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LCORL ligand dependent nuclear receptor corepressor like [ Homo sapiens (human) ]

Gene ID: 254251, updated on 9-Aug-2020

Summary

Official Symbol
LCORLprovided by HGNC
Official Full Name
ligand dependent nuclear receptor corepressor likeprovided by HGNC
Primary source
HGNC:HGNC:30776
See related
Ensembl:ENSG00000178177 MIM:611799
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
MLR1
Summary
This gene encodes a transcription factor that appears to function in spermatogenesis. Polymorphisms in this gene are associated with measures of skeletal frame size and adult height. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in testis (RPKM 2.1), small intestine (RPKM 1.8) and 25 other tissues See more
Orthologs

Genomic context

See LCORL in Genome Data Viewer
Location:
4p15.31
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (17841198..18023287, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (17844839..18023483, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 184 member B Neighboring gene mediator complex subunit 28 Neighboring gene DDB1 and CUL4 associated factor 16 Neighboring gene non-SMC condensin I complex subunit G Neighboring gene keratin 18 pseudogene 63 Neighboring gene uncharacterized LOC107986220 Neighboring gene uncharacterized LOC107986262

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 Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
NHGRI GWA Catalog
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
NHGRI GWA Catalog
Genome-wide association analysis identifies 20 loci that influence adult height.
NHGRI GWA Catalog
Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe).
NHGRI GWA Catalog
Genome-wide association study of height and body mass index in Australian twin families.
NHGRI GWA Catalog
Genome-wide diet-gene interaction analyses for risk of colorectal cancer.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
NHGRI GWA Catalog
New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30696

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ligand-dependent nuclear receptor corepressor-like protein
Names
LCOR-like protein
MBLK1-related protein
transcription factor MLR1

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.

Genomic

  1. NG_015822.2 RefSeqGene

    Range
    4986..185662
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166139.2NP_001159611.1  ligand-dependent nuclear receptor corepressor-like protein isoform 1

    See identical proteins and their annotated locations for NP_001159611.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). There are no full-length human transcripts representing this variant; it is supported by partial human transcript alignments and by full-length homologous mouse transcripts (GeneID:209707).
    Source sequence(s)
    AC005768, AK055258, AL700364, BC037322, BC062661, BU902997, BX107807
    Consensus CDS
    CCDS54749.1
    UniProtKB/Swiss-Prot
    Q8N3X6
    Related
    ENSP00000371661.5, ENST00000382226.5
    Conserved Domains (1) summary
    pfam05225
    Location:526571
    HTH_psq; helix-turn-helix, Psq domain
  2. NM_001365658.1NP_001352587.1  ligand-dependent nuclear receptor corepressor-like protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variant 5, encodes isoform 3.
    Source sequence(s)
    AC005768, AC079399
    Conserved Domains (1) summary
    pfam05225
    Location:366411
    HTH_psq; helix-turn-helix, Psq domain
  3. NM_001365659.1NP_001352588.1  ligand-dependent nuclear receptor corepressor-like protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variant 4, encodes isoform 3.
    Source sequence(s)
    AC005768, AC079399
    Conserved Domains (1) summary
    pfam05225
    Location:366411
    HTH_psq; helix-turn-helix, Psq domain
  4. NM_001365660.1NP_001352589.1  ligand-dependent nuclear receptor corepressor-like protein isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  5. NM_001365661.1NP_001352590.1  ligand-dependent nuclear receptor corepressor-like protein isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC079399
  6. NM_001365662.1NP_001352591.1  ligand-dependent nuclear receptor corepressor-like protein isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  7. NM_001365663.1NP_001352592.1  ligand-dependent nuclear receptor corepressor-like protein isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  8. NM_001365665.1NP_001352594.1  ligand-dependent nuclear receptor corepressor-like protein isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  9. NM_153686.8NP_710153.2  ligand-dependent nuclear receptor corepressor-like protein isoform 2

    See identical proteins and their annotated locations for NP_710153.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 3' terminal exon compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC005768, AK299939, AL133031, BC037322, BU902997
    Consensus CDS
    CCDS3425.1
    UniProtKB/Swiss-Prot
    Q8N3X6
    UniProtKB/TrEMBL
    B4DSW0
    Related
    ENSP00000317566.3, ENST00000326877.8

RNA

  1. NR_136669.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two non-consecutive exons and contains an alternate 3' terminal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC005768, AK299939, AL133031, BC037322
  2. NR_158563.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  3. NR_158564.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  4. NR_158565.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  5. NR_158566.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  6. NR_158567.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399
  7. NR_158568.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC005768, AC079399

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    17841198..18023287 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007961.2XP_016863450.1  ligand-dependent nuclear receptor corepressor-like protein isoform X3

  2. XM_017007965.1XP_016863454.1  ligand-dependent nuclear receptor corepressor-like protein isoform X7

  3. XM_017007962.2XP_016863451.1  ligand-dependent nuclear receptor corepressor-like protein isoform X4

    Conserved Domains (1) summary
    pfam15090
    Location:13291779
    DUF4553; Domain of unknown function (DUF4553)
  4. XM_011513822.3XP_011512124.1  ligand-dependent nuclear receptor corepressor-like protein isoform X2

    UniProtKB/TrEMBL
    A0A1B0GVP4
    Related
    ENSP00000490600.1, ENST00000635767.1
    Conserved Domains (1) summary
    pfam15090
    Location:14161866
    DUF4553; Domain of unknown function (DUF4553)
  5. XM_011513821.3XP_011512123.1  ligand-dependent nuclear receptor corepressor-like protein isoform X1

    Conserved Domains (1) summary
    pfam15090
    Location:14161866
    DUF4553; Domain of unknown function (DUF4553)
  6. XM_011513823.3XP_011512125.1  ligand-dependent nuclear receptor corepressor-like protein isoform X4

    Conserved Domains (1) summary
    pfam15090
    Location:13291779
    DUF4553; Domain of unknown function (DUF4553)
  7. XM_017007963.2XP_016863452.1  ligand-dependent nuclear receptor corepressor-like protein isoform X4

    Conserved Domains (1) summary
    pfam15090
    Location:13291779
    DUF4553; Domain of unknown function (DUF4553)
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