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MATR3 matrin 3 [ Homo sapiens (human) ]

Gene ID: 9782, updated on 9-Jul-2017
Official Symbol
MATR3provided by HGNC
Official Full Name
matrin 3provided by HGNC
Primary source
HGNC:HGNC:6912
See related
Ensembl:ENSG00000015479 Ensembl:ENSG00000280987 MIM:164015; Vega:OTTHUMG00000129229; Vega:OTTHUMG00000189583
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
MPD2; ALS21; VCPDM
Summary
This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
Orthologs
Location:
5q31.2
Exon count:
19
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (139273752..139331677)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138609441..138667366)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SIL1 nucleotide exchange factor Neighboring gene ribosomal protein L12 pseudogene 21 Neighboring gene RNA, U6 small nuclear 572, pseudogene Neighboring gene small nucleolar RNA, H/ACA box 74A Neighboring gene small nucleolar RNA host gene 4 Neighboring gene RNA, 5S ribosomal pseudogene 195 Neighboring gene RNA, 7SK small nuclear pseudogene 64 Neighboring gene poly(A) binding protein interacting protein 2 Neighboring gene solute carrier family 23 member 1

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Replication interactions

Interaction Pubs
siRNA knockdown of MATR3 improves the ZAP-induced degradation of HIV-1 transcripts; MATR3 enhances HIV-1 replication PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify matrin 3 (MATR3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify matrin 3 (MATR3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify matrin 3 (MATR3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify matrin 3 (MATR3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
gag Overexpression of Matrin 3 increases HIV-1 Gag expression; knockdown of Matrin 3 decreases HIV-1 Gag expression PubMed
Rev rev Association of PSF with MATR3 is involved in nuclear retention of unspliced HIV-1 RNA and Rev activity PubMed
rev The interaction of HIV-1 Rev and Matrin 3 specifically requires the presence of a Rev-dependent RRE-containing RNA. Two RNA recognition motifs (residues 586-612) in Matrin 3 are required for activity on Rev/RRE PubMed
rev HIV-1 Rev interacting protein, matrin 3 (MATR3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with MATR3 is increased by RRE PubMed
Tat tat Matrin 3 protein (MATR3) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of matrin 3 (MATR3) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
vpr HIV-1 Vpr is identified to have a physical interaction with matrin 3 (MATR3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC9105, KIAA0723, DKFZp686K0542, DKFZp686K23100

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity TAS
Traceable Author Statement
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
posttranscriptional regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear inner membrane TAS
Traceable Author Statement
more info
PubMed 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
matrin-3
Names
vocal cord and pharyngeal weakness with distal myopathy

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

  1. NG_012846.1 RefSeqGene

    Range
    4650..62575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001194954.1NP_001181883.1  matrin-3 isoform a

    See identical proteins and their annotated locations for NP_001181883.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
    Source sequence(s)
    AA233906, AB018266, AC011404, AK307872, BX537365, DC333260
    Consensus CDS
    CCDS4210.1
    UniProtKB/Swiss-Prot
    P43243
    UniProtKB/TrEMBL
    A0A0R4J2E8
    Related
    ENSP00000423533.1, OTTHUMP00000223743, ENST00000509990.5, OTTHUMT00000373020
    Conserved Domains (3) summary
    smart00451
    Location:798833
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:398473
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:496575
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
  2. NM_001194955.1NP_001181884.1  matrin-3 isoform a

    See identical proteins and their annotated locations for NP_001181884.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
    Source sequence(s)
    AA233906, AB018266, AC011404, AK316420, BX537365
    Consensus CDS
    CCDS4210.1
    UniProtKB/Swiss-Prot
    P43243
    UniProtKB/TrEMBL
    A0A0R4J2E8
    Related
    ENSP00000482895.1, ENST00000618441.5
    Conserved Domains (3) summary
    smart00451
    Location:798833
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:398473
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:496575
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
  3. NM_001194956.1NP_001181885.1  matrin-3 isoform b

    See identical proteins and their annotated locations for NP_001181885.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AA233906, AC011404, AK316420, BX537365
    Consensus CDS
    CCDS54908.1
    UniProtKB/Swiss-Prot
    P43243
    Related
    ENSP00000423587.1, OTTHUMP00000223738, ENST00000503811.5, OTTHUMT00000373015
    Conserved Domains (3) summary
    smart00451
    Location:510545
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:110185
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:208287
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
  4. NM_001282278.1NP_001269207.1  matrin-3 isoform c

    See identical proteins and their annotated locations for NP_001269207.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an exon which contains a portion of the 5' UTR and 5' coding region including the start codon, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (c) with a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AA233906, AB018266, AC011404, AK293952, AK307872, BX537365, DC333260
    Consensus CDS
    CCDS75316.1
    UniProtKB/Swiss-Prot
    P43243
    UniProtKB/TrEMBL
    B3KM87, B4DF66
    Related
    ENSP00000421218.1, OTTHUMP00000223742, ENST00000504203.5, OTTHUMT00000373019
    Conserved Domains (3) summary
    smart00451
    Location:460495
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:60135
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:158237
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
  5. NM_018834.5NP_061322.2  matrin-3 isoform a

    See identical proteins and their annotated locations for NP_061322.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
    Source sequence(s)
    AA233906, AC011404, AY007157, BX537365, DC401586
    Consensus CDS
    CCDS4210.1
    UniProtKB/Swiss-Prot
    P43243
    UniProtKB/TrEMBL
    A0A0R4J2E8, Q9H4N1
    Related
    ENSP00000378284.3, OTTHUMP00000159532, ENST00000394805.7, OTTHUMT00000251324
    Conserved Domains (3) summary
    smart00451
    Location:798833
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:398473
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:496575
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
  6. NM_199189.2NP_954659.1  matrin-3 isoform a

    See identical proteins and their annotated locations for NP_954659.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1-4 encode the same isoform (a).
    Source sequence(s)
    AA233906, AB018266, AC011404, AK307872, BX537365, DC333260
    Consensus CDS
    CCDS4210.1
    UniProtKB/Swiss-Prot
    P43243
    UniProtKB/TrEMBL
    A0A0R4J2E8
    Related
    ENSP00000354346.4, OTTHUMP00000281588, ENST00000361059.7, OTTHUMT00000488733
    Conserved Domains (3) summary
    smart00451
    Location:798833
    ZnF_U1; U1-like zinc finger
    cd12714
    Location:398473
    RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
    cd12715
    Location:496575
    RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

    Range
    139273752..139331677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 Alternate CHM1_1.1

    Range
    138042040..138099954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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