LONRF3 LON peptidase N-terminal domain and ring finger 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LONRF3provided by HGNC
Official Full Name: LON peptidase N-terminal domain and ring finger 3provided by HGNC
Primary source: HGNC:HGNC:21152
See related: Ensembl:ENSG00000175556 AllianceGenome:HGNC:21152
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: RNF127
Summary: The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Multiple alternatively spliced transcript variants have been suggested, but their full length natures are not clear. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 3.2), liver (RPKM 3.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq24

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (118974614..119018355)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (117352354..117396078)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (118108577..118152318)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat downregulates the expression of LON peptidase N-terminal domain and ring finger 3 (LONRF3) in human primary T cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

LONRF3 (e-PCR)
- UniSTS:506634

RNF127_2789 (e-PCR)
- UniSTS:462494

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

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LON peptidase N-terminal domain and RING finger protein 3

Names: ring finger protein 127

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.

Genomic

NG_012577.1 RefSeqGene

Range

4869..48606

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001031855.3 → NP_001027026.1 LON peptidase N-terminal domain and RING finger protein 3 isoform 1

See identical proteins and their annotated locations for NP_001027026.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK290198, BC100671, DA249558

Consensus CDS

CCDS35374.1

UniProtKB/Swiss-Prot

Q496Y0, Q5JPN6, Q8NB00, Q9H647

UniProtKB/TrEMBL

A8K2D3

Related

ENSP00000360690.3, ENST00000371628.8

Conserved Domains (6) summary

cd00162
Location:466 → 505

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 ...

cl19481
Location:566 → 744

LON; Found in ATP-dependent protease La (LON)

sd00006
Location:243 → 271

TPR; TPR repeat [structural motif]

pfam02190
Location:555 → 756

LON_substr_bdg; ATP-dependent protease La (LON) substrate-binding domain

pfam13414
Location:242 → 308

TPR_11; TPR repeat

cl17238
Location:158 → 195

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 ...
NM_001289109.1 → NP_001276038.1 LON peptidase N-terminal domain and RING finger protein 3 isoform 3

See identical proteins and their annotated locations for NP_001276038.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding region, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This results in a protein (isoform 3) which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK097641, AK290198, AL772284, BC098283

Consensus CDS

CCDS76014.1

UniProtKB/TrEMBL

B3KUN7

Related

ENSP00000408894.2, ENST00000422289.3

Conserved Domains (3) summary

cd00162
Location:210 → 249

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 ...

cl19481
Location:300 → 488

LON; Found in ATP-dependent protease La (LON)

pfam02190
Location:299 → 500

LON_substr_bdg; ATP-dependent protease La (LON) substrate-binding domain
NM_024778.5 → NP_079054.3 LON peptidase N-terminal domain and RING finger protein 3 isoform 2

See identical proteins and their annotated locations for NP_079054.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AK290198, BC103491, DA249558

Consensus CDS

CCDS14575.1

UniProtKB/TrEMBL

A8K2D3

Related

ENSP00000307732.7, ENST00000304778.11

Conserved Domains (6) summary

cd00162
Location:425 → 464

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 ...

cl19481
Location:525 → 703

LON; Found in ATP-dependent protease La (LON)

sd00006
Location:243 → 271

TPR; TPR repeat [structural motif]

pfam02190
Location:514 → 715

LON_substr_bdg; ATP-dependent protease La (LON) substrate-binding domain

pfam13414
Location:242 → 308

TPR_11; TPR repeat

cl17238
Location:158 → 195

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 ...

RNA

NR_110311.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate 3' splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK091777, AK290198, DA249558

Related

ENST00000481285.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

118974614..119018355

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005262476.3 → XP_005262533.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X1

UniProtKB/TrEMBL

A8K2D3

Conserved Domains (6) summary

cd00162
Location:518 → 557

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 ...

cl19481
Location:618 → 796

LON; Found in ATP-dependent protease La (LON)

sd00006
Location:243 → 271

TPR; TPR repeat [structural motif]

pfam02190
Location:607 → 808

LON_substr_bdg; ATP-dependent protease La (LON) substrate-binding domain

pfam13414
Location:242 → 308

TPR_11; TPR repeat

cl17238
Location:158 → 195

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 ...
XM_047442517.1 → XP_047298473.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X2
XM_017029845.1 → XP_016885334.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X4
XM_011531398.3 → XP_011529700.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X3

Conserved Domains (6) summary

cd00162
Location:518 → 557

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 ...

cl19481
Location:618 → 653

LON; Found in ATP-dependent protease La (LON)

sd00006
Location:243 → 271

TPR; TPR repeat [structural motif]

pfam02190
Location:607 → 650

LON_substr_bdg; ATP-dependent protease La (LON) substrate-binding domain

pfam13414
Location:242 → 308

TPR_11; TPR repeat

cl17238
Location:158 → 195

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 ...
XM_047442518.1 → XP_047298474.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X5
XM_047442519.1 → XP_047298475.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X6

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

117352354..117396078

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327872.1 → XP_054183847.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X1
XM_054327873.1 → XP_054183848.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X2
XM_054327875.1 → XP_054183850.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X4
XM_054327874.1 → XP_054183849.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X3
XM_054327876.1 → XP_054183851.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X5
XM_054327877.1 → XP_054183852.1 LON peptidase N-terminal domain and RING finger protein 3 isoform X6