U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 8861, updated on 19-Sep-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See LDB1 in Genome Data Viewer
Location:
10q24.32
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102102088..102121442, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (102987097..103006358, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (103866246..103880125, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene armadillo like helical domain containing 3 Neighboring gene uncharacterized LOC124902492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2735 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103698366-103699565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103795088-103795895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2738 Neighboring gene HPS6 biogenesis of lysosomal organelles complex 2 subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:103867277-103867778 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103870016-103871215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2739 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103876901-103877603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103877604-103878305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2745 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103880011-103880762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103880763-103881514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103881515-103882264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103887116-103887946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2750 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103897995-103899194 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103911632-103912831 Neighboring gene PPARG related coactivator 1 Neighboring gene nucleolar and coiled-body phosphoprotein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2751 Neighboring gene ELOVL fatty acid elongase 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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 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
 
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 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 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
 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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 positive regulation of transcription elongation 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 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
 
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
 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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)

  1. NM_001113407.3NP_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
    B4DUC4, O75479, O96010, Q1EQX1, Q86U70, Q9UGM4
    Related
    ENSP00000501277.1, ENST00000673968.1
    Conserved Domains (2) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:336364
    LID; LIM interaction domain (LID)
  2. NM_001321612.2NP_001308541.1  LIM domain-binding protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL500527
    Consensus CDS
    CCDS91327.1
    UniProtKB/TrEMBL
    A0A6E1WJ75
    Related
    ENSP00000392466.2, ENST00000425280.2
    Conserved Domains (2) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:334362
    LID; LIM interaction domain (LID)
  3. NM_003893.5NP_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:34235
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:300328
    LID; LIM interaction domain (LID)

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
    102102088..102121442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  2. XM_017016868.2XP_016872357.1  LIM domain-binding protein 1 isoform X3

    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  3. XM_047425980.1XP_047281936.1  LIM domain-binding protein 1 isoform X1

  4. XM_047425979.1XP_047281935.1  LIM domain-binding protein 1 isoform X1

  5. XM_017016869.2XP_016872358.1  LIM domain-binding protein 1 isoform X4

    Conserved Domains (1) summary
    pfam01803
    Location:7102
    LIM_bind; LIM-domain binding protein

RNA

  1. XR_001747255.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    102987097..103006358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367095.1XP_054223070.1  LIM domain-binding protein 1 isoform X2

  2. XM_054367096.1XP_054223071.1  LIM domain-binding protein 1 isoform X3

  3. XM_054367097.1XP_054223072.1  LIM domain-binding protein 1 isoform X1

  4. XM_054367094.1XP_054223069.1  LIM domain-binding protein 1 isoform X1

  5. XM_054367098.1XP_054223073.1  LIM domain-binding protein 1 isoform X4

RNA

  1. XR_008488307.1 RNA Sequence