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TLX1NB TLX1 neighbor [ Homo sapiens (human) ]

Gene ID: 100038246, updated on 22-Oct-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 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)

Genotypes

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