LDB1 LIM domain binding 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LDB1provided by HGNC
Official Full Name: LIM domain binding 1provided by HGNC
Primary source: HGNC:HGNC:6532
See related: Ensembl:ENSG00000198728 MIM:603451
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NLI; CLIM2; LDB-1; CLIM-2
Expression: Ubiquitous expression in skin (RPKM 42.1), ovary (RPKM 38.8) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 10q24.32

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	10	NC_000010.11 (102102100..102120368, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (103866315..103880210, complement)

Chromosome 10 - NC_000010.11 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?

LDB1 dimerization supports long-range connections between enhancers and genes involved in erythropoiesis, including the beta-globin genes. Single-stranded DNA binding proteins (SSBPs) interact specifically with the LDB/Chip conserved domain (LCCD) of LDB proteins and stabilize LDBs by preventing their proteasomal degradation, thus promoting their functions in gene regulation.
Title: Crystal structure of human LDB1 in complex with SSBP2.
Data indicate that LIM-domain-binding protein 1 (LDB1) has a strong role in colorectal cancer (CRC) progression.
Title: LDB1 overexpression is a negative prognostic factor in colorectal cancer.
LDB1 maintains the terminally differentiated state of beta cells and is a component of active enhancers in both murine and human islets.
Title: LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells.
SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic beta-Cell Target Genes
Title: SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic β-Cell Target Genes.
Alanine scanning mutagenesis of the LIM interaction domain of LDB1 revealed a discrete motif, R(320)LITR, required for LMO2 binding.
Title: LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding.
Clim2, in a complex with LMO4, supports mammary stem cells by directly targeting the Fgfr2 promoter in basal cells to increase its expression
Title: The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis.
In t(8;21) leukemia cells, LDB1 functions as a component of the stable AML1-ETO-containing transcription factor complex (AETFC). The AETFC components cooperatively regulate gene expression and contribute to leukemogenesis.
Title: A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis.
We investigated NLI (Ldb1 homolog) complex occupancy and chromatin conformation of the beta-globin locus in human erythroid cells.
Title: Distinct Ldb1/NLI complexes orchestrate γ-globin repression and reactivation through ETO2 in human adult erythroid cells.
These studies are consistent with a model in which TIF1gamma acts to ubiquitinate LDB1 leading to degradation of LDB1 and changes in transcription of LDB1-dependent promoters.
Title: Transcription intermediary factor 1gamma decreases protein expression of the transcriptional cofactor, LIM-domain-binding 1.
Expression of LDB1 (LIM-domain-binding 1) protein in which Lys134 is replaced with arginine leads to enhanced expression of the mutant protein compared with the wild-type protein.
Title: Regulation of LIM-domain-binding 1 protein expression by ubiquitination of Lys134.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_26540-26541:1033662278:1 (e-PCR)
- UniSTS:269017

LDB1_2220 (e-PCR)
- UniSTS:280819

Homology

Homologs of the LDB1 gene: The LDB1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 307 organisms have orthologs with human gene LDB1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
LIM domain binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
LIM domain binding	IPI Inferred from Physical Interaction more info	PubMed
LIM domain binding	ISS Inferred from Sequence or Structural Similarity more info
RNA polymerase II activating transcription factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
RNA polymerase II activating transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
transcription corepressor activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
histone H3-K4 acetylation	ISS Inferred from Sequence or Structural Similarity more info
multicellular organism development	NAS Non-traceable Author Statement more info	PubMed
negative regulation of erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
negative regulation of transcription, DNA-templated	IBA Inferred from Biological aspect of Ancestor more info	PubMed
negative regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
nervous system development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of hemoglobin biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
regulation of DNA-templated transcription, elongation	ISS Inferred from Sequence or Structural Similarity more info
regulation of cell migration	ISS Inferred from Sequence or Structural Similarity more info
regulation of focal adhesion assembly	ISS Inferred from Sequence or Structural Similarity more info
regulation of hematopoietic stem cell differentiation	TAS Traceable Author Statement more info
regulation of kinase activity	ISS Inferred from Sequence or Structural Similarity more info
regulation of transcription, DNA-templated	NAS Non-traceable Author Statement more info	PubMed
transcription, DNA-templated	NAS Non-traceable Author Statement more info	PubMed
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
beta-catenin-TCF complex	IDA Inferred from Direct Assay more info	PubMed
cell leading edge	ISS Inferred from Sequence or Structural Similarity more info
nuclear chromatin	IDA Inferred from Direct Assay more info	PubMed
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleus	ISS Inferred from Sequence or Structural Similarity more info
protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info
transcription factor complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transcription factor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: LIM domain-binding protein 1

Names: LIM domain-binding factor CLIM2; LIM domain-binding factor-1; carboxy terminal LIM domain protein 2; carboxyl-terminal LIM domain-binding protein 2; nuclear LIM interactor

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.

mRNA and Protein(s)

NM_001113407.3 → NP_001106878.1 LIM domain-binding protein 1 isoform 1

See identical proteins and their annotated locations for NP_001106878.1

Status: VALIDATED

Source sequence(s)

AL500527

Consensus CDS

CCDS44472.1

UniProtKB/Swiss-Prot

Q86U70

Related

ENSP00000501277.1, ENST00000673968.1

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
NM_001321612.2 → NP_001308541.1 LIM domain-binding protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL500527

Related

ENSP00000392466.2, ENST00000425280.2

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
NM_003893.5 → NP_003884.1 LIM domain-binding protein 1 isoform 3

See identical proteins and their annotated locations for NP_003884.1

Status: VALIDATED

Source sequence(s)

AL500527, BC009246

Consensus CDS

CCDS7528.1

UniProtKB/Swiss-Prot

Q86U70

Related

ENSP00000354616.5, ENST00000361198.9

Conserved Domains (1) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p13 Primary Assembly

Range

102102100..102120368 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017016868.1 → XP_016872357.1 LIM domain-binding protein 1 isoform X2

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
XM_017016867.1 → XP_016872356.1 LIM domain-binding protein 1 isoform X1

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
XM_017016869.1 → XP_016872358.1 LIM domain-binding protein 1 isoform X3

Conserved Domains (1) summary

pfam01803
Location:7 → 102

LIM_bind; LIM-domain binding protein