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

    Gene ID: 10743, updated on 10-Dec-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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    See RAI1 in Genome Data Viewer
    Location:
    17p11.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17681458..17811453)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17628072..17758044)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Smith-Magenis syndrome: haploinsufficiency of RAI1 results in altered gene regulation in neurological and metabolic pathways. Elsea SH, et al. Expert Rev Mol Med, 2011 Apr 19. PMID 21545756
    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 (95) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Overlapping hearing and communication profiles for the deletion and the RAI1 variant form of Smith-Magenis Syndrome (SMS).
      Title: Overlapping hearing and communication profiles for the deletion and the RAI1 variant form of Smith-Magenis Syndrome (SMS).
    2. N[6]-methyladenosine demethylase ALKBH5 suppresses malignancy of esophageal cancer by regulating microRNA biogenesis and RAI1 expression.
      Title: N(6)-methyladenosine demethylase ALKBH5 suppresses malignancy of esophageal cancer by regulating microRNA biogenesis and RAI1 expression.
    3. Allele-Specific Regulation of the Candidate Autism Liability Gene RAI1 by the Enhancer Variant rs4925102 (C/G).
      Title: Allele-Specific Regulation of the Candidate Autism Liability Gene RAI1 by the Enhancer Variant rs4925102 (C/G).
    4. 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.
    5. 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.
    6. Possible underreporting of pathogenic variants in RAI1 causing Smith-Magenis syndrome.
      Title: Possible underreporting of pathogenic variants in RAI1 causing Smith-Magenis syndrome.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    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
    		not available

    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)

    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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    NEW Try the new Transcript table

    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_2024_08

    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 [email protected] for further information.

    2. NM_152256.1: Suppressed sequence

      Description
      NM_152256.1: This RefSeq record was removed by NCBI staff. Contact [email protected] 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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