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    BORCS5 BLOC-1 related complex subunit 5 [ Homo sapiens (human) ]

    Gene ID: 118426, updated on 27-Nov-2024

    Summary

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    Official Symbol
    BORCS5provided by HGNC
    Official Full Name
    BLOC-1 related complex subunit 5provided by HGNC
    Primary source
    HGNC:HGNC:17950
    See related
    Ensembl:ENSG00000165714 MIM:616598; AllianceGenome:HGNC:17950
    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
    LOH12CR1; LOH1CR12
    Summary
    Involved in lysosome localization and organelle transport along microtubule. Located in cytoplasmic side of lysosomal membrane; plasma membrane; and plus-end kinesin complex. Part of BORC complex. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 2.1), bone marrow (RPKM 1.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BORCS5 in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (12357078..12471233)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (12226205..12340409)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (12510012..12624167)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MANSC domain containing 1 Neighboring gene ribosomal protein L23a pseudogene 66 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4252 Neighboring gene CRISPRi-validated cis-regulatory element chr12.586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12509797-12510475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6011 Neighboring gene loss of heterozygosity on chromosome 12, region 2 Neighboring gene Sharpr-MPRA regulatory region 10643 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12560630-12560819 Neighboring gene Sharpr-MPRA regulatory region 7135 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:12592110-12593309 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25257 Neighboring gene adaptor related protein complex 3 subunit sigma 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:12610012-12610690 Neighboring gene dual specificity phosphatase 16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12686984-12687949 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12688131-12688632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4258 Neighboring gene ribosomal protein L19 pseudogene 17

    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. LOH12CR1 is a Novel Tumor Suppressor Inhibiting Tumor Growth Through Deregulation of G1/S Checkpoint in Human Colorectal Carcinoma. Huang H, et al. Curr Mol Med, 2018. PMID 29879888
    2. Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression. Dupain C, et al. Oncogene, 2019 Nov. PMID 31488873
    3. A detailed transcriptional map of the chromosome 12p12 tumour suppressor locus. Montpetit A, et al. Eur J Hum Genet, 2002 Jan. PMID 11896457
    4. Mutational and expression analysis of the chromosome 12p candidate tumor suppressor genes in pre-B acute lymphoblastic leukemia. Montpetit A, et al. Leukemia, 2004 Sep. PMID 15284860
    5. BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain. Tunganuntarat J, et al. Sci Rep, 2023 Jan 30. PMID 36717601, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
      Title: BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain.
    2. our results suggest that LMO3-BORCS5 fusion oncogene plays an essential role in tumorigenesis
      Title: Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression.
    3. The present results suggest that LOH12CR1 might function as a tumor suppressor. Thus, loss of function of LOH12CR1 might be a potential driver in the development of colorectal carcinoma.
      Title: LOH12CR1 is a Novel Tumor Suppressor Inhibiting Tumor Growth Through Deregulation of G1/S Checkpoint in Human Colorectal Carcinoma.
    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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lysosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lysosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosome localization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in organelle transport along microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in organelle transport along microtubule IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in organelle transport along microtubule NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of anterograde synaptic vesicle transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of endosome size NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of lysosome size NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of BORC complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of BORC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of BORC complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    is_active_in cytoplasmic side of lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic side of lysosomal membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cytoplasmic side of lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    part_of plus-end kinesin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    BLOC-1-related complex subunit 5
    Names
    loss of heterozygosity 12 chromosomal region 1 protein
    loss of heterozygosity, 12, chromosomal region 1
    myristoylated lysosomal protein
    myrlysin

    NCBI Reference Sequences (RefSeq)

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    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_001300742.3 → NP_001287671.1  BLOC-1-related complex subunit 5 isoform 2

      See identical proteins and their annotated locations for NP_001287671.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in the use of an alternate start codon compared to variant 1. The encoded isoform (2) has a distinct N-terminus, and is shorter compared to isoform 1.
      Source sequence(s)
      AC007619, AC007621, AK075028, AW449789, BP260903
      Consensus CDS
      CCDS73448.1
      UniProtKB/TrEMBL
      G3V1P3
      Related
      ENSP00000443023.1, ENST00000542728.5
      Conserved Domains (1) summary
      pfam10158
      Location:42 → 172
      LOH1CR12; tumor suppressor protein

    2. NM_001330356.2 → NP_001317285.1  BLOC-1-related complex subunit 5 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) has the same N- and C-termini, but is shorter than isoform 1.
      Source sequence(s)
      AC007619, AC007621, AK075028, AW449789, AY037866
      Consensus CDS
      CCDS81669.1
      UniProtKB/Swiss-Prot
      Q969J3
      Related
      ENSP00000298571.6, ENST00000298571.6
      Conserved Domains (1) summary
      pfam10158
      Location:20 → 143
      LOH1CR12; tumor suppressor protein

    3. NM_058169.6 → NP_477517.1  BLOC-1-related complex subunit 5 isoform 1

      See identical proteins and their annotated locations for NP_477517.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC007619, AC007621, AK075028, AW449789
      Consensus CDS
      CCDS8649.1
      UniProtKB/Swiss-Prot
      Q969J3, Q96QS5
      Related
      ENSP00000321546.4, ENST00000314565.9
      Conserved Domains (1) summary
      pfam10158
      Location:61 → 191
      LOH1CR12; tumor suppressor protein

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      12357078..12471233
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520551.3 → XP_011518853.1  BLOC-1-related complex subunit 5 isoform X1

      See identical proteins and their annotated locations for XP_011518853.1

      Conserved Domains (1) summary
      pfam10158
      Location:31 → 161
      LOH1CR12; tumor suppressor protein

    2. XM_011520553.3 → XP_011518855.1  BLOC-1-related complex subunit 5 isoform X2

      See identical proteins and their annotated locations for XP_011518855.1

      Conserved Domains (1) summary
      pfam10158
      Location:61 → 120
      LOH1CR12; Tumour suppressor protein

    3. XM_047428271.1 → XP_047284227.1  BLOC-1-related complex subunit 5 isoform X1

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_011332696.1 Reference GRCh38.p14 PATCHES

      Range
      326073..440236
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331697.1 → XP_054187672.1  BLOC-1-related complex subunit 5 isoform X1

    2. XM_054331698.1 → XP_054187673.1  BLOC-1-related complex subunit 5 isoform X2

    3. XM_054331696.1 → XP_054187671.1  BLOC-1-related complex subunit 5 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      12226205..12340409
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371042.1 → XP_054227017.1  BLOC-1-related complex subunit 5 isoform X1

    2. XM_054371043.1 → XP_054227018.1  BLOC-1-related complex subunit 5 isoform X2

    3. XM_054371040.1 → XP_054227015.1  BLOC-1-related complex subunit 5 isoform X3

      UniProtKB/TrEMBL
      G3V1P3

    4. XM_054371041.1 → XP_054227016.1  BLOC-1-related complex subunit 5 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969J3.1 GenPept UniProtKB/Swiss-Prot:Q969J3

    Gene LinkOut

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

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