Cdx1 caudal type homeo box 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cdx1provided by RGD
Official Full Name: caudal type homeo box 1provided by RGD
Primary source: RGD:621233
See related: EnsemblRapid:ENSRNOG00000060334 AllianceGenome:RGD:621233
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 DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and methyl-CpG binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II and regulation of somitogenesis. Predicted to act upstream of or within anterior/posterior pattern specification and bone morphogenesis. Predicted to be located in nucleus. Orthologous to human CDX1 (caudal type homeobox 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 4.8), Thymus (RPKM 0.6) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 18q12.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (56742970..56761299, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (54472587..54490913, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (56337485..56355477, complement)

Chromosome 18 - NC_086036.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Downregulation of Cdx2 at the time of cloacal separation into the primitive rectum and UGS might thus be related to the development of ARM.
Title: Temporal and spatial expression of caudal-type homeobox gene-2 during hindgut development in rat embryos with ethylenethiourea-induced anorectal malformations.
Perinatal undernutrition associated with reduced gene expression of Cdx1 in adult offspring fed a high-fat diet.
Title: Perinatal undernutrition alters intestinal alkaline phosphatase and its main transcription factors KLF4 and Cdx1 in adult offspring fed a high-fat diet.
Downregulation of Cdx1 at the time of cloacal separation into rectum and urethra might be related to the development of ARM in the rat.
Title: Temporal and spatial expression of caudal-type homeobox gene-1 in the development of anorectal malformations in rat embryos.
Cdx1 has a role in apoB mrna editing, which is part of the cytodifferentiation function of the small intestine
Title: Developmental regulation of apolipoprotein B mRNA editing is an autonomous function of small intestine involving homeobox gene Cdx1.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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	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	TAS Traceable Author Statement more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables methyl-CpG binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables methyl-CpG binding	ISS Inferred from Sequence or Structural Similarity 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 cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in bone morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pattern specification process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of somitogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of somitogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of somitogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein CDX-1

Names: caudal type homeobox transcription factor 1; caudal-type homeobox protein 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.