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    TH2LCRR T helper type 2 locus control region associated RNA [ Homo sapiens (human) ]

    Gene ID: 101927761, updated on 10-Oct-2023

    Summary

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    Official Symbol
    TH2LCRRprovided by HGNC
    Official Full Name
    T helper type 2 locus control region associated RNAprovided by HGNC
    Primary source
    HGNC:HGNC:40495
    See related
    Ensembl:ENSG00000223442 AllianceGenome:HGNC:40495
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TH2-LCR
    Expression
    Ubiquitous expression in testis (RPKM 5.8), thyroid (RPKM 3.5) and 25 other tissues See more
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    Genomic context

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    See TH2LCRR in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132630589..132656154, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (133150391..133175955, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131966281..131991846, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:131821689-131822888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131825338-131825985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131827280-131827925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131832117-131833091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23085 Neighboring gene interferon regulatory factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131892292-131892952 Neighboring gene interleukin 5 Neighboring gene RAD50 double strand break repair protein Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131954089-131954264 Neighboring gene Th2 cytokine locus control region Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131985148-131985325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:132000651-132001178 Neighboring gene uncharacterized LOC105379176 Neighboring gene interleukin 13 Neighboring gene interleukin 4

    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. Convergent Evidence Supports TH2LCRR as a Novel Asthma Susceptibility Gene. Li YK, et al. Am J Respir Cell Mol Biol, 2022 Mar. PMID 34851809
    2. Expression and functions of long noncoding RNAs during human T helper cell differentiation. Spurlock CF 3rd, et al. Nat Commun, 2015 Apr 23. PMID 25903499, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Convergent Evidence Supports TH2LCRR as a Novel Asthma Susceptibility Gene.
      Title: Convergent Evidence Supports TH2LCRR as a Novel Asthma Susceptibility Gene.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    General gene information

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    Clone Names

    • AC004041.2

    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.

    RNA

    1. NR_132124.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents a non-coding transcript.
      Source sequence(s)
      AA496113, DB527752
      Related
      ENST00000457489.1

    2. NR_132125.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences compared to variant 1.
      Source sequence(s)
      BC042122
      Related
      ENST00000458509.1

    3. NR_132126.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences compared to variant 1.
      Source sequence(s)
      AA470013, BC042122, BX095327
      Related
      ENST00000417516.1

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      132630589..132656154 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      133150391..133175955 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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

    Molecular Biology Databases