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

    Gene ID: 11342, updated on 9-Dec-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.