Display Settings:

Format

Send to:

Choose Destination

MATR3 matrin 3 [ Homo sapiens (human) ]

Gene ID: 9782, updated on 19-Nov-2014
Official Symbol
MATR3provided by HGNC
Official Full Name
matrin 3provided by HGNC
Primary source
HGNC:HGNC:6912
See related
Ensembl:ENSG00000015479; HPRD:05270; MIM:164015; Vega:OTTHUMG00000129229
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]
See MATR3 in Epigenomics, MapViewer
Location:
5q31.2
Exon count:
19
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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 catenin (cadherin-associated protein), alpha 1, 102kDa Neighboring gene leucine rich repeat transmembrane neuronal 2 Neighboring gene SIL1 nucleotide exchange factor Neighboring gene ribosomal protein L12 pseudogene 21 Neighboring gene small nucleolar RNA, H/ACA box 74A Neighboring gene RNA, 5S ribosomal pseudogene 195 Neighboring gene small nucleolar RNA host gene 4 (non-protein coding) Neighboring gene poly(A) binding protein interacting protein 2 Neighboring gene solute carrier family 23 (ascorbic acid transporter), member 1 Neighboring gene marginal zone B and B1 cell-specific protein

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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
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
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
poly(A) RNA binding IDA
Inferred from Direct Assay
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
 
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
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
matrin-3
Names
matrin-3
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 

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

mRNA and Protein(s)

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

    See proteins identical to 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
    Conserved Domains (4) 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
    pfam04931
    Location:584678
    DNA_pol_phi; DNA polymerase phi
  2. NM_001194955.1NP_001181884.1  matrin-3 isoform a

    See proteins identical to 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
    Related
    ENSP00000482895, ENST00000618441
    Conserved Domains (4) 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
    pfam04931
    Location:584678
    DNA_pol_phi; DNA polymerase phi
  3. NM_001194956.1NP_001181885.1  matrin-3 isoform b

    See proteins identical to 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
    Conserved Domains (4) 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
    pfam04931
    Location:296390
    DNA_pol_phi; DNA polymerase phi
  4. NM_001282278.1NP_001269207.1  matrin-3 isoform c

    See proteins identical to 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/TrEMBL
    B3KM87
    UniProtKB/TrEMBL
    B4DF66
    UniProtKB/Swiss-Prot
    P43243
    Conserved Domains (4) 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
    pfam04931
    Location:246340
    DNA_pol_phi; DNA polymerase phi
  5. NM_018834.5NP_061322.2  matrin-3 isoform a

    See proteins identical to 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
    Q9H4N1
    Related
    ENSP00000378284, OTTHUMP00000159532, ENST00000394805, OTTHUMT00000251324
    Conserved Domains (4) 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
    pfam04931
    Location:584678
    DNA_pol_phi; DNA polymerase phi
  6. NM_199189.2NP_954659.1  matrin-3 isoform a

    See proteins identical to 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
    Related
    ENSP00000354346, ENST00000361059
    Conserved Domains (4) 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
    pfam04931
    Location:584678
    DNA_pol_phi; DNA polymerase phi

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Alternate HuRef

Genomic

  1. AC_000137.1 

    Range
    133798796..133857165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000005.10 

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

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 

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