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BLOC1S6 biogenesis of lysosomal organelles complex 1 subunit 6 [ Homo sapiens (human) ]

Gene ID: 26258, updated on 15-Jun-2019

Summary

Official Symbol
BLOC1S6provided by HGNC
Official Full Name
biogenesis of lysosomal organelles complex 1 subunit 6provided by HGNC
Primary source
HGNC:HGNC:8549
See related
Ensembl:ENSG00000104164 MIM:604310
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
PA; HPS9; PLDN; BLOS6; PALLID
Summary
The protein encoded by this gene may play a role in intracellular vesicle trafficking. It interacts with Syntaxin 13 which mediates intracellular membrane fusion. Mutations in this gene cause symptoms associated with Hermansky-Pudlak syndrome-9. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on the X chromosome. [provided by RefSeq, Aug 2015]
Expression
Ubiquitous expression in thyroid (RPKM 21.0), prostate (RPKM 17.5) and 25 other tissues See more
Orthologs

Genomic context

See BLOC1S6 in Genome Data Viewer
Location:
15q21.1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (45587123..45609716)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (45879417..45901909)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 46 Neighboring gene small nucleolar RNA, H/ACA box 41B Neighboring gene developmental pluripotency associated 5 pseudogene 2 Neighboring gene sulfide quinone oxidoreductase Neighboring gene uncharacterized LOC105370802 Neighboring gene uncharacterized LOC107984794

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

  • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
    Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
  • Golgi Associated Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Golgi Associated Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
    trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
anterograde axonal transport ISS
Inferred from Sequence or Structural Similarity
more info
 
anterograde synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
 
endosome to melanosome transport IDA
Inferred from Direct Assay
more info
PubMed 
melanosome organization NAS
Non-traceable Author Statement
more info
PubMed 
melanosome transport IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of pigment cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
synaptic vesicle docking NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
BLOC-1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
BLOC-1 complex IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with SNARE complex IDA
Inferred from Direct Assay
more info
PubMed 
axon cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extrinsic component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extrinsic component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
presynapse IEA
Inferred from Electronic Annotation
more info
 
transport vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transport vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
biogenesis of lysosome-related organelles complex 1 subunit 6
Names
BLOC-1 subunit 6
BLOC-1 subunit pallidin
biogenesis of lysosomal organelles complex-1, subunit 5, pallidin
biogenesis of lysosomal organelles complex-1, subunit 6, pallidin
pallid protein homolog
syntaxin 13 binding protein 1
syntaxin 13-interacting protein pallid

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_028194.2 RefSeqGene

    Range
    4905..27498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_883

mRNA and Protein(s)

  1. NM_001311255.1NP_001298184.1  biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AK128626, AL596952, BC026289, BP423071, DA230439
    Consensus CDS
    CCDS81878.1
    UniProtKB/TrEMBL
    B3KY40, H3BST1
    Related
    ENSP00000456851.1, ENST00000565323.5
    Conserved Domains (1) summary
    pfam14712
    Location:56145
    Snapin_Pallidin; Snapin/Pallidin
  2. NM_001311256.1NP_001298185.1  biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) lacks an alternate exon in the central coding region, which results in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK128626, BC026289, BP423071, DA226593, DA230439, DA523523
    UniProtKB/TrEMBL
    B3KY40
    Conserved Domains (1) summary
    pfam14712
    Location:5680
    Snapin_Pallidin; Snapin/Pallidin
  3. NM_012388.3NP_036520.1  biogenesis of lysosome-related organelles complex 1 subunit 6 isoform 2

    See identical proteins and their annotated locations for NP_036520.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF080470, AK128626, BC026289, BP423071, DA468279
    Consensus CDS
    CCDS10126.1
    UniProtKB/Swiss-Prot
    Q9UL45
    UniProtKB/TrEMBL
    B3KY40
    Related
    ENSP00000220531.3, ENST00000220531.7
    Conserved Domains (1) summary
    pfam14712
    Location:51140
    Snapin_Pallidin; Snapin/Pallidin

RNA

  1. NR_132350.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK128626, BC026289, BP423071, DA230439
    Related
    ENST00000568816.5
  2. NR_132351.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' terminal exon and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF080470, AK057545, AK128626, BC026289, BP423071, DA468279
  3. NR_132352.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF080470, AK128626, BC026289, BP423071, DA247079, DA468279
  4. NR_132353.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AK128626, BC026289, BP423071, DA468279, DB212570
  5. NR_132354.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains multiple differences, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AF080470, AK128626, BC026289, BP423071, DA468279, DA798595
  6. NR_132355.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains an alternate 5' exon and lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AF080470, AK128626, BC026289, BP423071, DA468279, DB287075
  7. NR_132356.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an alternate 5' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK128626, BC026289, BP423071, DA237963, DB289156
  8. NR_132357.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) contains an alternate 5' exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AK128626, BC026289, BP423071, DA237963, DA859617
  9. NR_132358.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK128626, BC026289, BP423071, DA226593, DA230439
  10. NR_132359.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) contains an alternate 5' terminal exon and lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AK128626, BC026289, BP423071, DA233328, DA237963

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.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    45587123..45609716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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