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    PHC3 polyhomeotic homolog 3 [ Homo sapiens (human) ]

    Gene ID: 80012, updated on 3-Dec-2024

    Summary

    Official Symbol
    PHC3provided by HGNC
    Official Full Name
    polyhomeotic homolog 3provided by HGNC
    Primary source
    HGNC:HGNC:15682
    See related
    Ensembl:ENSG00000173889 MIM:620031; 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 DNA-templated transcription. Located in nucleoplasm. Part of PRC1 complex. [provided by Alliance of Genome Resources, Nov 2024]
    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
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (170087584..170181733, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172872255..172966417, complement)
    RS_2024_09 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 H3K4me1 hESC enhancer GRCh37_chr3:169779520-169780041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169780042-169780562 Neighboring gene G protein-coupled receptor 160 Neighboring gene MPRA-validated peak4913 silencer Neighboring gene uncharacterized LOC124909456 Neighboring gene KMT5A pseudogene 3 Neighboring gene MPRA-validated peak4915 silencer Neighboring gene uncharacterized LOC105374209 Neighboring gene RNA, U6 small nuclear 315, pseudogene Neighboring gene RNA, U7 small nuclear 32 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14883 Neighboring gene protein kinase C iota Neighboring gene Sharpr-MPRA regulatory region 5121 Neighboring gene MPRA-validated peak4916 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:170079595-170080095 Neighboring gene MPRA-validated peak4917 silencer Neighboring gene SKI like proto-oncogene

    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

    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
     
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    Component Evidence Code Pubs
    part_of PRC1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    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
      A2RRP9, Q5HYF0, Q6NSG2, Q8NDX5, Q8NFT7, Q8NFZ1, Q8TBM2, Q9H971, Q9H9I4
      UniProtKB/TrEMBL
      A5YM43
      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/TrEMBL
      A5YM43
      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: GCF_000001405.40-RS_2024_08

    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

      UniProtKB/TrEMBL
      A5YM43
    2. XM_047448987.1XP_047304943.1  polyhomeotic-like protein 3 isoform X10

      UniProtKB/TrEMBL
      A5YM43
    3. XM_047448986.1XP_047304942.1  polyhomeotic-like protein 3 isoform X8

      UniProtKB/TrEMBL
      A5YM43
    4. XM_047448984.1XP_047304940.1  polyhomeotic-like protein 3 isoform X6

      UniProtKB/TrEMBL
      A5YM43
    5. XM_047448983.1XP_047304939.1  polyhomeotic-like protein 3 isoform X4

      UniProtKB/TrEMBL
      A5YM43
    6. XM_017007235.3XP_016862724.1  polyhomeotic-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A5YM43
    7. XM_017007238.3XP_016862727.1  polyhomeotic-like protein 3 isoform X11

      UniProtKB/TrEMBL
      A5YM43
    8. XM_006713756.4XP_006713819.1  polyhomeotic-like protein 3 isoform X9

      UniProtKB/TrEMBL
      A5YM43
      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

      UniProtKB/TrEMBL
      A5YM43
    10. XM_011513188.4XP_011511490.1  polyhomeotic-like protein 3 isoform X5

      UniProtKB/TrEMBL
      A5YM43
      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

      UniProtKB/TrEMBL
      A5YM43
      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

      UniProtKB/TrEMBL
      A5YM43
      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

      UniProtKB/TrEMBL
      A5YM43
      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

      UniProtKB/TrEMBL
      A5YM43
    15. XM_047448990.1XP_047304946.1  polyhomeotic-like protein 3 isoform X16

      UniProtKB/TrEMBL
      B4E2T1
    16. XM_047448989.1XP_047304945.1  polyhomeotic-like protein 3 isoform X14

      UniProtKB/TrEMBL
      B4E2T1
    17. XM_005247791.5XP_005247848.1  polyhomeotic-like protein 3 isoform X13

      UniProtKB/TrEMBL
      B4E2T1
      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
      B4E2T1, 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)

    mRNA and Protein(s)

    1. XM_054347955.1XP_054203930.1  polyhomeotic-like protein 3 isoform X12

      UniProtKB/TrEMBL
      A5YM43
    2. XM_054347953.1XP_054203928.1  polyhomeotic-like protein 3 isoform X10

      UniProtKB/TrEMBL
      A5YM43
    3. XM_054347951.1XP_054203926.1  polyhomeotic-like protein 3 isoform X8

      UniProtKB/TrEMBL
      A5YM43
    4. XM_054347949.1XP_054203924.1  polyhomeotic-like protein 3 isoform X6

      UniProtKB/TrEMBL
      A5YM43
    5. XM_054347947.1XP_054203922.1  polyhomeotic-like protein 3 isoform X4

      UniProtKB/TrEMBL
      A5YM43
    6. XM_054347943.1XP_054203918.1  polyhomeotic-like protein 3 isoform X2

      UniProtKB/TrEMBL
      A5YM43
    7. XM_054347954.1XP_054203929.1  polyhomeotic-like protein 3 isoform X11

      UniProtKB/TrEMBL
      A5YM43
    8. XM_054347952.1XP_054203927.1  polyhomeotic-like protein 3 isoform X9

      UniProtKB/TrEMBL
      A5YM43
    9. XM_054347950.1XP_054203925.1  polyhomeotic-like protein 3 isoform X7

      UniProtKB/TrEMBL
      A5YM43
    10. XM_054347948.1XP_054203923.1  polyhomeotic-like protein 3 isoform X5

      UniProtKB/TrEMBL
      A5YM43
    11. XM_054347942.1XP_054203917.1  polyhomeotic-like protein 3 isoform X1

      UniProtKB/TrEMBL
      A5YM43
    12. XM_054347944.1XP_054203919.1  polyhomeotic-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A5YM43
    13. XM_054347945.1XP_054203920.1  polyhomeotic-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A5YM43
    14. XM_054347946.1XP_054203921.1  polyhomeotic-like protein 3 isoform X3

      UniProtKB/TrEMBL
      A5YM43
    15. XM_054347958.1XP_054203933.1  polyhomeotic-like protein 3 isoform X20

      UniProtKB/TrEMBL
      A5YM43
    16. XM_054347960.1XP_054203935.1  polyhomeotic-like protein 3 isoform X16

      UniProtKB/TrEMBL
      B4E2T1
    17. XM_054347957.1XP_054203932.1  polyhomeotic-like protein 3 isoform X14

      UniProtKB/TrEMBL
      B4E2T1
    18. XM_054347956.1XP_054203931.1  polyhomeotic-like protein 3 isoform X13

      UniProtKB/TrEMBL
      B4E2T1
    19. XM_054347959.1XP_054203934.1  polyhomeotic-like protein 3 isoform X15

      UniProtKB/TrEMBL
      B4E2T1, E7EX82
    20. XM_054347961.1XP_054203936.1  polyhomeotic-like protein 3 isoform X17

    21. XM_054347963.1XP_054203938.1  polyhomeotic-like protein 3 isoform X19

    22. XM_054347962.1XP_054203937.1  polyhomeotic-like protein 3 isoform X18