Zhx3 zinc fingers and homeoboxes 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Zhx3provided by RGD
Full Name: zinc fingers and homeoboxes 3provided by RGD
Primary source: RGD:631431
See related: EnsemblRapid:ENSRNOG00000027988 AllianceGenome:RGD:631431
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
Also known as: Tix1
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Is active in nucleus. Orthologous to human ZHX3 (zinc fingers and homeoboxes 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 144.0), Adrenal (RPKM 122.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (169837497..169968371, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (149417787..149548671, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (156759820..156868173, complement)

Chromosome 3 - NC_086021.1 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?

ZHX proteins 1, 2 and 3 are major transcriptional mediators of podocyte disease
Title: ZHX proteins regulate podocyte gene expression during the development of nephrotic syndrome.

Submit: New GeneRIF Correction

General gene information

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Markers

Zhx3 (e-PCR), detects polymorphism
- UniSTS:547390

RH137720 (e-PCR)
- UniSTS:219807

RH137781 (e-PCR)
- UniSTS:219868

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IC Inferred by Curator more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of osteoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: zinc fingers and homeoboxes protein 3

Names: triple homeobox 1; zinc finger and homeodomain protein 3

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_001047097.2 → NP_001040562.1 zinc fingers and homeoboxes protein 3

See identical proteins and their annotated locations for NP_001040562.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6

Related

ENSRNOP00000073211.3, ENSRNOT00000091208.3

Conserved Domains (3) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

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_086021.1 Reference GRCr8

Range

169837497..169968371 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063283858.1 → XP_063139928.1 zinc fingers and homeoboxes protein 3 isoform X2

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6
XM_008762344.4 → XP_008760566.1 zinc fingers and homeoboxes protein 3 isoform X2

See identical proteins and their annotated locations for XP_008760566.1

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6

Conserved Domains (3) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez
XM_063283861.1 → XP_063139931.1 zinc fingers and homeoboxes protein 3 isoform X2

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6
XM_063283860.1 → XP_063139930.1 zinc fingers and homeoboxes protein 3 isoform X2

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6
XM_063283859.1 → XP_063139929.1 zinc fingers and homeoboxes protein 3 isoform X2

UniProtKB/Swiss-Prot

Q1I1B1, Q80Z36

UniProtKB/TrEMBL

A6JWZ6
XM_039105096.2 → XP_038961024.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_006235480.5 → XP_006235542.1 zinc fingers and homeoboxes protein 3 isoform X1

See identical proteins and their annotated locations for XP_006235542.1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_006235475.5 → XP_006235537.1 zinc fingers and homeoboxes protein 3 isoform X1

See identical proteins and their annotated locations for XP_006235537.1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_039105098.2 → XP_038961026.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_063283856.1 → XP_063139926.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5
XM_063283855.1 → XP_063139925.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5
XM_063283854.1 → XP_063139924.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5
XM_063283853.1 → XP_063139923.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5
XM_006235476.4 → XP_006235538.1 zinc fingers and homeoboxes protein 3 isoform X1

See identical proteins and their annotated locations for XP_006235538.1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_006235474.5 → XP_006235536.1 zinc fingers and homeoboxes protein 3 isoform X1

See identical proteins and their annotated locations for XP_006235536.1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_039105099.2 → XP_038961027.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_063283857.1 → XP_063139927.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5
XM_039105097.2 → XP_038961025.1 zinc fingers and homeoboxes protein 3 isoform X1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain
XM_006235477.5 → XP_006235539.1 zinc fingers and homeoboxes protein 3 isoform X1

See identical proteins and their annotated locations for XP_006235539.1

UniProtKB/TrEMBL

A0A0G2K4X5

Conserved Domains (4) summary

smart00389
Location:614 → 659

HOX; Homeodomain

cd00086
Location:493 → 546

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.

pfam11569
Location:845 → 887

Homez; Homeodomain leucine-zipper encoding, Homez

pfam18387
Location:105 → 157

zf_C2H2_ZHX; Zinc-fingers and homeoboxes C2H2 finger domain