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PRDM2 PR/SET domain 2 [ Homo sapiens (human) ]

Gene ID: 7799, updated on 4-Sep-2021

Summary

Official Symbol
PRDM2provided by HGNC
Official Full Name
PR/SET domain 2provided by HGNC
Primary source
HGNC:HGNC:9347
See related
Ensembl:ENSG00000116731 MIM:601196
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
RIZ; KMT8; RIZ1; RIZ2; KMT8A; MTB-ZF; HUMHOXY1
Summary
This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 10.7), ovary (RPKM 8.6) and 25 other tissues See more
Orthologs
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Genomic context

See PRDM2 in Genome Data Viewer
Location:
1p36.21
Exon count:
17
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (13698874..13825079)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (14026683..14151574)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378612 Neighboring gene uncharacterized LOC105376756 Neighboring gene kazrin, periplakin interacting protein Neighboring gene RNA, U6 small nuclear 1265, pseudogene Neighboring gene uncharacterized LOC107985467

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of PR domain containing 2, with ZNF domain (PRDM2) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
PR domain zinc finger protein 2
Names
GATA-3 binding protein G3B
MTE-binding protein
PR domain 2
PR domain containing 2, with ZNF domain
PR domain-containing protein 2
lysine N-methyltransferase 8
retinoblastoma protein-binding zinc finger protein
retinoblastoma protein-interacting zinc finger protein
zinc finger protein RIZ
zinc-finger DNA-binding protein
NP_001007258.1
NP_001129082.1
NP_001380915.1
NP_001380916.1
NP_001380917.1
NP_036363.2
NP_056950.2
XP_016857744.1
XP_016857746.1
XP_016857748.1
XP_016857749.1
XP_016857750.1
XP_016857752.1
XP_016857753.1

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)

  1. NM_001007257.3NP_001007258.1  PR domain zinc finger protein 2 isoform c

    See identical proteins and their annotated locations for NP_001007258.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is shorter at the 5' end and differs in the 3' UTR and coding region compared to variant 1. Expression of this transcript is under the control of an internal promoter in the gene (PMID: 9006946), which is why it is shorter at the 5' end than variant 1. The resulting isoform (c, also called RIZ2) is shorter at the N-terminus and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AI651991, AL031277, BC014468, BC032768, D45132, U17838
    Consensus CDS
    CCDS30603.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000411103.1, ENST00000413440.5
    Conserved Domains (3) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
  2. NM_001135610.2NP_001129082.1  PR domain zinc finger protein 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' UTR and lacks two internal coding exons compared to variant 1. The resulting isoform (d) is much shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK307377, AL031277, AL359771, BC014468, BU621515
    Consensus CDS
    CCDS44061.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000365216.5, ENST00000376048.9
    Conserved Domains (1) summary
    smart00317
    Location:28147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  3. NM_001393986.1NP_001380915.1  PR domain zinc finger protein 2 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL031277, AL359771, AL583942
    Conserved Domains (5) summary
    sd00017
    Location:11361156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19188
    Location:23145
    PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
    pfam00096
    Location:360382
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:483506
    zf-C2H2_4; C2H2-type zinc finger
  4. NM_001393987.1NP_001380916.1  PR domain zinc finger protein 2 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL031277
    Conserved Domains (4) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:282305
    zf-C2H2_4; C2H2-type zinc finger
  5. NM_001393988.1NP_001380917.1  PR domain zinc finger protein 2 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL031277
    Conserved Domains (3) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
  6. NM_012231.5NP_036363.2  PR domain zinc finger protein 2 isoform a

    See identical proteins and their annotated locations for NP_036363.2

    Status: REVIEWED

    Source sequence(s)
    AL031277, AL359771, AL583942
    Consensus CDS
    CCDS150.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000235372.6, ENST00000235372.11
    Conserved Domains (5) summary
    sd00017
    Location:11361156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19188
    Location:23145
    PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
    pfam00096
    Location:360382
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:483506
    zf-C2H2_4; C2H2-type zinc finger
  7. NM_015866.6NP_056950.2  PR domain zinc finger protein 2 isoform b

    See identical proteins and their annotated locations for NP_056950.2

    Status: REVIEWED

    Source sequence(s)
    AL031277, AL359771, AL583942
    Consensus CDS
    CCDS151.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000312352.5, ENST00000311066.9
    Conserved Domains (4) summary
    smart00317
    Location:28147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:11361156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360382
    zf-C2H2; Zinc finger, C2H2 type

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    13698874..13825079
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002264.2XP_016857753.1  PR domain zinc finger protein 2 isoform X5

  2. XM_017002255.1XP_016857744.1  PR domain zinc finger protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (5) summary
    sd00017
    Location:11361156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19188
    Location:23145
    PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
    pfam00096
    Location:360382
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:483506
    zf-C2H2_4; C2H2-type zinc finger
  3. XM_017002257.1XP_016857746.1  PR domain zinc finger protein 2 isoform X2

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    smart00317
    Location:28147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:11361156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360382
    zf-C2H2; Zinc finger, C2H2 type
  4. XM_017002259.2XP_016857748.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:282305
    zf-C2H2_4; C2H2-type zinc finger
  5. XM_017002261.2XP_016857750.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:282305
    zf-C2H2_4; C2H2-type zinc finger
  6. XM_017002263.2XP_016857752.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:282305
    zf-C2H2_4; C2H2-type zinc finger
  7. XM_017002260.2XP_016857749.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    sd00017
    Location:935955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:161181
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159181
    zf-C2H2; Zinc finger, C2H2 type
    pfam13894
    Location:282305
    zf-C2H2_4; C2H2-type zinc finger

RNA

  1. XR_002957562.1 RNA Sequence

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