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

Gene ID: 89866, updated on 23-Nov-2023

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; 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
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Genomic context

See SEC16B in Genome Data Viewer
Location:
1q25.2
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (177928788..177984284, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (177283553..177339057, complement)
105.20220307 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

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 Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough CRYZL2P-SEC16B

Readthrough gene: CRYZL2P-SEC16B, Included gene: CRYZL2P

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 
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

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_001356499.2NP_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:328593
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  2. NM_001390833.1NP_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:327683
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  3. NM_001390834.1NP_001377763.1  protein transport protein Sec16B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL160007, AL356279
    Conserved Domains (1) summary
    cd09233
    Location:328684
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  4. NM_001390835.1NP_001377764.1  protein transport protein Sec16B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL160007, AL356279, AL359075
    Conserved Domains (1) summary
    cd09233
    Location:328684
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16
  5. NM_033127.4NP_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, 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:327683
    ACE1-Sec16-like; Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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.