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; AllianceGenome:HGNC:6532
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
Summary: Enables LIM domain binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and enzyme binding activity. Involved in negative regulation of transcription, DNA-templated and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in skin (RPKM 42.1), ovary (RPKM 38.8) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 10q24.32

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (102102088..102121442, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (102991499..103005382, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (103866246..103880125, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Ldb1 transcriptional co-regulator is required for establishment and maintenance of the pancreatic endocrine lineage.
Title: The Ldb1 transcriptional co-regulator is required for establishment and maintenance of the pancreatic endocrine lineage.
LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia.
Title: LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia.
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.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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: 432 organisms have orthologs with human gene LDB1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables LIM domain binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables LIM domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables LIM domain binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein self-association	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in anterior/posterior axis specification	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cellular component assembly	IEA Inferred from Electronic Annotation more info
involved_in cerebellar Purkinje cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in epithelial structure maintenance	IEA Inferred from Electronic Annotation more info
involved_in gastrulation with mouth forming second	IEA Inferred from Electronic Annotation more info
involved_in hair follicle development	IEA Inferred from Electronic Annotation more info
involved_in histone H3-K4 acetylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in mesendoderm development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of hemoglobin biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of focal adhesion assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription elongation by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in somatic stem cell population maintenance	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in 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
part_of beta-catenin-TCF complex	IDA Inferred from Direct Assay more info	PubMed
located_in cell leading edge	ISS Inferred from Sequence or Structural Similarity more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

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.

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, Q9UGM4

Related

ENSP00000501277.1, ENST00000673968.1

Conserved Domains (2) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein

pfam17916
Location:336 → 364

LID; LIM interaction domain (LID)
NM_001321612.2 → NP_001308541.1 LIM domain-binding protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL500527

UniProtKB/TrEMBL

A0A6E1WJ75

Related

ENSP00000392466.2, ENST00000425280.2

Conserved Domains (2) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein

pfam17916
Location:334 → 362

LID; LIM interaction domain (LID)
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 (2) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

pfam17916
Location:300 → 328

LID; LIM interaction domain (LID)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

102102088..102121442 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017016867.2 → XP_016872356.1 LIM domain-binding protein 1 isoform X2

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
XM_017016868.2 → XP_016872357.1 LIM domain-binding protein 1 isoform X3

Conserved Domains (1) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein
XM_047425980.1 → XP_047281936.1 LIM domain-binding protein 1 isoform X1
XM_047425979.1 → XP_047281935.1 LIM domain-binding protein 1 isoform X1
XM_017016869.2 → XP_016872358.1 LIM domain-binding protein 1 isoform X4

Conserved Domains (1) summary

pfam01803
Location:7 → 102

LIM_bind; LIM-domain binding protein