ALX1 ALX homeobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALX1provided by HGNC
Official Full Name: ALX homeobox 1provided by HGNC
Primary source: HGNC:HGNC:1494
See related: Ensembl:ENSG00000180318 MIM:601527
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FND3; CART1; HEL23
Summary: The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse gene lead to neural tube defects such as acrania and meroanencephaly. [provided by RefSeq, Jul 2008]
Expression: Biased expression in kidney (RPKM 1.7), ovary (RPKM 0.6) and 5 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 12q21.31

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	12	NC_000012.12 (85280220..85301784)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (85673713..85695562)

Chromosome 12 - NC_000012.12 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ALX1 is highly expressed in human melanoma tissues and cell lines. Knockdown of ALX1 suppressed the proliferation and invasion of melanoma cells.
Title: Knockdown of aristaless-like homeobox1 inhibits epithelial-mesenchymal transition through Wnt/β-catenin signaling pathway in melanoma cells.
According to our analysis, three proteins, namely aristaless-like homeobox1 isoform X1 (ALX1), major histocompatibility complex polypeptide-related sequence A (MICA), and uncharacterized protein C14orf105 isoform X12 were found to be potential markers for Opisthorchis viverrini (OV)- infection, as they were predominantly found in all OV-infected groups
Title: Novel Potential Biomarkers for <i>Opisthorchis viverrini</i> Infection and Associated Cholangiocarcinoma.
Our study concludes that the splice site variant identified in the ALX1 gene causes mild form of Frontonasal dysplasia.
Title: Exome sequencing revealed a novel splice site variant in the ALX1 gene underlying frontonasal dysplasia.
we identify critical roles of ALX1 in lung cancer development and progression
Title: ALX1 promotes migration and invasion of lung cancer cells through increasing snail expression.
Knockdown of the CART1 gene significantly inhibited cell invasion and proliferation and induce cell cycle arrest in S phase.
Title: [Knockdown of CART1 induces S phase arrest and inhibits invasion and migration of MDA-MB-231 breast cancer cells].
we found that depletion of ALX1 caused a dramatic cell cycle arrest, followed by massive apoptotic cell death, and eventually resulted in a significant decrease in migration and invasion of the osteosarcoma cell line studied.
Title: Depletion of ALX1 causes inhibition of migration and induction of apoptosis in human osteosarcoma.
hypermethylation of HIST1H4F, PCDHGB6, NPBWR1, ALX1, and HOXA9 was significantly associated with shorter survival in stage 1 Non-small-cell lung cancer
Title: A prognostic DNA methylation signature for stage I non-small-cell lung cancer.
ALX1 upregulated expression of the key EMT regulator Snail (SNAI1) and that it mediated EMT activation and cell invasion by ALX1.
Title: ALX1 induces snail expression to promote epithelial-to-mesenchymal transition and invasion of ovarian cancer cells.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genes encoding critical transcriptional activators for murine neural tube development and human spina bifida: a case-control study.
Disruption of CART1 (ALX1) causes extreme microphthalmia and severe facial clefting.
Title: Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Frontonasal dysplasia 3 MedGen: C3150706 OMIM: 613456 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of ALX homeobox 1 (ALX1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-N20106 (e-PCR)
- UniSTS:55859

RH68918 (e-PCR)
- UniSTS:33504

Homology

Homologs of the ALX1 gene: The ALX1 gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 317 organisms have orthologs with human gene ALX1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
RNA polymerase II regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
RNA polymerase II regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein homodimerization activity	IEA Inferred from Electronic Annotation more info
transcription corepressor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
cartilage condensation	TAS Traceable Author Statement more info	PubMed
embryonic limb morphogenesis	IEA Inferred from Electronic Annotation more info
embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
multicellular organism development	TAS Traceable Author Statement more info	PubMed
negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
negative regulation of transcription, DNA-templated	IBA Inferred from Biological aspect of Ancestor more info	PubMed
neural crest cell migration	IEA Inferred from Electronic Annotation more info
neural tube closure	IEA Inferred from Electronic Annotation more info
positive regulation of epithelial to mesenchymal transition	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription, DNA-templated	IMP Inferred from Mutant Phenotype more info	PubMed
roof of mouth development	IEA Inferred from Electronic Annotation more info
transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
Golgi apparatus	IDA Inferred from Direct Assay more info
nuclear body	IDA Inferred from Direct Assay more info
nuclear chromatin	ISA Inferred from Sequence Alignment more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed
transcription factor complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ALX homeobox protein 1

Names: CART-1; cartilage paired-class homeoprotein 1; epididymis luminal protein 23

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.