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PHC1 polyhomeotic homolog 1 [ Homo sapiens (human) ]

Gene ID: 1911, updated on 7-Jan-2024

Summary

Official Symbol
PHC1provided by HGNC
Official Full Name
polyhomeotic homolog 1provided by HGNC
Primary source
HGNC:HGNC:3182
See related
Ensembl:ENSG00000111752 MIM:602978; AllianceGenome:HGNC:3182
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
EDR1; HPH1; RAE28; MCPH11
Summary
This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 40.0), endometrium (RPKM 27.7) and 25 other tissues See more
Orthologs
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Genomic context

See PHC1 in Genome Data Viewer
Location:
12p13.31
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (8913843..8941467)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (8896088..8923703)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9067105..9094063)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8940741-8941280 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8941281-8941820 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8942577-8943254 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8941899-8942576 Neighboring gene A2ML1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8947958-8948568 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8957581-8958288 Neighboring gene long intergenic non-protein coding RNA 2972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8958995-8959702 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8962654-8963394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8963395-8964136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8967023-8967549 Neighboring gene Sharpr-MPRA regulatory region 8322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8980966-8981708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8984681-8985424 Neighboring gene alpha-2-macroglobulin like 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9057572-9058228 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:9060851-9061506 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:9064238-9064790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9101505-9102410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9102411-9103315 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:9108425-9109624 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene killer cell lectin like receptor G1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4222 Neighboring gene VDAC2 pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 612

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

Phenotypes

Associated conditions

Description Tests
Microcephaly 11, primary, autosomal recessive
MedGen: C3809431 OMIM: 615414 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 nuclear body IEA
Inferred from Electronic Annotation
more info
 
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 
part_of sex chromatin IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
polyhomeotic-like protein 1
Names
early development regulator 1 (homolog of polyhomeotic 1)
early development regulatory protein 1
polyhomeotic-like 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.

Genomic

  1. NG_042273.1 RefSeqGene

    Range
    4790..31748
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001413738.1NP_001400667.1  polyhomeotic-like protein 1 isoform a

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/Swiss-Prot
    D3DUV4, P78364, Q8WVM3, Q9BU63
    UniProtKB/TrEMBL
    B2RXH1
  2. NM_001413739.1NP_001400668.1  polyhomeotic-like protein 1 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  3. NM_001413740.1NP_001400669.1  polyhomeotic-like protein 1 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  4. NM_001413741.1NP_001400670.1  polyhomeotic-like protein 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    J3KQH6
    Related
    ENSP00000399194.2, ENST00000433083.6
  5. NM_001413742.1NP_001400671.1  polyhomeotic-like protein 1 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  6. NM_001413743.1NP_001400672.1  polyhomeotic-like protein 1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  7. NM_001413744.1NP_001400673.1  polyhomeotic-like protein 1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  8. NM_001413745.1NP_001400674.1  polyhomeotic-like protein 1 isoform h

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  9. NM_001413746.1NP_001400675.1  polyhomeotic-like protein 1 isoform i

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  10. NM_001413747.1NP_001400676.1  polyhomeotic-like protein 1 isoform j

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  11. NM_001413748.1NP_001400677.1  polyhomeotic-like protein 1 isoform k

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  12. NM_001413749.1NP_001400678.1  polyhomeotic-like protein 1 isoform k

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  13. NM_001413750.1NP_001400679.1  polyhomeotic-like protein 1 isoform l

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  14. NM_001413751.1NP_001400680.1  polyhomeotic-like protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  15. NM_001413752.1NP_001400681.1  polyhomeotic-like protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    B2RXH1
  16. NM_001413753.1NP_001400682.1  polyhomeotic-like protein 1 isoform n

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    J3KQH6
  17. NM_001413754.1NP_001400683.1  polyhomeotic-like protein 1 isoform o

    Status: REVIEWED

    Source sequence(s)
    AC006581
    UniProtKB/TrEMBL
    J3KQH6
  18. NM_004426.3NP_004417.2  polyhomeotic-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_004417.2

    Status: REVIEWED

    Source sequence(s)
    AC006581, BC073964, BM473731, BX640639, CN388283, CN388285, CN388316, U89277
    Consensus CDS
    CCDS8597.1
    UniProtKB/Swiss-Prot
    D3DUV4, P78364, Q8WVM3, Q9BU63
    UniProtKB/TrEMBL
    B2RXH1
    Related
    ENSP00000437659.1, ENST00000544916.6
    Conserved Domains (4) summary
    cd09577
    Location:9351003
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9371004
    SAM; Sterile alpha motif
    pfam06467
    Location:792827
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:828934
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RNA

  1. NR_182209.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC006581

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    8913843..8941467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520603.3XP_011518905.1  polyhomeotic-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011518905.1

    UniProtKB/TrEMBL
    B2RXH1
    Conserved Domains (4) summary
    cd09577
    Location:9521020
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9541021
    SAM; Sterile alpha motif
    pfam06467
    Location:809844
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:845951
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  2. XM_011520599.3XP_011518901.1  polyhomeotic-like protein 1 isoform X2

    UniProtKB/TrEMBL
    B2RXH1
    Conserved Domains (4) summary
    cd09577
    Location:9441012
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9461013
    SAM; Sterile alpha motif
    pfam06467
    Location:801836
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:837943
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  3. XM_011520600.3XP_011518902.1  polyhomeotic-like protein 1 isoform X3

    UniProtKB/TrEMBL
    B2RXH1
    Conserved Domains (4) summary
    cd09577
    Location:902970
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:904971
    SAM; Sterile alpha motif
    pfam06467
    Location:759794
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:795901
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  4. XM_017018957.2XP_016874446.1  polyhomeotic-like protein 1 isoform X4

    UniProtKB/TrEMBL
    B2RXH1
  5. XM_047428475.1XP_047284431.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    B2RXH1
  6. XM_017018955.3XP_016874444.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    B2RXH1
    Conserved Domains (4) summary
    cd09577
    Location:9521020
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9541021
    SAM; Sterile alpha motif
    pfam06467
    Location:809844
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:845951
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    8896088..8923703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371354.1XP_054227329.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    B2RXH1
  2. XM_054371356.1XP_054227331.1  polyhomeotic-like protein 1 isoform X2

    UniProtKB/TrEMBL
    B2RXH1
  3. XM_054371358.1XP_054227333.1  polyhomeotic-like protein 1 isoform X3

    UniProtKB/TrEMBL
    B2RXH1
  4. XM_054371360.1XP_054227335.1  polyhomeotic-like protein 1 isoform X5

    UniProtKB/TrEMBL
    B2RXH1
  5. XM_054371361.1XP_054227336.1  polyhomeotic-like protein 1 isoform X4

    UniProtKB/TrEMBL
    B2RXH1
  6. XM_054371362.1XP_054227337.1  polyhomeotic-like protein 1 isoform X6

    UniProtKB/TrEMBL
    B2RXH1
  7. XM_054371353.1XP_054227328.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    B2RXH1
  8. XM_054371357.1XP_054227332.1  polyhomeotic-like protein 1 isoform X3

    UniProtKB/TrEMBL
    B2RXH1
  9. XM_054371359.1XP_054227334.1  polyhomeotic-like protein 1 isoform X5

    UniProtKB/TrEMBL
    B2RXH1
  10. XM_054371355.1XP_054227330.1  polyhomeotic-like protein 1 isoform X1

    UniProtKB/TrEMBL
    B2RXH1