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Phc1 polyhomeotic 1 [ Mus musculus (house mouse) ]

Gene ID: 13619, updated on 21-Dec-2022

Summary

Official Symbol
Phc1provided by MGI
Official Full Name
polyhomeotic 1provided by MGI
Primary source
MGI:MGI:103248
See related
Ensembl:ENSMUSG00000040669 AllianceGenome:MGI:103248
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Edr; Edr1; Mph1; rae28; Rae-28
Summary
Enables chromatin binding activity. Acts upstream of or within cellular response to leukemia inhibitory factor and cellular response to retinoic acid. Located in nuclear body and sex chromatin. Is expressed in several structures, including alimentary system; genitourinary system; hemolymphoid system; nervous system; and sensory organ. Used to study dilated cardiomyopathy and tetralogy of Fallot. 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, Apr 2022]
Expression
Broad expression in testis adult (RPKM 55.8), CNS E14 (RPKM 22.1) and 20 other tissues See more
Orthologs
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Genomic context

See Phc1 in Genome Data Viewer
Location:
6 F1; 6 57.52 cM
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (122294690..122317946, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (122317731..122340227, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6637 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene RIKEN cDNA 1700063H04 gene Neighboring gene VISTA enhancer mm94 Neighboring gene mitochondrial ribosomal protein S36 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of PRC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in sex chromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
polyhomeotic-like protein 1
Names
early development regulator1 (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.

mRNA and Protein(s)

  1. NM_001042623.3NP_001036088.1  polyhomeotic-like protein 1 isoform b

    See identical proteins and their annotated locations for NP_001036088.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. It encodes isoform b which is shorter than isoform a. Variants 2, 6, and 7 all encode the same isoform (b).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS39620.1
    UniProtKB/TrEMBL
    Q3TJ47, Q3V116
    Related
    ENSMUSP00000123911.2, ENSMUST00000161054.8
    Conserved Domains (3) summary
    cd09577
    Location:889957
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:427557
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:782889
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  2. NM_001271579.2NP_001258508.1  polyhomeotic-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_001258508.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same isoform (a).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS20494.1
    UniProtKB/Swiss-Prot
    Q64028, Q8BZ80
    UniProtKB/TrEMBL
    Q7TT35
    Related
    ENSMUSP00000078514.4, ENSMUST00000079560.10
    Conserved Domains (4) summary
    cd09577
    Location:9411009
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9431010
    SAM; Sterile alpha motif
    pfam06467
    Location:798833
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:834940
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  3. NM_001355215.2NP_001342144.1  polyhomeotic-like protein 1 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate in-frame exon in the coding region which results in the use of a novel translation start site compared to variant 1. It encodes isoform c which has a longer N-terminus than isoform a. Variants 5 and 8 both encode the same isoform (c).
    Source sequence(s)
    AC153579
    Conserved Domains (3) summary
    cd09577
    Location:9571025
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    pfam16616
    Location:850956
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
    cl26464
    Location:495625
    Atrophin-1; Atrophin-1 family
  4. NM_001408247.1NP_001395176.1  polyhomeotic-like protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC153579
    UniProtKB/TrEMBL
    Q3V116
  5. NM_001408248.1NP_001395177.1  polyhomeotic-like protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC153579
    UniProtKB/TrEMBL
    Q3V116
  6. NM_001408249.1NP_001395178.1  polyhomeotic-like protein 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AC153579
  7. NM_001408250.1NP_001395179.1  polyhomeotic-like protein 1 isoform d

    Status: VALIDATED

    Source sequence(s)
    AC153579
  8. NM_007905.4NP_031931.2  polyhomeotic-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_031931.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (a). Both variants 1 and 3 encode the same isoform (a).
    Source sequence(s)
    AC153579
    Consensus CDS
    CCDS20494.1
    UniProtKB/Swiss-Prot
    Q8BZ80
    UniProtKB/TrEMBL
    Q7TT35
    Related
    ENSMUSP00000125568.2, ENSMUST00000161739.8
    Conserved Domains (4) summary
    cd09577
    Location:9411009
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    smart00454
    Location:9431010
    SAM; Sterile alpha motif
    pfam06467
    Location:798833
    zf-FCS; MYM-type Zinc finger with FCS sequence motif
    pfam16616
    Location:834940
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RNA

  1. NR_073364.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate donor splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC153579
    Related
    ENSMUST00000160163.8
  2. NR_176619.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC153579
  3. NR_176620.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC153579

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    122294690..122317946 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036165806.1XP_036021699.1  polyhomeotic-like protein 1 isoform X5

    Conserved Domains (3) summary
    cd09577
    Location:889957
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:427557
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:782889
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  2. XM_030255141.2XP_030111001.1  polyhomeotic-like protein 1 isoform X4

    Conserved Domains (3) summary
    cd09577
    Location:916984
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:454584
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:809915
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  3. XM_006505499.5XP_006505562.1  polyhomeotic-like protein 1 isoform X2

    Conserved Domains (3) summary
    cd09577
    Location:9681036
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:506636
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:861967
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  4. XM_006505498.2XP_006505561.1  polyhomeotic-like protein 1 isoform X1

    Conserved Domains (3) summary
    cd09577
    Location:9711039
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:509639
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:864970
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  5. XM_006505500.2XP_006505563.1  polyhomeotic-like protein 1 isoform X3

    Conserved Domains (3) summary
    cd09577
    Location:919987
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:457587
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:812918
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  6. XM_017321382.3XP_017176871.1  polyhomeotic-like protein 1 isoform X6

    Conserved Domains (3) summary
    cd09577
    Location:839907
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:377507
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:732838
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
  7. XM_030255142.2XP_030111002.1  polyhomeotic-like protein 1 isoform X7

    Conserved Domains (3) summary
    cd09577
    Location:764832
    SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group
    PHA03247
    Location:302432
    PHA03247; large tegument protein UL36; Provisional
    pfam16616
    Location:657763
    PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2