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

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; AllianceGenome:HGNC:18064
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: mouse all
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Genomic context

Location:: 6p22.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (30070270..30075769, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (29934544..29940043, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (30038047..30043546, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The findings provide evidence that hypermethylation in an independent MHC locus, RNF39, is also associated with relapsing-remitting multiple sclerosis.
Title: Differential methylation at MHC in CD4(+) T cells is associated with multiple sclerosis independently of HLA-DRB1.
Results identified RNF39 as cis methylation quantitative trait loci in both allergic rhinitis and asthma.
Title: Combining omics data to identify genes associated with allergic rhinitis.
these findings suggest that RNF39 and TRIM39 are involved in the etiology of Behcet's disease.
Title: TRIM39 and RNF39 are associated with Behçet's disease independently of HLA-B∗51 and -A∗26.
Observational study of gene-disease association. (HuGE Navigator)
Title: A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH99256 (e-PCR)
- UniSTS:88348

G29206 (e-PCR)
- UniSTS:22052

NoName (e-PCR)
- UniSTS:494653

STS-R63837 (e-PCR)
- UniSTS:43096

RNF39_1552.2 (e-PCR)
- UniSTS:280973

G31541 (e-PCR)
- UniSTS:72855

STS-W44579 (e-PCR)
- UniSTS:53704

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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

Process	Evidence Code	Pubs
involved_in innate immune response	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

General protein information

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Preferred Names: RING finger protein 39

Names: LTP (long-term potentiation) induced RING finger protein; protein HZFw

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_025236.4 → NP_079512.3 RING finger protein 39 isoform 1

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)

AL669914

Consensus CDS

CCDS4673.2

UniProtKB/Swiss-Prot

A2BEK3, A6NCD6, B0S858, Q5SPM8, Q5SPM9, Q5SPN0, Q5SRJ9, Q5SRK1, Q5SS29, Q9H2S3, Q9H2S4, Q9H2S5

UniProtKB/TrEMBL

Q96QB5

Related

ENSP00000244360.7, ENST00000244360.8

Conserved Domains (4) summary

TIGR00599
Location:14 → 186

rad18; DNA repair protein rad18

cd12888
Location:161 → 347

SPRY_PRY_TRIM7_like; PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41

cd00162
Location:20 → 66

RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]

cl17238
Location:18 → 66

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
NM_170769.3 → NP_739575.3 RING finger protein 39 isoform 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)

AL669914

Consensus CDS

CCDS4674.2

UniProtKB/TrEMBL

A0A1U9X8G2

Related

ENSP00000365942.4, ENST00000376751.8

Conserved Domains (4) summary

TIGR00599
Location:14 → 186

rad18; DNA repair protein rad18

cd00162
Location:20 → 66

RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]

cl02614
Location:161 → 257

SPRY; SPRY domain

cl17238
Location:18 → 66

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

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

30070270..30075769 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017011325.2 → XP_016866814.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

1328362..1333861 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054328523.1 → XP_054184498.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

1550041..1555540 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329914.1 → XP_054185889.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

1326186..1331685 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330406.1 → XP_054186381.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

1331020..1336519 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330685.1 → XP_054186660.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

1414360..1419859 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330899.1 → XP_054186874.1 RING finger protein 39 isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

1325430..1330924 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

1369189..1374688 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331419.1 → XP_054187394.1 RING finger protein 39 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

29934544..29940043 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356472.1 → XP_054212447.1 RING finger protein 39 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.