TBL1XR1 TBL1X/Y related 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBL1XR1provided by HGNC
Official Full Name: TBL1X/Y related 1provided by HGNC
Primary source: HGNC:HGNC:29529
See related: Ensembl:ENSG00000177565 MIM:608628; AllianceGenome:HGNC:29529
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: C21; DC42; IRA1; MRD41; TBLR1
Summary: This gene is a member of the WD40 repeat-containing gene family and shares sequence similarity with transducin (beta)-like 1X-linked (TBL1X). The protein encoded by this gene is thought to be a component of both nuclear receptor corepressor (N-CoR) and histone deacetylase 3 (HDAC 3) complexes, and is required for transcriptional activation by a variety of transcription factors. Mutations in these gene have been associated with some autism spectrum disorders, and one finding suggests that haploinsufficiency of this gene may be a cause of intellectual disability with dysmorphism. Mutations in this gene as well as recurrent translocations involving this gene have also been observed in some tumors. [provided by RefSeq, Mar 2016]
Expression: Ubiquitous expression in thyroid (RPKM 21.1), prostate (RPKM 13.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q26.32

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (177019344..177201800, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (179822332..180000612, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (176737132..176915270, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The spectrum of neurological presentation in individuals affected by TBL1XR1 gene defects.
Title: The spectrum of neurological presentation in individuals affected by TBL1XR1 gene defects.
lncRNA799/TBL1XR1/ZEB1 Axis Forms a Feedback Loop to Promote the Epithelial-Mesenchymal Transition of Cervical Cancer Cells.
Title: lncRNA799/TBL1XR1/ZEB1 Axis Forms a Feedback Loop to Promote the Epithelial-Mesenchymal Transition of Cervical Cancer Cells.
Exploring TBL1XR1 and NCOR1 Expression in B-cell Lymphoma Subtypes: Interaction With DNA Damage Repair Genes.
Title: Exploring TBL1XR1 and NCOR1 Expression in B-cell Lymphoma Subtypes: Interaction With DNA Damage Repair Genes.
Expanding the genotypic and phenotypic spectrum associated with TBL1XR1 de novo variants.
Title: Expanding the genotypic and phenotypic spectrum associated with TBL1XR1 de novo variants.
TBL1X: At the crossroads of transcriptional and posttranscriptional regulation.
Title: TBL1X: At the crossroads of transcriptional and posttranscriptional regulation.
Knockdown of circ_0026579 ameliorates lipopolysaccharide (bacterial origin)-induced inflammatory injury in bronchial epithelium cells by targeting miR-338-3p/TBL1XR1 axis.
Title: Knockdown of circ_0026579 ameliorates lipopolysaccharide (bacterial origin)-induced inflammatory injury in bronchial epithelium cells by targeting miR-338-3p/TBL1XR1 axis.
TBL1XR1 associated intellectual disability, a new missense variant with dysmorphic features plus autism: Expanding the phenotypic spectrum.
Title: TBL1XR1 associated intellectual disability, a new missense variant with dysmorphic features plus autism: Expanding the phenotypic spectrum.
MicroRNA-1178-3p suppresses the growth of hepatocellular carcinoma by regulating transducin (beta)-like 1 X-linked receptor 1.
Title: MicroRNA-1178-3p suppresses the growth of hepatocellular carcinoma by regulating transducin (beta)-like 1 X-linked receptor 1.
A novel fusion protein TBLR1-RARalpha acts as an oncogene to induce murine promyelocytic leukemia: identification and treatment strategies.
Title: A novel fusion protein TBLR1-RARα acts as an oncogene to induce murine promyelocytic leukemia: identification and treatment strategies.
TBL1XR1 Mutations in Primary Marginal Zone Lymphomas of Ocular Adnexa are Associated with Unique Morphometric Phenotypes.
Title: TBL1XR1 Mutations in Primary Marginal Zone Lymphomas of Ocular Adnexa are Associated with Unique Morphometric Phenotypes.

Submit: New GeneRIF Correction See all GeneRIFs (51)

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

Associated conditions

Description	Tests
Intellectual disability, autosomal dominant 41 MedGen: C4310784 OMIM: 616944 GeneReviews: Not available	Compare labs
Pierpont syndrome MedGen: C1865644 OMIM: 602342 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity Little evidence for dosage pathogenicity (Last evaluated 2019-03-27) ClinGen Genome Curation PagePubMed Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-03-27) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	HIV-1 Rev is identified to have a physical interaction with transducin (beta)-like 1 X-linked receptor 1 (TBL1XR1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH41472 (e-PCR)
- UniSTS:91942

SGC34530 (e-PCR)
- UniSTS:809

A009S15 (e-PCR)
- UniSTS:35897

D3S3097 (e-PCR)
- UniSTS:60495

NoName (e-PCR)
- UniSTS:483421

RH65544 (e-PCR)
- UniSTS:40030

RH122782 (e-PCR)
- UniSTS:135016

SHGC-77559 (e-PCR)
- UniSTS:15992

SHGC-149434 (e-PCR)
- UniSTS:183681

SHGC-12205 (e-PCR)
- UniSTS:11909

G32804 (e-PCR)
- UniSTS:117383

RH65477 (e-PCR)
- UniSTS:87980

TBL1XR1 (e-PCR)
- UniSTS:505519

SHGC-77560 (e-PCR)
- UniSTS:32706

RH47416 (e-PCR)
- UniSTS:12236

SHGC-77561 (e-PCR)
- UniSTS:10714

SHGC-2932 (e-PCR)
- UniSTS:17371

G63142 (e-PCR)
- UniSTS:140259

D3S4234 (e-PCR)
- UniSTS:15331

RH11791 (e-PCR)
- UniSTS:15332

RH122844 (e-PCR)
- UniSTS:135142

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
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 cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info
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

Process	Evidence Code	Pubs
involved_in blastocyst hatching	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in fat pad development	IEA Inferred from Electronic Annotation more info
involved_in lipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of triglyceride metabolic process	IEA Inferred from Electronic Annotation more info
involved_in response to dietary excess	IEA Inferred from Electronic Annotation more info
involved_in white fat cell differentiation	IEA Inferred from Electronic Annotation more info

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

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Preferred Names: F-box-like/WD repeat-containing protein TBL1XR1

Names: TBL1-related protein 1; TBL1X receptor 1; nuclear receptor co-repressor/HDAC3 complex subunit; nuclear receptor corepressor/HDAC3 complex subunit TBLR1; transducin beta like 1 X-linked receptor 1

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

NG_047195.1 RefSeqGene

Range

4779..182917

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001321193.3 → NP_001308122.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (2), as well as variants 1, 3, 5, 6, and 7, encodes isoform 1.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Related

ENSP00000405574.1, ENST00000430069.5

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
NM_001321194.3 → NP_001308123.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2, 3, 5, 6, and 7 all encode the same isoform (1).

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Related

ENSP00000387849.3, ENST00000422442.6

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
NM_001321195.3 → NP_001308124.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1. Variants 4 and 8 both encode the same isoform (2).

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS93428.1

UniProtKB/TrEMBL

B7Z475, C9JLJ1

Conserved Domains (2) summary

cd00200
Location:77 → 383

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 ...

sd00039
Location:182 → 219

7WD40; WD40 repeat [structural motif]
NM_001374327.1 → NP_001361256.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (5), as well as variants 1, 2, 3, 6, and 7, encodes isoform 1.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Related

ENSP00000263964.11, ENST00000352800.10

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
NM_001374328.1 → NP_001361257.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (6), as well as variants 1, 2, 3, 5, and 7, encodes isoform 1.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
NM_001374329.1 → NP_001361258.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (7), as well as variants 1, 2, 3, 5, and 6, encodes isoform 1.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
NM_001374330.1 → NP_001361259.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (8), as well as variant 4, encodes isoform 2.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS93428.1

UniProtKB/TrEMBL

B7Z475, C9JLJ1

Related

ENSP00000402402.2, ENST00000431421.6

Conserved Domains (2) summary

cd00200
Location:77 → 383

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 ...

sd00039
Location:182 → 219

7WD40; WD40 repeat [structural motif]
NM_024665.7 → NP_078941.2 F-box-like/WD repeat-containing protein TBL1XR1 isoform 1

See identical proteins and their annotated locations for NP_078941.2

Status: REVIEWED

Description

Transcript Variant: This variant (1), as well as variants 2, 3, 5, 6, and 7, encodes isoform 1.

Source sequence(s)

AC023235, AC078799, KF457713

Consensus CDS

CCDS46961.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Related

ENSP00000413251.3, ENST00000457928.7

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

177019344..177201800 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047448940.1 → XP_047304896.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X1

UniProtKB/TrEMBL

C9JLJ1
XM_011513142.3 → XP_011511444.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

See identical proteins and their annotated locations for XP_011511444.1

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

UniProtKB/TrEMBL

A0A0D9SF63

Conserved Domains (3) summary

cd00200
Location:164 → 470

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 ...

sd00039
Location:228 → 264

7WD40; WD40 repeat [structural motif]

pfam08513
Location:7 → 31

LisH
XM_047448941.1 → XP_047304897.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X2
XM_047448949.1 → XP_047304905.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

Related

ENSP00000515886.1, ENST00000704384.1
XM_047448942.1 → XP_047304898.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X3
XM_047448943.1 → XP_047304899.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X3
XM_047448947.1 → XP_047304903.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

Related

ENSP00000486324.1, ENST00000631253.2
XM_047448945.1 → XP_047304901.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_047448946.1 → XP_047304902.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_047448944.1 → XP_047304900.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

179822332..180000612 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347894.1 → XP_054203869.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_054347889.1 → XP_054203864.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X3
XM_054347888.1 → XP_054203863.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X3
XM_054347887.1 → XP_054203862.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X2
XM_054347893.1 → XP_054203868.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_054347891.1 → XP_054203866.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_054347892.1 → XP_054203867.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1
XM_054347890.1 → XP_054203865.1 F-box-like/WD repeat-containing protein TBL1XR1 isoform X4

UniProtKB/Swiss-Prot

D3DNQ9, Q14DC3, Q9BZK7, Q9H2I1, Q9H9A1