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RNF39 ring finger protein 39 [ Homo sapiens (human) ]

Gene ID: 80352, updated on 7-Jun-2020

Summary

Official Symbol
RNF39provided by HGNC
Official Full Name
ring finger protein 39provided by HGNC
Primary source
HGNC:HGNC:18064
See related
Ensembl:ENSG00000204618 MIM:607524
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HZF; HZFW; LIRF; FAP216
Summary
This gene lies within the major histocompatibility complex class I region on chromosome 6. Studies of a similar rat protein suggest that this gene encodes a protein that plays a role in an early phase of synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in small intestine (RPKM 5.5), duodenum (RPKM 5.3) and 25 other tissues See more
Orthologs

Genomic context

See RNF39 in Genome Data Viewer
Location:
6p22.1
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (30070266..30080625, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30038043..30043628, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc ribbon domain containing 1 antisense, pseudogene Neighboring gene eukaryotic translation termination factor 1 pseudogene 1 Neighboring gene RNA polymerase I subunit H Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 11 Neighboring gene TRIM31 antisense RNA 1 Neighboring gene tripartite motif containing 31 Neighboring gene tripartite motif containing 40

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?

Phenotypes

NHGRI GWAS Catalog

Description
Common genetic variation and the control of HIV-1 in humans.
NHGRI GWA Catalog
Genome-wide association study of proneness to anger.
NHGRI GWA Catalog
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
RING finger protein 39
Names
LTP (long-term potentiation) induced RING finger protein
protein HZFw

NCBI Reference Sequences (RefSeq)

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_025236.3NP_079512.2  RING finger protein 39 isoform 1

    See identical proteins and their annotated locations for NP_079512.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1), also known as HZFw1, represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF238315, AL669914
    Consensus CDS
    CCDS4673.1
    UniProtKB/Swiss-Prot
    Q9H2S5
    UniProtKB/TrEMBL
    Q96QB5
    Related
    ENSP00000244360.6, ENST00000244360.6
    Conserved Domains (2) summary
    cd12888
    Location:229415
    SPRY_PRY_TRIM7_like; PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41
    cl17238
    Location:88134
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
  2. NM_170769.2NP_739575.2  RING finger protein 39 isoform 2

    See identical proteins and their annotated locations for NP_739575.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2), also known as HZFw2, lacks an in-frame segment in the coding region, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AF238316, AL669914
    Consensus CDS
    CCDS4674.1
    UniProtKB/Swiss-Prot
    Q9H2S5
    UniProtKB/TrEMBL
    A0A1U9X8G2
    Related
    ENSP00000365942.3, ENST00000376751.7
    Conserved Domains (3) summary
    cl02614
    Location:229325
    SPRY; SPRY domain
    cl17238
    Location:86134
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    cl28410
    Location:63254
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    30070266..30080625 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011325.1XP_016866814.1  RING finger protein 39 isoform X1

  2. XM_017011326.1XP_016866815.1  RING finger protein 39 isoform X2

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    1328358..1333943 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    1550037..1555622 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    1326182..1331767 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    1331016..1336601 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    1414356..1419941 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    1325426..1331006 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    1369185..1374770 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_170770.1: Suppressed sequence

    Description
    NM_170770.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
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