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

Gene ID: 118426, updated on 2-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
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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 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)

Genotypes

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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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

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