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

    Gene ID: 89866, updated on 10-Dec-2024

    Summary

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    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; AllianceGenome:HGNC:30301
    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
    mouse all
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    Genomic context

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    See SEC16B in Genome Data Viewer
    Location:
    1q25.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (177928788..177984284, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (177283553..177339057, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (177897923..177953419, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:177624802-177625303 Neighboring gene long intergenic non-protein coding RNA 1741 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:177763543-177764294 Neighboring gene CRYZL2P-SEC16B readthrough Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:177883789-177884988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:177905975-177906476 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:177928928-177929429 Neighboring gene MPRA-validated peak475 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:178019054-178019211 Neighboring gene crystallin zeta like 2, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2141 Neighboring gene uncharacterized LOC124904459

    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. Genetic variants in SEC16B are associated with body composition in black South Africans. Sahibdeen V, et al. Nutr Diabetes, 2018 Jul 19. PMID 30026463, Free PMC Article
    2. Female-Specific Susceptibility Locus in BOC and SEC16B are Associated with Adolescent Idiopathic Scoliosis. Dai Z, et al. Spine (Phila Pa 1976), 2021 Nov 15. PMID 33958541
    3. Novel protein RGPR-p117: its role as the regucalcin gene transcription factor. Yamaguchi M. Mol Cell Biochem, 2009 Jul. PMID 19214710
    4. Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants. Mei H, et al. Biomed Res Int, 2022. PMID 35295960, Free PMC Article
    5. Molecular cloning and sequencing of the cDNA coding for a novel regucalcin gene promoter region-related protein in rat, mouse and human liver. Misawa H, et al. Int J Mol Med, 2001 Nov. PMID 11605020

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants.
      Title: Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants.
    2. Female-Specific Susceptibility Locus in BOC and SEC16B are Associated with Adolescent Idiopathic Scoliosis.
      Title: Female-Specific Susceptibility Locus in BOC and SEC16B are Associated with Adolescent Idiopathic Scoliosis.
    3. SNPs in several gene loci, including SEC16B were similarly associated (albeit not at array-wide signficance (P </= 6.7 x 10(-7)) with various phenotypes including fat mass, percentage fat mass, waist-to-hip ratio linked to body composition in this African cohort
      Title: Genetic variants in SEC16B are associated with body composition in black South Africans.
    4. Significant associations were identified at 3.5 years for SEC16B rs10913469 with dietary parameters
      Title: Validation of obesity susceptibility loci identified by genome-wide association studies in early childhood in South Brazilian children.
    5. SEC16B, MC4R, MAP2K5 and KCTD15 (rs17782313, rs543874, rs2241423 and rs11084753) polymorphisms are associated with the risk for children obesity in China.
      Title: Genetic variations in SEC16B, MC4R, MAP2K5 and KCTD15 were associated with childhood obesity and interacted with dietary behaviors in Chinese school-age population.
    6. Data show the synthetic effect of SNPs on the indices of adiposity and risk of obesity in Chinese girls, but failed to replicate the effect of five separate variants of SEC16B rs10913469, SH2B1 rs4788102, PCSK1 rs6235, KCTD15 rs29941 and BAT2 rs2844479.
      Title: Sex-dependent associations of genetic variants identified by GWAS with indices of adiposity and obesity risk in a Chinese children population.
    7. describe characterization of the localization and dynamics of Sec16B relative to Sec16A, provide evidence that Sec16B is likely a minor or perhaps specialized form of Sec16, and that it is not functionally redundant with S
      Title: Characterization of human Sec16B: indications of specialized, non-redundant functions.
    8. Data show that knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes, and suppressed expression of Pex3.
      Title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.
    9. Data show that SNPs in SEC16B and TMEM18 were significantly associated with obesity, and the SNPs in GNPDA2, BDNF, FAIM2 and MC4R were marginally associated with obesity in Japanese.
      Title: Association between obesity and polymorphisms in SEC16B, TMEM18, GNPDA2, BDNF, FAIM2 and MC4R in a Japanese population.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analyses of shared genetic factors between asthma and obesity in children.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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

    General protein information

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    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)

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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_001356499.2 → NP_001343428.1  protein transport protein Sec16B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL160007, AL356279, BC009106
      Consensus CDS
      CCDS86035.1
      UniProtKB/TrEMBL
      E9PK14
      Related
      ENSP00000431727.2, ENST00000464631.6
      Conserved Domains (1) summary
      cd09233
      Location:328 → 593
      ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

    2. NM_001390833.1 → NP_001377762.1  protein transport protein Sec16B isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL160007, AL356279
      Consensus CDS
      CCDS44281.1
      UniProtKB/Swiss-Prot
      A3EYF1, Q5HYF6, Q8N7D6, Q96GX6, Q96JE7
      Conserved Domains (1) summary
      cd09233
      Location:327 → 683
      ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

    3. NM_001390834.1 → NP_001377763.1  protein transport protein Sec16B isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL160007, AL356279
      Conserved Domains (1) summary
      cd09233
      Location:328 → 684
      ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

    4. NM_001390835.1 → NP_001377764.1  protein transport protein Sec16B isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL160007, AL356279, AL359075
      Conserved Domains (1) summary
      cd09233
      Location:328 → 684
      ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

    5. NM_033127.4 → NP_149118.2  protein transport protein Sec16B isoform 1

      Status: VALIDATED

      Source sequence(s)
      AA086201, AB063357, AK090971, AK098627, AL356279, AV697113, BX481418
      Consensus CDS
      CCDS44281.1
      UniProtKB/Swiss-Prot
      A3EYF1, Q5HYF6, Q8N7D6, Q96GX6, Q96JE7
      Related
      ENSP00000308339.6, ENST00000308284.11
      Conserved Domains (1) summary
      cd09233
      Location:327 → 683
      ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      177928788..177984284 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      177283553..177339057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001356500.2: Suppressed sequence

      Description
      NM_001356500.2: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JE7.2 GenPept UniProtKB/Swiss-Prot:Q96JE7

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
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