Phc1 polyhomeotic 1 [Mus musculus (house mouse)] - Gene

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: human all
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Genomic context

Location:: 6 F1; 6 57.52 cM

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (122294690..122317551, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (122317731..122340227, complement)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PcG complex 1, involving Rae28 and Cdt1, supports the activity of hematopoietic stem cells by enhancing cycling capability and hematopoietic activity through direct regulation of Geminin
Title: Polycomb-group complex 1 acts as an E3 ubiquitin ligase for Geminin to sustain hematopoietic stem cell activity.
rae28 has a crucial role in sustaining the activity of hematopoietic stem cells to maintain hematopoiesis
Title: Polycomb group gene rae28 is required for sustaining activity of hematopoietic stem cells.
in vivo results clearly indicate that Polycomb-group gene rae28 is indispensable for the long-term repopulating ability of HSCs
Title: Defective long-term repopulating ability in hematopoietic stem cells lacking the Polycomb-group gene rae28.
Gene rae28 is involved in cardiac morphogenesis through a non cardiomyocyte pathway. However, cardiomyocyte-specific overexpression of rae28 caused dilated cardiomyopathy.
Title: Overexpression of Polycomb-group gene rae28 in cardiomyocytes does not complement abnormal cardiac morphogenesis in mice lacking rae28 but causes dilated cardiomyopathy.
The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis.
Title: The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis.
polymeric Scm complexes could extend beyond the local domains of polymeric Ph complexes on chromatin, possibly playing a role in long range repression
Title: Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer.
functional overlap between Phc2 and Phc1 along with a strict dose-dependent requirement during anterior-posterior (A-P) patterning
Title: Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate polycomb repression of Hox genes.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW557034 (e-PCR)
- UniSTS:179456

Phc1 (e-PCR), detects polymorphism
- UniSTS:536543

Gene Ontology Provided by MGI

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	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
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

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cellular response to retinoic acid	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of sex chromatin	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

NM_001042623.3 → NP_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:889 → 957

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:427 → 557

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:782 → 889

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
NM_001271579.2 → NP_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

P70359, Q64028, Q64307, Q7TT35, Q8BZ80

UniProtKB/TrEMBL

Q3TJ47

Related

ENSMUSP00000078514.4, ENSMUST00000079560.10

Conserved Domains (4) summary

cd09577
Location:941 → 1009

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:943 → 1010

SAM; Sterile alpha motif

pfam06467
Location:798 → 833

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:834 → 940

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
NM_001355215.2 → NP_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

UniProtKB/TrEMBL

Q3TJ47

Conserved Domains (3) summary

cd09577
Location:957 → 1025

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

pfam16616
Location:850 → 956

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

cl26464
Location:495 → 625

Atrophin-1; Atrophin-1 family
NM_001408247.1 → NP_001395176.1 polyhomeotic-like protein 1 isoform b

Status: VALIDATED

Source sequence(s)

AC153579

UniProtKB/TrEMBL

Q3V116

Related

ENSMUSP00000080532.4, ENSMUST00000081849.10
NM_001408248.1 → NP_001395177.1 polyhomeotic-like protein 1 isoform b

Status: VALIDATED

Source sequence(s)

AC153579

UniProtKB/TrEMBL

Q3V116

Related

ENSMUSP00000108219.3, ENSMUST00000112600.9
NM_001408249.1 → NP_001395178.1 polyhomeotic-like protein 1 isoform c

Status: VALIDATED

Source sequence(s)

AC153579
NM_001408250.1 → NP_001395179.1 polyhomeotic-like protein 1 isoform d

Status: VALIDATED

Source sequence(s)

AC153579
NM_007905.4 → NP_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

P70359, Q64028, Q64307, Q7TT35, Q8BZ80

UniProtKB/TrEMBL

Q3TJ47

Related

ENSMUSP00000125568.2, ENSMUST00000161739.8

Conserved Domains (4) summary

cd09577
Location:941 → 1009

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

smart00454
Location:943 → 1010

SAM; Sterile alpha motif

pfam06467
Location:798 → 833

zf-FCS; MYM-type Zinc finger with FCS sequence motif

pfam16616
Location:834 → 940

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2

RNA

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
NR_176619.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC153579
NR_176620.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC153579

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

122294690..122317551 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030255141.2 → XP_030111001.1 polyhomeotic-like protein 1 isoform X4

UniProtKB/TrEMBL

Q3TJ47

Conserved Domains (3) summary

cd09577
Location:916 → 984

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:454 → 584

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:809 → 915

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_006505498.2 → XP_006505561.1 polyhomeotic-like protein 1 isoform X1

UniProtKB/TrEMBL

Q3TJ47

Conserved Domains (3) summary

cd09577
Location:971 → 1039

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:509 → 639

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:864 → 970

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_006505500.2 → XP_006505563.1 polyhomeotic-like protein 1 isoform X3

UniProtKB/TrEMBL

Q3TJ47

Conserved Domains (3) summary

cd09577
Location:919 → 987

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:457 → 587

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:812 → 918

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_017321382.3 → XP_017176871.1 polyhomeotic-like protein 1 isoform X6

UniProtKB/TrEMBL

E0CXV8

Conserved Domains (3) summary

cd09577
Location:839 → 907

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:377 → 507

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:732 → 838

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2
XM_030255142.2 → XP_030111002.1 polyhomeotic-like protein 1 isoform X7

UniProtKB/TrEMBL

E0CXV8

Conserved Domains (3) summary

cd09577
Location:764 → 832

SAM_Ph1,2,3; SAM domain of Ph (polyhomeotic) proteins of Polycomb group

PHA03247
Location:302 → 432

PHA03247; large tegument protein UL36; Provisional

pfam16616
Location:657 → 763

PHC2_SAM_assoc; Unstructured region on Polyhomeotic-like protein 1 and 2