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

Gene ID: 8861, updated on 9-Dec-2018

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

Genomic context

See LDB1 in Genome Data Viewer
Location:
10q24.32
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (102102100..102120473, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (103866315..103880210, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927445 Neighboring gene armadillo-like helical domain containing 3 Neighboring gene HPS6, biogenesis of lysosomal organelles complex 2 subunit 3 Neighboring gene peroxisome proliferator-activated receptor gamma, coactivator-related 1 Neighboring gene nucleolar and coiled-body phosphoprotein 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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enhancer sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
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
 
protein self-association IEA
Inferred from Electronic Annotation
more info
 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
anterior/posterior axis specification IEA
Inferred from Electronic Annotation
more info
 
cellular component assembly IEA
Inferred from Electronic Annotation
more info
 
cerebellar Purkinje cell differentiation IEA
Inferred from Electronic Annotation
more info
 
epithelial structure maintenance IEA
Inferred from Electronic Annotation
more info
 
gastrulation with mouth forming second IEA
Inferred from Electronic Annotation
more info
 
hair follicle development IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 acetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell adhesion IEA
Inferred from Electronic Annotation
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 
somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
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

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)

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_001113407.2NP_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, AW137421, BC009246, CB988590, CV575131
    Consensus CDS
    CCDS44472.1
    UniProtKB/Swiss-Prot
    Q86U70
    Related
    ENSP00000392466.1, ENST00000425280.1
    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  2. NM_001321612.1NP_001308541.1  LIM domain-binding protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL500527
    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  3. NM_003893.4NP_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:34235
    LIM_bind; LIM-domain binding protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    102102100..102120473 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  2. XM_017016867.1XP_016872356.1  LIM domain-binding protein 1 isoform X1

    Conserved Domains (1) summary
    pfam01803
    Location:70271
    LIM_bind; LIM-domain binding protein
  3. XM_017016869.1XP_016872358.1  LIM domain-binding protein 1 isoform X3

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

RNA

  1. XR_001747255.2 RNA Sequence

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