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

Gene ID: 11342, updated on 27-Nov-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See RNF13 in Genome Data Viewer
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_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14807 Neighboring gene COMM domain containing 2 Neighboring gene ankyrin repeat and ubiquitin domain containing 1 Neighboring gene RNA, U6 small nuclear 507, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:149508028-149509227 Neighboring gene Sharpr-MPRA regulatory region 5490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:149530359-149530870 Neighboring gene MPRA-validated peak4858 silencer Neighboring gene RNA, U6 small nuclear 720, pseudogene Neighboring gene nucleophosmin 1 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14812 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:149688883-149689414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:149689415-149689945 Neighboring gene uncharacterized LOC646903 Neighboring gene profilin 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ93817, MGC13689

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 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

Preferred Names
E3 ubiquitin-protein ligase RNF13
Names
RING zinc finger protein
RING-type E3 ubiquitin transferase RNF13
NP_001365214.1
NP_001365215.1
NP_001365216.1
NP_001365217.1
NP_001365218.1
NP_001365219.1
NP_001365220.1
NP_009213.1
NP_899237.1
NP_899239.2
XP_011510675.1
XP_016861150.1
XP_047303335.1
XP_047303336.1
XP_047303337.1
XP_047303338.1
XP_054201085.1
XP_054201086.1
XP_054201087.1
XP_054201088.1
XP_054201089.1
XP_054201090.1
XP_054201091.1
XP_054201092.1

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_001378285.1NP_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: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_001378286.1NP_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: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
  3. NM_001378287.1NP_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:121162
    RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]
    cl28883
    Location:2161
    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:119164
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  4. NM_001378288.1NP_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:121162
    RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]
    cl28883
    Location:2161
    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:119164
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  5. NM_001378289.1NP_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:121162
    RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]
    cl28883
    Location:2161
    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:119164
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  6. NM_001378290.1NP_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:121162
    RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]
    cl28883
    Location:2161
    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:119164
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  7. NM_001378291.1NP_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:149
    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:107152
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  8. NM_007282.4NP_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: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
  9. NM_183381.3NP_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: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
  10. NM_183383.2NP_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:121162
    RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]
    cl28883
    Location:2161
    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:119164
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RNA

  1. 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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    149812688..149962139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  2. XM_011512373.3XP_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: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
  3. XM_047447379.1XP_047303335.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  4. XM_047447381.1XP_047303337.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  5. XM_047447382.1XP_047303338.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  6. XM_017005661.3XP_016861150.1  E3 ubiquitin-protein ligase RNF13 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    152563773..152713514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  2. XM_054345110.1XP_054201085.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  3. XM_054345112.1XP_054201087.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  4. XM_054345116.1XP_054201091.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  5. XM_054345111.1XP_054201086.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  6. XM_054345115.1XP_054201090.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  7. XM_054345113.1XP_054201088.1  E3 ubiquitin-protein ligase RNF13 isoform X1

    UniProtKB/Swiss-Prot
    A6NC87, B3KR12, O43567, Q05D66, Q6IBJ9
  8. XM_054345117.1XP_054201092.1  E3 ubiquitin-protein ligase RNF13 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_183382.1: Suppressed sequence

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