456.3NP_001291385.1  E3 ubiquitin-protein ligase RNF13 isoform d

    See identical proteins and their annotated locations for NP_001291385.1

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Consensus CDS
    CCDS84622.1
    UniProtKB/TrEMBL
    Q8C4F9
    Related
    ENSMUSP00000143498.2, ENSMUST00000198214.5
    Conserved Domains (1) summary
    cd02123
    Location:23180
    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 ...
  4. NM_001357080.2NP_001344009.1  E3 ubiquitin-protein ligase RNF13 isoform a precursor

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Consensus CDS
    CCDS50913.1
    UniProtKB/Swiss-Prot
    O54965, O54966, Q6PEA8
    UniProtKB/TrEMBL
    Q3TJV7
    Conserved Domains (2) summary
    cd02123
    Location:23180
    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:238283
    RING-H2_RNF167; RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins
  5. NM_001428659.1NP_001415588.1  E3 ubiquitin-protein ligase RNF13 isoform e

    Status: VALIDATED

    Source sequence(s)
    AC165888
    UniProtKB/TrEMBL
    Q3TJV7
  6. NM_011883.6NP_036013.1  E3 ubiquitin-protein ligase RNF13 isoform b precursor

    See identical proteins and their annotated locations for NP_036013.1

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Consensus CDS
    CCDS79910.1
    UniProtKB/TrEMBL
    Q3UTG4
    Related
    ENSMUSP00000142335.2, ENSMUST00000199041.2
    Conserved Domains (2) summary
    cd02123
    Location:23180
    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:240260
    zf-RING_11; RING-like zinc finger

RNA

  1. NR_130743.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC165888
    Related
    ENSMUST00000197205.5

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    57643468..57742846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    Q3TJV7
    Conserved Domains (2) summary
    cd02123
    Location:37153
    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:211256
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  2. XM_006501458.5XP_006501521.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    Conserved Domains (2) summary
    cd02123
    Location:37153
    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:211256
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain