Pitx1 paired-like homeodomain transcription factor 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pitx1provided by MGI
Official Full Name: paired-like homeodomain transcription factor 1provided by MGI
Primary source: MGI:MGI:107374
See related: Ensembl:ENSMUSG00000021506 AllianceGenome:MGI:107374
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: Bft; Potx; Ptx1; P-OTX
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in embryonic hindlimb morphogenesis; negative regulation of DNA-templated transcription; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including branchiomeric skeletal muscle development; hindlimb morphogenesis; and myoblast fate commitment. Located in cytoplasm and nucleus. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; brain; branchial arch; limb; and sensory organ. Used to study clubfoot. Human ortholog(s) of this gene implicated in clubfoot. Orthologous to human PITX1 (paired like homeodomain 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in stomach adult (RPKM 95.5), bladder adult (RPKM 23.0) and 5 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13 B1; 13 30.06 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (55972857..55984002, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (55825044..55836190, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer.
Title: Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer.
Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.
Title: Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.
Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition.
Title: Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition.
The PITX1 is specifically expressed in TPCs, where it co-localizes with SOX2 and TRP63 and determines cell fate in mouse and human squamous cell carcinoma (SCC).
Title: De Novo PITX1 Expression Controls Bi-Stable Transcriptional Circuits to Govern Self-Renewal and Differentiation in Squamous Cell Carcinoma.
Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. Forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs.
Title: Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis.
Pitx1 distal enhancer loss have only mild effects on Pitx1 expression in the hindlimb and no overt effects on hindlimb or mandibular morphology.
Title: Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development.
data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.
Title: PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets.
Results indicate autonomously programmed differences in forelimb and hindlimb cartilage precursors of the limb skeleton are controlled, at least in part, by Pitx1 and suggest this has an important role in generating distinct limb-type morphologies.
Title: Pitx1 determines characteristic hindlimb morphologies in cartilage micromass culture.
Pitx1 targets sites that are in a similar chromatin state in Forelimbs (FLs) and hindlimbs and controls expression of patterning genes as well as the chondrogenic program.
Title: Pitx1 directly modulates the core limb development program to implement hindlimb identity.
Pitx1 influences hindlimb morphology both through the activation of hindlimb-specific enhancers as well as through the hindlimb-specific modulation of enhancers that are active in both sets of limbs
Title: Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (6) 1 citation
Targeted (2) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

Pitx1 (e-PCR), detects polymorphism
- UniSTS:144184

U71206 (e-PCR)
- UniSTS:180541

Pitx1 (e-PCR), detects polymorphism
- UniSTS:546944

Pitx1 (e-PCR), detects polymorphism
- UniSTS:527004

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within branchiomeric skeletal muscle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic hindlimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in embryonic hindlimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindlimb morphogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within hindlimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myoblast fate commitment	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pituitary gland development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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 transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: pituitary homeobox 1

Names: hindlimb-expressed homeobox protein backfoot; homeobox protein P-OTX; homeobox protein PITX1; pituitary OTX-related factor

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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)

NM_011097.2 → NP_035227.1 pituitary homeobox 1

See identical proteins and their annotated locations for NP_035227.1

Status: VALIDATED

Source sequence(s)

AC129780

Consensus CDS

CCDS26556.1

UniProtKB/Swiss-Prot

O54742, P70314, P70427

UniProtKB/TrEMBL

Q3UQH0

Related

ENSMUSP00000021968.6, ENSMUST00000021968.7

Conserved Domains (3) summary

pfam00046
Location:94 → 147

Homeobox; Homeobox domain

pfam03826
Location:277 → 294

OAR; OAR domain

pfam08430
Location:196 → 275

Forkhead_N; Forkhead N-terminal region

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_000079.7 Reference GRCm39 C57BL/6J

Range

55972857..55984002 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006517157.5 → XP_006517220.1 pituitary homeobox 1 isoform X1

See identical proteins and their annotated locations for XP_006517220.1

UniProtKB/Swiss-Prot

O54742, P70314, P70427

UniProtKB/TrEMBL

Q3UQH0

Conserved Domains (3) summary

pfam00046
Location:94 → 147

Homeobox; Homeobox domain

pfam03826
Location:277 → 294

OAR; OAR domain

pfam08430
Location:196 → 275

Forkhead_N; Forkhead N-terminal region
XM_006517158.5 → XP_006517221.1 pituitary homeobox 1 isoform X1

See identical proteins and their annotated locations for XP_006517221.1

UniProtKB/Swiss-Prot

O54742, P70314, P70427

UniProtKB/TrEMBL

Q3UQH0

Conserved Domains (3) summary

pfam00046
Location:94 → 147

Homeobox; Homeobox domain

pfam03826
Location:277 → 294

OAR; OAR domain

pfam08430
Location:196 → 275

Forkhead_N; Forkhead N-terminal region