Pbx1 PBX homeobox 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pbx1provided by RGD
Official Full Name: PBX homeobox 1provided by RGD
Primary source: RGD:1308213
See related: EnsemblRapid:ENSRNOG00000070119 AllianceGenome:RGD:1308213
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and transcription corepressor binding activity. Predicted to contribute to RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including natural killer cell differentiation; nervous system development; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including hematopoietic or lymphoid organ development; positive regulation of G2/M transition of mitotic cell cycle; and regionalization. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. Biomarker of brain infarction and glaucoma. Human ortholog(s) of this gene implicated in congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay. Orthologous to human PBX1 (PBX homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Uterus (RPKM 319.2), Adrenal (RPKM 251.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q24

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (82811664..83121447, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (80278766..80588563, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (86390741..86671460, complement)

Chromosome 13 - NC_086031.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-kappaB activation.
Title: Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-κB activation.

Submit: New GeneRIF Correction

General gene information

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Markers

RH142689 (e-PCR)
- UniSTS:231936

Pbx1 (e-PCR), detects polymorphism
- UniSTS:528306

BE097482 (e-PCR)
- UniSTS:244676

AW535487 (e-PCR)
- UniSTS:260816

BI281745 (e-PCR)
- UniSTS:249570

AL033591 (e-PCR)
- UniSTS:93438

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adrenal gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic hemopoiesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system development	ISO Inferred from Sequence Orthology more info
involved_in natural killer cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of G2/M transition of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within proximal/distal pattern formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of ossification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spleen development	ISO Inferred from Sequence Orthology more info
acts_upstream_of stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within thymus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within urogenital system development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: pre-B-cell leukemia transcription factor 1

Names: pre-B-cell leukemia homeobox 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_001100681.2 → NP_001094151.1 pre-B-cell leukemia transcription factor 1 isoform b

See identical proteins and their annotated locations for NP_001094151.1

Status: VALIDATED

Source sequence(s)

BC098847, BC161983, JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I6AM04, B1WC30

Related

ENSRNOP00000096551.1, ENSRNOT00000106300.2

Conserved Domains (2) summary

cd00086
Location:234 → 294

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:40 → 232

PBC; PBC domain
NM_001134862.2 → NP_001128334.1 pre-B-cell leukemia transcription factor 1 isoform a

See identical proteins and their annotated locations for NP_001128334.1

Status: VALIDATED

Source sequence(s)

BC098847, FN805837, JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I5ZR45

Related

ENSRNOP00000080916.1, ENSRNOT00000103202.2

Conserved Domains (2) summary

cd00086
Location:234 → 294

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:40 → 232

PBC; PBC domain

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

NC_086031.1 Reference GRCr8

Range

82811664..83121447 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090792.2 → XP_038946720.1 pre-B-cell leukemia transcription factor 1 isoform X1

UniProtKB/TrEMBL

F7EV88

Related

ENSRNOP00000027996.5, ENSRNOT00000027996.6

Conserved Domains (2) summary

cd00086
Location:234 → 294

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:40 → 232

PBC; PBC domain
XM_039090794.2 → XP_038946722.1 pre-B-cell leukemia transcription factor 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AM04, B1WC30

Conserved Domains (2) summary

cd00086
Location:234 → 294

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:40 → 232

PBC; PBC domain