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    TLX1NB TLX1 neighbor [ Homo sapiens (human) ]

    Gene ID: 100038246, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TLX1NBprovided by HGNC
    Official Full Name
    TLX1 neighborprovided by HGNC
    Primary source
    HGNC:HGNC:37183
    See related
    Ensembl:ENSG00000236311 MIM:612734; AllianceGenome:HGNC:37183
    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
    TD1; TDI; APT-B7
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See TLX1NB in Genome Data Viewer
    Location:
    10q24.31
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (101089321..101141266, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101972704..102024651, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102849078..102901023, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984262 Neighboring gene Sharpr-MPRA regulatory region 11881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102821610-102822498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2718 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:102829506-102830705 Neighboring gene Kazal type serine peptidase inhibitor domain 1 Neighboring gene Sharpr-MPRA regulatory region 9711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102880827-102881554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102902239-102903043 Neighboring gene T cell leukemia homeobox 1 Neighboring gene RNY5 pseudogene 7 Neighboring gene long intergenic non-protein coding RNA 1514 Neighboring gene SMARCE1 pseudogene 7

    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. The long non-coding RNA T cell leukemia homeobox 1 neighbor enhances signal transducer and activator of transcription 5A phosphorylation to promote colon cancer cell invasion, migration, and metastasis. Chen G, et al. Bioengineered, 2022 Apr. PMID 35502613, Free PMC Article
    2. A promoter with bidirectional activity is located between TLX1/HOX11 and a divergently transcribed novel human gene. Greene WK, et al. Gene, 2007 Apr 15. PMID 17303350
    3. The DNA sequence and comparative analysis of human chromosome 10. Deloukas P, et al. Nature, 2004 May 27. PMID 15164054
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The long non-coding RNA T cell leukemia homeobox 1 neighbor enhances signal transducer and activator of transcription 5A phosphorylation to promote colon cancer cell invasion, migration, and metastasis.
      Title: The long non-coding RNA T cell leukemia homeobox 1 neighbor enhances signal transducer and activator of transcription 5A phosphorylation to promote colon cancer cell invasion, migration, and metastasis.
    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)

    General gene information

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    Markers

    Homology

    Other Names

    • TLX1 divergent gene protein
    • putative TLX1 neighbor protein

    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_130722.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      BC019674, BI770592

    2. NR_130723.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' terminal exon, compared to variant 1.
      Source sequence(s)
      BC019674, BI770592
      Related
      ENST00000445873.5

    3. NR_130724.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains alternate 5' and 3' terminal exons, compared to variant 1.
      Source sequence(s)
      AI184724, AL357395, BX117337
      Related
      ENST00000747505.1

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      101089321..101141266 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      101972704..102024651 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001085398.1: Suppressed sequence

      Description
      NM_001085398.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0CAT3.1 GenPept UniProtKB/Swiss-Prot:P0CAT3

    Gene LinkOut

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

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials