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TBL1X transducin beta like 1 X-linked [ Homo sapiens (human) ]

Gene ID: 6907, updated on 3-Dec-2023

Summary

Official Symbol
TBL1Xprovided by HGNC
Official Full Name
transducin beta like 1 X-linkedprovided by HGNC
Primary source
HGNC:HGNC:11585
See related
Ensembl:ENSG00000101849 MIM:300196; AllianceGenome:HGNC:11585
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
EBI; TBL1; CHNG8; SMAP55
Summary
The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This encoded protein is found as a subunit in corepressor SMRT (silencing mediator for retinoid and thyroid receptors) complex along with histone deacetylase 3 protein. This gene is located adjacent to the ocular albinism gene and it is thought to be involved in the pathogenesis of the ocular albinism with late-onset sensorineural deafness phenotype. Four transcript variants encoding two different isoforms have been found for this gene. This gene is highly similar to the Y chromosome TBL1Y gene. [provided by RefSeq, Nov 2008]
Expression
Ubiquitous expression in endometrium (RPKM 23.1), prostate (RPKM 12.2) and 24 other tissues See more
Orthologs
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Genomic context

See TBL1X in Genome Data Viewer
Location:
Xp22.31-p22.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (9463295..9719740)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (9045885..9302376)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (9431335..9687780)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905242 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9260651-9261238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29398 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:9320474-9321673 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:9374111-9375310 Neighboring gene uncharacterized LOC107985634 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9382495-9382700 Neighboring gene chromodomain Y like protein pseudogene Neighboring gene MPRA-validated peak7356 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9420158-9420316 Neighboring gene Sharpr-MPRA regulatory region 2097 Neighboring gene Sharpr-MPRA regulatory region 7028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9431698-9432526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9471641-9472141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9490972-9491496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29402 Neighboring gene Sharpr-MPRA regulatory region 11092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9500568-9501137 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528031-9528532 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528533-9529032 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9536306-9537137 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9537138-9537968 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9554716-9555236 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9555237-9555756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561459-9561960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561961-9562460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9603687-9604186 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:9629664-9630863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9650484-9650984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9675799-9676456 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9676457-9677113 Neighboring gene uncharacterized LOC105373126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9732793-9733294 Neighboring gene G protein-coupled receptor 143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9761068-9761591 Neighboring gene shroom family member 2 Neighboring gene eukaryotic translation initiation factor 5 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hypothyroidism, congenital, nongoitrous, 8
MedGen: C5231395 OMIM: 301033 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of transducin (beta)-like 1X-linked (TBL1X) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription corepressor activity IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in mitotic spindle IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
F-box-like/WD repeat-containing protein TBL1X
Names
transducin beta like 1X-linked
transducin beta-like protein 1X
transducin-beta-like protein 1, X-linked

NCBI Reference Sequences (RefSeq)

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_053005.1 RefSeqGene

    Range
    6764..261446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001139466.1NP_001132938.1  F-box-like/WD repeat-containing protein TBL1X isoform a

    See identical proteins and their annotated locations for NP_001132938.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform a.
    Source sequence(s)
    AC003036, AK289409, AK290962, BC052304
    Consensus CDS
    CCDS14133.1
    UniProtKB/Swiss-Prot
    A8K044, A8K4J7, O60907, Q86UY2
    UniProtKB/TrEMBL
    A0A2R8YFW3
    Related
    ENSP00000385988.2, ENST00000407597.7
    Conserved Domains (4) summary
    COG2319
    Location:215577
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:227533
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam08513
    Location:5783
    LisH; LisH
    sd00039
    Location:235282
    7WD40; WD40 repeat [structural motif]
  2. NM_001139467.1NP_001132939.1  F-box-like/WD repeat-containing protein TBL1X isoform b

    See identical proteins and their annotated locations for NP_001132939.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks the alternate first coding exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode isoform b.
    Source sequence(s)
    AC003036, AK289409, BC052304
    Consensus CDS
    CCDS48078.1
    UniProtKB/TrEMBL
    A0A2R8YFW3
    Related
    ENSP00000394097.1, ENST00000424279.6
    Conserved Domains (4) summary
    COG2319
    Location:164526
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:176482
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam08513
    Location:632
    LisH; LisH
    sd00039
    Location:184231
    7WD40; WD40 repeat [structural motif]
  3. NM_001139468.1NP_001132940.1  F-box-like/WD repeat-containing protein TBL1X isoform b

    See identical proteins and their annotated locations for NP_001132940.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks the alternate first coding exon compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode isoform b.
    Source sequence(s)
    AC003036, AK289409, BC032708, BC052304
    Consensus CDS
    CCDS48078.1
    UniProtKB/TrEMBL
    A0A2R8YFW3
    Related
    ENSP00000370348.1, ENST00000380961.5
    Conserved Domains (4) summary
    COG2319
    Location:164526
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:176482
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam08513
    Location:632
    LisH; LisH
    sd00039
    Location:184231
    7WD40; WD40 repeat [structural motif]
  4. NM_005647.4NP_005638.1  F-box-like/WD repeat-containing protein TBL1X isoform a

    See identical proteins and their annotated locations for NP_005638.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode isoform a.
    Source sequence(s)
    AC003036, AC073488, BC052304
    Consensus CDS
    CCDS14133.1
    UniProtKB/Swiss-Prot
    A8K044, A8K4J7, O60907, Q86UY2
    UniProtKB/TrEMBL
    A0A2R8YFW3
    Related
    ENSP00000496215.1, ENST00000645353.2
    Conserved Domains (4) summary
    COG2319
    Location:215577
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:227533
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam08513
    Location:5783
    LisH; LisH
    sd00039
    Location:235282
    7WD40; WD40 repeat [structural motif]

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    9463295..9719740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    9045885..9302376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)