U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PHC3 polyhomeotic homolog 3 [ Homo sapiens (human) ]

Gene ID: 80012, updated on 5-Aug-2022

Summary

Official Symbol
PHC3provided by HGNC
Official Full Name
polyhomeotic homolog 3provided by HGNC
Primary source
HGNC:HGNC:15682
See related
Ensembl:ENSG00000173889 AllianceGenome:HGNC:15682
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EDR3; HPH3
Summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of PRC1 complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 7.6), thyroid (RPKM 6.5) and 25 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See PHC3 in Genome Data Viewer
Location:
3q26.2
Exon count:
18
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (170087584..170181733, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172872255..172966417, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (169805372..169899521, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor 160 Neighboring gene uncharacterized LOC124909456 Neighboring gene KMT5A pseudogene 3 Neighboring gene uncharacterized LOC105374209 Neighboring gene RNA, U6 small nuclear 315, pseudogene Neighboring gene RNA, U7 small nuclear 32 pseudogene Neighboring gene protein kinase C iota Neighboring gene Sharpr-MPRA regulatory region 5121

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12729, FLJ12967, MGC88144, DKFZp313K1221

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of PRC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of PRC1 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of PcG protein complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
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 

General protein information

Preferred Names
polyhomeotic-like protein 3
Names
early development regulator 3
early development regulatory protein 3
homolog of polyhomeotic 3
polyhomeotic like 3

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_001308116.2NP_001295045.1  polyhomeotic-like protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001295045.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC008040, AI042019, AJ320486, AK304411
    Consensus CDS
    CCDS77858.1
    UniProtKB/Swiss-Prot
    Q8NDX5, Q9H9I4
    UniProtKB/TrEMBL
    B4E2T1
    Related
    ENSP00000420271.1, ENST00000494943.5
    Conserved Domains (2) summary
    cd09577
    Location:914982
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:916983
    SAM; Sterile alpha motif
  2. NM_024947.4NP_079223.3  polyhomeotic-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_079223.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC008040, BC026001, BC131772, BP200133
    Consensus CDS
    CCDS46952.1
    UniProtKB/Swiss-Prot
    Q8NDX5
    Related
    ENSP00000420294.1, ENST00000495893.7
    Conserved Domains (2) summary
    cd09577
    Location:926994
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:928995
    SAM; Sterile alpha motif

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    170087584..170181733 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448988.1XP_047304944.1  polyhomeotic-like protein 3 isoform X12

  2. XM_047448987.1XP_047304943.1  polyhomeotic-like protein 3 isoform X10

  3. XM_047448986.1XP_047304942.1  polyhomeotic-like protein 3 isoform X8

  4. XM_047448984.1XP_047304940.1  polyhomeotic-like protein 3 isoform X6

  5. XM_047448983.1XP_047304939.1  polyhomeotic-like protein 3 isoform X4

  6. XM_017007235.3XP_016862724.1  polyhomeotic-like protein 3 isoform X2

  7. XM_017007238.3XP_016862727.1  polyhomeotic-like protein 3 isoform X11

  8. XM_006713756.4XP_006713819.1  polyhomeotic-like protein 3 isoform X9

    Conserved Domains (2) summary
    cd09577
    Location:856924
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:858925
    SAM; Sterile alpha motif
  9. XM_017007237.3XP_016862726.1  polyhomeotic-like protein 3 isoform X7

  10. XM_011513188.4XP_011511490.1  polyhomeotic-like protein 3 isoform X5

    Conserved Domains (2) summary
    cd09577
    Location:889957
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:891958
    SAM; Sterile alpha motif
  11. XM_005247789.4XP_005247846.1  polyhomeotic-like protein 3 isoform X1

    Conserved Domains (2) summary
    cd09577
    Location:9421010
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9441011
    SAM; Sterile alpha motif
  12. XM_006713753.3XP_006713816.1  polyhomeotic-like protein 3 isoform X3

    See identical proteins and their annotated locations for XP_006713816.1

    Conserved Domains (2) summary
    cd09577
    Location:930998
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:932999
    SAM; Sterile alpha motif
  13. XM_006713754.5XP_006713817.1  polyhomeotic-like protein 3 isoform X3

    See identical proteins and their annotated locations for XP_006713817.1

    Conserved Domains (2) summary
    cd09577
    Location:930998
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:932999
    SAM; Sterile alpha motif
  14. XM_047448982.1XP_047304938.1  polyhomeotic-like protein 3 isoform X3

  15. XM_047448990.1XP_047304946.1  polyhomeotic-like protein 3 isoform X16

  16. XM_047448989.1XP_047304945.1  polyhomeotic-like protein 3 isoform X14

  17. XM_005247791.5XP_005247848.1  polyhomeotic-like protein 3 isoform X13

    Conserved Domains (1) summary
    pfam09770
    Location:423518
    PAT1; Topoisomerase II-associated protein PAT1
  18. XM_011513189.4XP_011511491.1  polyhomeotic-like protein 3 isoform X15

    UniProtKB/TrEMBL
    E7EX82
    Related
    ENSP00000419089.1, ENST00000467570.5
    Conserved Domains (1) summary
    pfam09770
    Location:370465
    PAT1; Topoisomerase II-associated protein PAT1
  19. XM_005247793.4XP_005247850.1  polyhomeotic-like protein 3 isoform X17

    Conserved Domains (1) summary
    pfam09770
    Location:423518
    PAT1; Topoisomerase II-associated protein PAT1
  20. XM_047448991.1XP_047304947.1  polyhomeotic-like protein 3 isoform X19

  21. XM_006713757.5XP_006713820.1  polyhomeotic-like protein 3 isoform X18

    Conserved Domains (1) summary
    pfam09770
    Location:423518
    PAT1; Topoisomerase II-associated protein PAT1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    172872255..172966417 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)