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RAI1 retinoic acid induced 1 [ Homo sapiens (human) ]

Gene ID: 10743, updated on 7-Apr-2024

Summary

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Official Symbol
RAI1provided by HGNC
Official Full Name
retinoic acid induced 1provided by HGNC
Primary source
HGNC:HGNC:9834
See related
Ensembl:ENSG00000108557 MIM:607642; AllianceGenome:HGNC:9834
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
SMS; SMCR
Summary
This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in spleen (RPKM 5.1), endometrium (RPKM 4.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
17p11.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17681458..17811453)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17628072..17758044)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17584772..17714767)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene phosphatidylethanolamine N-methyltransferase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17494467-17495208 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17506274-17506774 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17516315-17516931 Neighboring gene Sharpr-MPRA regulatory region 11476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17525146-17526020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17526021-17526896 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529033-17529938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529939-17530844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17570789-17571290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17571291-17571790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17578718-17579346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17584813-17585414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596270-17596984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596985-17597697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8250 Neighboring gene uncharacterized LOC124903943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602043-17602561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602562-17603079 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17603559-17604070 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 2 Neighboring gene Sharpr-MPRA regulatory region 3199 Neighboring gene Sharpr-MPRA regulatory region 10129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17620721-17621465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17628326-17629207 Neighboring gene Sharpr-MPRA regulatory region 1571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17643281-17643912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17646375-17646876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17655569-17656270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17665979-17666591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17666592-17667203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11810 Neighboring gene uncharacterized LOC124903942 Neighboring gene RAI1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17682070-17682959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17683849-17684738 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17685874-17686374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17687340-17687880 Neighboring gene Sharpr-MPRA regulatory region 10806 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17693241-17693447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17696322-17697048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17697049-17697773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17704013-17704802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17704803-17705590 Neighboring gene Sharpr-MPRA regulatory region 10333 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17716071-17716629 Neighboring gene microRNA 6777 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene microRNA 33b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Possible underreporting of pathogenic variants in RAI1 causing Smith-Magenis syndrome. Boot E, et al. Am J Med Genet A, 2021 Oct. PMID 34089220, Free PMC Article
  2. Twenty-four-hour motor activity and body temperature patterns suggest altered central circadian timekeeping in Smith-Magenis syndrome, a neurodevelopmental disorder. Smith ACM, et al. Am J Med Genet A, 2019 Feb. PMID 30690916, Free PMC Article
  3. Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men. Chen H, et al. Am J Respir Cell Mol Biol, 2018 Mar. PMID 29077507, Free PMC Article
  4. Association of premenstrual/menstrual symptoms with perinatal depression and a polymorphic repeat in the polyglutamine tract of the retinoic acid induced 1 gene. Tan EC, et al. J Affect Disord, 2014 Jun. PMID 24751306
  5. Expression in the human brain of retinoic acid induced 1, a protein associated with neurobehavioural disorders. Fragoso YD, et al. Brain Struct Funct, 2015 Mar. PMID 24519454, Free PMC Article

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pentanucleotide Repeat Insertions in RAI1 Cause Benign Adult Familial Myoclonic Epilepsy Type 8.
    Title: Pentanucleotide Repeat Insertions in RAI1 Cause Benign Adult Familial Myoclonic Epilepsy Type 8.
  2. Intellectual and Behavioral Phenotypes of Smith-Magenis Syndrome: Comparisons between Individuals with a 17p11.2 Deletion and Pathogenic RAI1 Variant.
    Title: Intellectual and Behavioral Phenotypes of Smith-Magenis Syndrome: Comparisons between Individuals with a 17p11.2 Deletion and Pathogenic RAI1 Variant.
  3. Possible underreporting of pathogenic variants in RAI1 causing Smith-Magenis syndrome.
    Title: Possible underreporting of pathogenic variants in RAI1 causing Smith-Magenis syndrome.
  4. Sleep disturbances and phase-advanced circadian rhythm in bodytemperature may be related to a complex biology that stems from theinterstitial deletion or mutation ofRAI1within chromosome 17p11.2.
    Title: Twenty-four-hour motor activity and body temperature patterns suggest altered central circadian timekeeping in Smith-Magenis syndrome, a neurodevelopmental disorder.
  5. This study identified from multiethnic meta-analyses stronger associations between the RAI1 locus and non-REM apnea-hypopnea index in men compared with women.
    Title: Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men.
  6. This study provides information about the inheritance pattern and recurrence risk for patients with identified variants and demonstrates clinical and genetic overlap of neurodevelopmental disorders
    Title: Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants.
  7. we report molecular and clinical characterizations of six subjects with the reciprocal phenomenon of deletions spanning both genes, i.e., PMP22-RAI1 deletions. Systematic clinical studies revealed features consistent with SMS, including features of intellectual disability, speech and gross motor delays, behavioral problems and ocular abnormalities.
    Title: Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy.
  8. RAI1 polymorphisms rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1, respectively, in Smith-Magenis and Potocki-Lupski syndromes patients.
    Title: Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain.
  9. Mutations in RAI1, OTOF, and SLC26A4 may have roles in nonsyndromic hearing loss in Altaian families in Siberia
    Title: Whole Exome Sequencing Reveals Homozygous Mutations in RAI1, OTOF, and SLC26A4 Genes Associated with Nonsyndromic Hearing Loss in Altaian Families (South Siberia).
  10. South American cohort did not confirm the effect of the four candidate loci as modifier of onset age: mithocondrial A10398G polymorphism and CAGn at RAI1, CACNA1A, ATXN3, and ATXN7 genes
    Title: ATXN3, ATXN7, CACNA1A, and RAI1 Genes and Mitochondrial Polymorphism A10398G Did Not Modify Age at Onset in Spinocerebellar Ataxia Type 2 Patients from South America.
Submit: New GeneRIF Correction See all GeneRIFs (31)

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
Smith-Magenis syndrome
MedGen: C0795864 OMIM: 182290 GeneReviews: Smith-Magenis Syndrome
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-10-13)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-10-13)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
EBI GWAS Catalog
Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1820, MGC12824, DKFZp434A139

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in circadian regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
retinoic acid-induced protein 1
Names
Smith-Magenis syndrome chromosome region

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.

Genomic

  1. NG_007101.2 RefSeqGene

    Range
    4986..134981
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_030665.4 → NP_109590.3  retinoic acid-induced protein 1

    See identical proteins and their annotated locations for NP_109590.3

    Status: REVIEWED

    Source sequence(s)
    AB058723, AC078903, AL834468, AY172136
    Consensus CDS
    CCDS11188.1
    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69
    Related
    ENSP00000323074.4, ENST00000353383.6
    Conserved Domains (1) summary
    cd15700
    Location:1687 → 1902
    ePHD_RAI1; Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    17681458..17811453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435151.1 → XP_047291107.1  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  2. XM_047435152.1 → XP_047291108.1  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  3. XM_047435153.1 → XP_047291109.1  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  4. XM_047435149.1 → XP_047291105.1  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  5. XM_017024027.2 → XP_016879516.2  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  6. XM_047435150.1 → XP_047291106.1  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

  7. XM_017024028.3 → XP_016879517.2  retinoic acid-induced protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z5J4, Q8N3B4, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    17628072..17758044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314742.1 → XP_054170717.1  retinoic acid-induced protein 1 isoform X1

  2. XM_054314743.1 → XP_054170718.1  retinoic acid-induced protein 1 isoform X1

  3. XM_054314744.1 → XP_054170719.1  retinoic acid-induced protein 1 isoform X1

  4. XM_054314738.1 → XP_054170713.1  retinoic acid-induced protein 1 isoform X1

  5. XM_054314739.1 → XP_054170714.1  retinoic acid-induced protein 1 isoform X1

  6. XM_054314741.1 → XP_054170716.1  retinoic acid-induced protein 1 isoform X1

  7. XM_054314740.1 → XP_054170715.1  retinoic acid-induced protein 1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017574.1: Suppressed sequence

    Description
    NM_017574.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.

  2. NM_152256.1: Suppressed sequence

    Description
    NM_152256.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z5J4.2 GenPept UniProtKB/Swiss-Prot:Q7Z5J4

Gene LinkOut

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