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

    Gene ID: 254251, updated on 5-May-2024

    Summary

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    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; AllianceGenome:HGNC:30776
    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
    mouse all
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    Genomic context

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    See LCORL in Genome Data Viewer
    Location:
    4p15.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (17841187..18021875, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (17823534..18004228, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (17842810..18023498, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15312 Neighboring gene family with sequence similarity 184 member B Neighboring gene mediator complex subunit 28 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812049-17812560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812561-17813073 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 ATAC-STARR-seq lymphoblastoid silent region 15313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21358 Neighboring gene uncharacterized LOC107986220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:18160933-18161439 Neighboring gene uncharacterized LOC107986262

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Identification and characterization of Mlr1,2: two mouse homologues of Mblk-1, a transcription factor from the honeybee brain(1). Kunieda T, et al. FEBS Lett, 2003 Jan 30. PMID 12560079
    2. A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity. Beck DB, et al. Neurogenetics, 2019 Aug. PMID 31041561, Free PMC Article
    3. New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism. Horikoshi M, et al. Nat Genet, 2013 Jan. PMID 23202124, Free PMC Article
    4. Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe). Carty CL, et al. Hum Mol Genet, 2012 Feb 1. PMID 22021425, Free PMC Article
    5. Genome-wide association study of height and body mass index in Australian twin families. Liu JZ, et al. Twin Res Hum Genet, 2010 Apr. PMID 20397748, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Identification and characterization of an homologous gene in mouse.
      Title: Identification and characterization of Mlr1,2: two mouse homologues of Mblk-1, a transcription factor from the honeybee brain(1).
    3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30696

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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

    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.

    Genomic

    1. NG_015822.2 RefSeqGene

      Range
      5106..185674
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001166139.2 → NP_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, Q96NK1
      Related
      ENSP00000371661.5, ENST00000382226.5
      Conserved Domains (1) summary
      pfam05225
      Location:526 → 571
      HTH_psq; helix-turn-helix, Psq domain

    2. NM_001365658.1 → NP_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:366 → 411
      HTH_psq; helix-turn-helix, Psq domain

    3. NM_001365659.1 → NP_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:366 → 411
      HTH_psq; helix-turn-helix, Psq domain

    4. NM_001365660.1 → NP_001352589.1  ligand-dependent nuclear receptor corepressor-like protein isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC005768, AC079399
      Consensus CDS
      CCDS93484.1
      UniProtKB/TrEMBL
      A0A6Q8PG24, A0A6Q8PHE0
      Related
      ENSP00000502692.1, ENST00000675143.1

    5. NM_001365661.1 → NP_001352590.1  ligand-dependent nuclear receptor corepressor-like protein isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC079399
      Consensus CDS
      CCDS93486.1
      UniProtKB/TrEMBL
      A0A6Q8PG24, A0A6Q8PHT2
      Related
      ENSP00000502833.1, ENST00000674942.1

    6. NM_001365662.1 → NP_001352591.1  ligand-dependent nuclear receptor corepressor-like protein isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC005768, AC079399
      UniProtKB/TrEMBL
      A0A6Q8PG24

    7. NM_001365663.1 → NP_001352592.1  ligand-dependent nuclear receptor corepressor-like protein isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC005768, AC079399
      UniProtKB/TrEMBL
      A0A6Q8PG24

    8. NM_001365665.1 → NP_001352594.1  ligand-dependent nuclear receptor corepressor-like protein isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC005768, AC079399

    9. NM_001394446.1 → NP_001381375.1  ligand-dependent nuclear receptor corepressor-like protein isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC005768, AC079399
      Consensus CDS
      CCDS93485.1
      UniProtKB/TrEMBL
      A0A1B0GVP4
      Related
      ENSP00000490600.1, ENST00000635767.2
      Conserved Domains (1) summary
      pfam15090
      Location:1416 → 1866
      DUF4553; Domain of unknown function (DUF4553)

    10. NM_153686.8 → NP_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/TrEMBL
      A0A6Q8PG24
      Related
      ENSP00000317566.3, ENST00000326877.8

    RNA

    1. NR_136669.3 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
      Related
      ENST00000675131.1

    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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      17841187..18021875 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449965.1 → XP_047305921.1  ligand-dependent nuclear receptor corepressor-like protein isoform X1

    2. XM_017007965.2 → XP_016863454.1  ligand-dependent nuclear receptor corepressor-like protein isoform X3

    3. XM_047449966.1 → XP_047305922.1  ligand-dependent nuclear receptor corepressor-like protein isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      17823534..18004228 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349513.1 → XP_054205488.1  ligand-dependent nuclear receptor corepressor-like protein isoform X1

    2. XM_054349515.1 → XP_054205490.1  ligand-dependent nuclear receptor corepressor-like protein isoform X3

    3. XM_054349514.1 → XP_054205489.1  ligand-dependent nuclear receptor corepressor-like protein isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N3X6.4 GenPept UniProtKB/Swiss-Prot:Q8N3X6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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    Tools
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