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SEC16B SEC16 homolog B, endoplasmic reticulum export factor [ Homo sapiens (human) ]

Gene ID: 89866, updated on 8-Dec-2018

Summary

Official Symbol
SEC16Bprovided by HGNC
Official Full Name
SEC16 homolog B, endoplasmic reticulum export factorprovided by HGNC
Primary source
HGNC:HGNC:30301
See related
Ensembl:ENSG00000120341 MIM:612855
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
RGPR; LZTR2; SEC16S; PGPR-p117; RGPR-p117
Summary
SEC16B is a mammalian homolog of S. cerevisiae Sec16 that is required for organization of transitional endoplasmic reticulum (ER) sites and protein export (Bhattacharyya and Glick, 2007 [PubMed 17192411]).[supplied by OMIM, Jun 2009]
Expression
Broad expression in small intestine (RPKM 16.8), duodenum (RPKM 16.0) and 22 other tissues See more
Orthologs

Genomic context

See SEC16B in Genome Data Viewer
Location:
1q25.2
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (177928788..177984303, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (177892825..177939188, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1645 Neighboring gene long intergenic non-protein coding RNA 1741 Neighboring gene CRYZL2P-SEC16B readthrough Neighboring gene crystallin zeta like 2, pseudogene Neighboring gene RASAL2 antisense RNA 1 Neighboring gene RAS protein activator like 2

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A comprehensive family-based replication study of schizophrenia genes.
NHGRI GWA Catalog
A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry.
NHGRI GWA Catalog
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
NHGRI GWA Catalog
Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations.
NHGRI GWA Catalog
Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course.
NHGRI GWA Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog
Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • 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...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough CRYZL2P-SEC16B

Readthrough gene: CRYZL2P-SEC16B, Included gene: CRYZL2P

Homology

Clone Names

  • FLJ23871, FLJ25761, FLJ33652, FLJ36620, DKFZp686C2486

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
COPII vesicle coating IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
COPII vesicle coating TAS
Traceable Author Statement
more info
 
ER to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
ER to Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
PubMed 
Golgi organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum organization IDA
Inferred from Direct Assay
more info
PubMed 
peroxisome fission IMP
Inferred from Mutant Phenotype
more info
PubMed 
peroxisome organization IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein exit from endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of protein exit from endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
ER to Golgi transport vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum exit site IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein transport protein Sec16B
Names
leucine zipper transcription regulator 2
protein SEC16 homolog B
regucalcin gene promoter region-related protein p117
regucalcin gene promotor region related protein

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.

mRNA and Protein(s)

  1. NM_001356499.1NP_001343428.1  protein transport protein Sec16B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL160007, AL356279, BC009106
    Consensus CDS
    CCDS86035.1
    Related
    ENSP00000431727.2, ENST00000464631.6
    Conserved Domains (1) summary
    cd09233
    Location:328593
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  2. NM_001356500.1NP_001343429.1  protein transport protein Sec16B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL160007, AL356279, AL359075
    Conserved Domains (1) summary
    cd09233
    Location:93342
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  3. NM_033127.3NP_149118.2  protein transport protein Sec16B isoform 1

    See identical proteins and their annotated locations for NP_149118.2

    Status: VALIDATED

    Source sequence(s)
    AA086201, AB063357, AK090971, AK098627, AV697113, BX481418
    Consensus CDS
    CCDS44281.1
    UniProtKB/Swiss-Prot
    Q96JE7
    Related
    ENSP00000308339.6, ENST00000308284.10
    Conserved Domains (1) summary
    cd09233
    Location:327683
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    177928788..177984303 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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