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PRDM10 PR/SET domain 10 [ Homo sapiens (human) ]

Gene ID: 56980, updated on 21-Jan-2024

Summary

Official Symbol
PRDM10provided by HGNC
Official Full Name
PR/SET domain 10provided by HGNC
Primary source
HGNC:HGNC:13995
See related
Ensembl:ENSG00000170325 MIM:618319; AllianceGenome:HGNC:13995
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
BHD2; PFM7; TRIS
Summary
The protein encoded by this gene is a transcription factor that contains C2H2-type zinc-fingers. It also contains a positive regulatory domain, which has been found in several other zinc-finger transcription factors including those involved in B cell differentiation and tumor suppression. Studies of the mouse counterpart suggest that this protein may be involved in the development of the central nerve system (CNS), as well as in the pathogenesis of neuronal storage disease. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 1.6), lymph node (RPKM 1.5) and 25 other tissues See more
Orthologs
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Genomic context

See PRDM10 in Genome Data Viewer
Location:
11q24.3
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (129899711..130002835, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (129935739..130038861, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (129769606..129872730, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 45B Neighboring gene TMEM45B-NFRKB intergenic CAGE-defined mid-level expression enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr11:129739277-129739466 Neighboring gene Sharpr-MPRA regulatory region 15352 Neighboring gene nuclear factor related to kappaB binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4068 Neighboring gene NANOG hESC enhancer GRCh37_chr11:129795831-129796332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129806281-129806994 Neighboring gene MPRA-validated peak1509 silencer Neighboring gene Sharpr-MPRA regulatory region 3666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:129841453-129842000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4072 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4073 Neighboring gene CRISPRi-validated cis-regulatory element chr11.6035 Neighboring gene PRDM10 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4074 Neighboring gene Sharpr-MPRA regulatory region 13105 Neighboring gene NANOG hESC enhancer GRCh37_chr11:129907707-129908249 Neighboring gene MPRA-validated peak1512 silencer Neighboring gene elongin B pseudogene 2 Neighboring gene uncharacterized LOC107984432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129938480-129938980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129938981-129939481

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 10 (PRDM10) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed
Knockdown of PR domain containing 10 (PRDM10) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1231, MGC131802

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of transcription repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
PR domain zinc finger protein 10
Names
PR domain 10
PR domain containing 10
PR domain-containing protein 10
PR-domain family member 7
PRDM zinc finger transcription factor
tristanin
NP_001354819.1
NP_001354820.1
NP_001354821.1
NP_001354822.1
NP_001354823.1
NP_001354824.1
NP_001354825.1
NP_001354826.1
NP_001354827.1
NP_001354828.1
NP_064613.2
NP_955469.1
NP_955470.1
NP_955471.1
XP_011541214.1
XP_047283267.1
XP_047283268.1
XP_054225408.1
XP_054225409.1
XP_054225410.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001367890.1NP_001354819.1  PR domain zinc finger protein 10 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    A0A2Z2E6H7
  2. NM_001367891.1NP_001354820.1  PR domain zinc finger protein 10 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    A0A2Z2E6H7
  3. NM_001367892.1NP_001354821.1  PR domain zinc finger protein 10 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    A0A2Z2E6H7
  4. NM_001367893.1NP_001354822.1  PR domain zinc finger protein 10 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/Swiss-Prot
    B7ZL71, G3XAE5, J3KP23, Q17R90, Q2KHR4, Q863Z2, Q9NQV6, Q9NXI4, Q9ULI9
    UniProtKB/TrEMBL
    A0A2Z2E6H7
  5. NM_001367894.1NP_001354823.1  PR domain zinc finger protein 10 isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    A0A2Z2E6H7
  6. NM_001367895.1NP_001354824.1  PR domain zinc finger protein 10 isoform 14

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    B7ZL72
  7. NM_001367896.1NP_001354825.1  PR domain zinc finger protein 10 isoform 13

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    B7ZL72
  8. NM_001367897.1NP_001354826.1  PR domain zinc finger protein 10 isoform 12

    Status: REVIEWED

    Source sequence(s)
    AP003041, AP003326, AP003327
    UniProtKB/TrEMBL
    B7ZL72
  9. NM_001367898.1NP_001354827.1  PR domain zinc finger protein 10 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AP003326, AP003327
    UniProtKB/TrEMBL
    B7ZL72
  10. NM_001367899.1NP_001354828.1  PR domain zinc finger protein 10 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP003326, AP003327, BC143612
    Consensus CDS
    CCDS91624.1
    UniProtKB/TrEMBL
    B7ZL72
    Related
    ENSP00000432237.1, ENST00000526082.5
  11. NM_020228.3NP_064613.2  PR domain zinc finger protein 10 isoform 1

    See identical proteins and their annotated locations for NP_064613.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AP003041, AP003326, AP003327
    Consensus CDS
    CCDS44771.1
    UniProtKB/TrEMBL
    A0A2Z2E6H7
    Related
    ENSP00000351686.5, ENST00000358825.9
    Conserved Domains (5) summary
    COG5048
    Location:559692
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:618638
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:644666
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:220325
    SET; SET domain
    pfam16638
    Location:405510
    Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers
  12. NM_199437.2NP_955469.1  PR domain zinc finger protein 10 isoform 2

    See identical proteins and their annotated locations for NP_955469.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1.
    Source sequence(s)
    AP003041, AP003326, AP003327
    Consensus CDS
    CCDS8484.1
    UniProtKB/TrEMBL
    A0A2Z2E6H7
    Related
    ENSP00000354118.3, ENST00000360871.8
    Conserved Domains (5) summary
    COG5048
    Location:555688
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:614634
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:640662
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:220325
    SET; SET domain
    pfam16638
    Location:405510
    Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers
  13. NM_199438.2NP_955470.1  PR domain zinc finger protein 10 isoform 3

    See identical proteins and their annotated locations for NP_955470.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences compared to the variant 1. The resulting isoform (3) has a distinct and shorter N-terminus, and lacks an internal region, as compared to isoform 1.
    Source sequence(s)
    AP003326, AP003327
    Consensus CDS
    CCDS44772.1
    UniProtKB/TrEMBL
    B7ZL72
    Related
    ENSP00000398431.2, ENST00000423662.6
    Conserved Domains (4) summary
    sd00017
    Location:532552
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:558580
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:134239
    SET; SET domain
    pfam16638
    Location:319424
    Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers
  14. NM_199439.2NP_955471.1  PR domain zinc finger protein 10 isoform 4

    See identical proteins and their annotated locations for NP_955471.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant 1. The resulting isoform (4) has a distinct and shorter N-terminus and lacks two internal regions, as compared to isoform 1.
    Source sequence(s)
    AP003326, AP003327
    Consensus CDS
    CCDS8485.1
    UniProtKB/TrEMBL
    B7ZL72
    Related
    ENSP00000302669.6, ENST00000304538.10
    Conserved Domains (4) summary
    sd00017
    Location:528548
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:554576
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:134239
    SET; SET domain
    pfam16638
    Location:319424
    Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers

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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    129899711..130002835 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427312.1XP_047283268.1  PR domain zinc finger protein 10 isoform X3

    UniProtKB/TrEMBL
    A0A2Z2E6H7
  2. XM_011542912.3XP_011541214.1  PR domain zinc finger protein 10 isoform X1

    UniProtKB/TrEMBL
    A0A2Z2E6H7
    Related
    ENSP00000431262.1, ENST00000528746.5
    Conserved Domains (4) summary
    sd00017
    Location:614634
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:640662
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:220325
    SET; SET domain
    pfam16638
    Location:405510
    Tristanin_u2; Unstructured region on methyltransferase between zinc-fingers
  3. XM_047427311.1XP_047283267.1  PR domain zinc finger protein 10 isoform X2

    UniProtKB/TrEMBL
    A0A2Z2E6H7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    129935739..130038861 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369435.1XP_054225410.1  PR domain zinc finger protein 10 isoform X3

    UniProtKB/TrEMBL
    A0A2Z2E6H7
  2. XM_054369433.1XP_054225408.1  PR domain zinc finger protein 10 isoform X1

    UniProtKB/TrEMBL
    A0A2Z2E6H7
  3. XM_054369434.1XP_054225409.1  PR domain zinc finger protein 10 isoform X2

    UniProtKB/TrEMBL
    A0A2Z2E6H7