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TLX1 T cell leukemia homeobox 1 [ Homo sapiens (human) ]

Gene ID: 3195, updated on 2-Nov-2024

Summary

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Official Symbol
TLX1provided by HGNC
Official Full Name
T cell leukemia homeobox 1provided by HGNC
Primary source
HGNC:HGNC:5056
See related
Ensembl:ENSG00000107807 MIM:186770; AllianceGenome:HGNC:5056
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
TCL3; HOX11
Summary
This gene encodes a nuclear transcription factor that belongs to the NK-linked or NK-like (NKL) subfamily of homeobox genes. The encoded protein is required for normal development of the spleen during embryogenesis. This protein is also involved in specification of neuronal cell fates. Ectopic expression of this gene due to chromosomal translocations is associated with certain T-cell acute lymphoblastic leukemias. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]
Expression
Biased expression in spleen (RPKM 14.4) and salivary gland (RPKM 3.2) See more
Orthologs
mouse all
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Genomic context

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See TLX1 in Genome Data Viewer
Location:
10q24.31
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (101131300..101137789)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (102014685..102021174)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102891057..102897546)

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 TLX1 neighbor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102880827-102881554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102902239-102903043 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association of TLX1 gene polymorphisms with the risk of acute lymphoblastic leukemia and B lineage acute lymphoblastic leukemia in Han Chinese children.
    Title: Association of TLX1 gene polymorphisms with the risk of acute lymphoblastic leukemia and B lineage acute lymphoblastic leukemia in Han Chinese children.
  2. Data show that among all long non-coding RNAs (lncRNAs), 82 are differentially regulated upon T cell leukemia homeobox 1 protein (TLX1) knockdown, of which 30 are directly bound by TLX1.
    Title: A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing.
  3. oncogenic kinase NUP214-ABL1, through its downstream effector STAT5, directly cooperates with TLX1 at the transcriptional level.
    Title: Cooperative Enhancer Activation by TLX1 and STAT5 Drives Development of NUP214-ABL1/TLX1-Positive T Cell Acute Lymphoblastic Leukemia.
  4. High TLX1 expression is associated with castration-resistant prostate cancer.
    Title: Orphan nuclear receptor TLX contributes to androgen insensitivity in castration-resistant prostate cancer via its repression of androgen receptor transcription.
  5. Our data suggest that loss of DLX5, TLX1 and HOXA10 expression in late gestation is required for proper placental differentiation and function.
    Title: Increased methylation and decreased expression of homeobox genes TLX1, HOXA10 and DLX5 in human placenta are associated with trophoblast differentiation.
  6. TLX1 hypermethylation is associated with colorectal cancer.
    Title: Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer.
  7. The occurrence of G-quadruplex structures at the HOX11 breakpoint region explain its fragility during the t(10;14) translocation.
    Title: G-quadruplex structures formed at the HOX11 breakpoint region contribute to its fragility during t(10;14) translocation in T-cell leukemia.
  8. these results place TLX1 and TLX3 at the top of an oncogenic transcriptional network controlling leukemia development, and identify RUNX1 as a tumor-suppressor gene in T-ALL
    Title: Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL.
  9. The cortical thymic maturation arrest in T-lineage Acute lymphoblastic leukemias (ALLs) that overexpress TLX1 or TLX3 is due to binding of TLX1/TLX3 to ETS1.
    Title: TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression.
  10. Suppression of TLX1 expression slowed the growth of TLX1 tumor cell lines. Suppression of TLX1 in vivo also transiently delayed leukemia progression.
    Title: Transient responses to NOTCH and TLX1/HOX11 inhibition in T-cell acute lymphoblastic leukemia/lymphoma.
Submit: New GeneRIF Correction See all GeneRIFs (29)

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

Variation

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See Variation Viewer (GRCh37.p13)

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

  • MGC163402

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in animal organ development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
T-cell leukemia homeobox protein 1
Names
T-cell leukemia/lymphoma protein 3
homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)
homeobox protein Hox-11
proto-oncogene TCL-3

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_027826.1 RefSeqGene

    Range
    4997..11486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195517.2 → NP_001182446.1  T-cell leukemia homeobox protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001182446.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 2, which has a shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AL357395, BC130530, BF514683
    Consensus CDS
    CCDS55725.1
    UniProtKB/Swiss-Prot
    P31314
    Related
    ENSP00000434914.2, ENST00000467928.2
    Conserved Domains (1) summary
    pfam00046
    Location:204 → 257
    Homeobox; Homeobox domain

  2. NM_005521.4 → NP_005512.1  T-cell leukemia homeobox protein 1 isoform 1

    See identical proteins and their annotated locations for NP_005512.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL357395, BC130530, BF514683, M62626, S38742
    Consensus CDS
    CCDS7510.1
    UniProtKB/Swiss-Prot
    A1L4G3, O75699, P31314, Q5VXP2, Q9HCA0, Q9UD59
    Related
    ENSP00000359215.6, ENST00000370196.11
    Conserved Domains (1) summary
    pfam00046
    Location:204 → 257
    Homeobox; Homeobox domain

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
    101131300..101137789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539744.4 → XP_011538046.1  T-cell leukemia homeobox protein 1 isoform X1

    Conserved Domains (1) summary
    pfam00046
    Location:216 → 269
    Homeobox; Homeobox domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    102014685..102021174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054365703.1 → XP_054221678.1  T-cell leukemia homeobox protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P31314.1 GenPept UniProtKB/Swiss-Prot:P31314

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