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Phc1 polyhomeotic homolog 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 312690, updated on 2-Nov-2024

Summary

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Official Symbol
Phc1provided by RGD
Official Full Name
polyhomeotic homolog 1provided by RGD
Primary source
RGD:1309203
See related
EnsemblRapid:ENSRNOG00000015191 AllianceGenome:RGD:1309203
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in chromatin remodeling and negative regulation of DNA-templated transcription. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and cellular response to retinoic acid. Predicted to be located in nuclear body and sex chromatin. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in primary autosomal recessive microcephaly 11. Orthologous to human PHC1 (polyhomeotic homolog 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Testes (RPKM 142.7), Adrenal (RPKM 77.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Phc1 in Genome Data Viewer
Location:
4q42
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (157182348..157205504, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (155510274..155532636, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (155093947..155118838, complement)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene killer cell lectin like receptor G1 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene alpha-ketoglutarate dehydrogenase component 4-like Neighboring gene transfer RNA alanine (anticodon AGC) 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. Awad S, et al. Hum Mol Genet, 2013 Jun 1. PMID 23418308
  2. The mouse YAF2 gene generates two distinct transcripts and is expressed in pre-and postimplantation embryos. Kaneko T, et al. Gene, 2003 Oct 2. PMID 14557078
  3. Isolation and characterization of retinoic acid-inducible cDNA clones in F9 cells: one of the early inducible clones encodes a novel protein sharing several highly homologous regions with a Drosophila polyhomeotic protein. Nomura M, et al. Differentiation, 1994 Jun. PMID 8070621
  4. PRC1 complex diversity: where is it taking us? Gil J, et al. Trends Cell Biol, 2014 Nov. PMID 25065329
  5. Distinct roles of Polycomb group gene products in transcriptionally repressed and active domains of Hoxb8. Fujimura Y, et al. Development, 2006 Jun. PMID 16687444

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cellular response to retinoic acid ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
part_of PcG protein complex ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in sex chromatin ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
polyhomeotic-like protein 1
Names
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.

mRNA and Protein(s)

  1. NM_001107886.1 → NP_001101356.1  polyhomeotic-like protein 1

    See identical proteins and their annotated locations for NP_001101356.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473964
    UniProtKB/TrEMBL
    A0A8I6AHM8, A6ILE3, D3ZVD1
    Related
    ENSRNOP00000020529.5, ENSRNOT00000020529.7
    Conserved Domains (4) summary
    cd09577
    Location:973 → 1041
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:975 → 1042
    SAM; Sterile alpha motif
    pfam06467
    Location:830 → 865
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:866 → 972
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086022.1 Reference GRCr8

    Range
    157182348..157205504 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063286125.1 → XP_063142195.1  polyhomeotic-like protein 1 isoform X3

  2. XM_063286129.1 → XP_063142199.1  polyhomeotic-like protein 1 isoform X7

  3. XM_063286126.1 → XP_063142196.1  polyhomeotic-like protein 1 isoform X4

  4. XM_039107670.2 → XP_038963598.1  polyhomeotic-like protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A8I6AHM8
    Conserved Domains (2) summary
    cd09577
    Location:946 → 1014
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam16616
    Location:839 → 946
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

  5. XM_063286128.1 → XP_063142198.1  polyhomeotic-like protein 1 isoform X6

  6. XM_063286127.1 → XP_063142197.1  polyhomeotic-like protein 1 isoform X5

    Related
    ENSRNOP00000087501.2, ENSRNOT00000104598.2

  7. XM_063286123.1 → XP_063142193.1  polyhomeotic-like protein 1 isoform X1

  8. XM_063286124.1 → XP_063142194.1  polyhomeotic-like protein 1 isoform X2

Nucleotide Protein Strain
Heading Accession and Version

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