Human Gene SEC61B (ENST00000223641.5_4) from GENCODE V47lift37
  Description: SEC61 translocon subunit beta (from RefSeq NM_006808.3)
Gencode Transcript: ENST00000223641.5_4
Gencode Gene: ENSG00000106803.10_7
Transcript (Including UTRs)
   Position: hg19 chr9:101,984,564-101,992,897 Size: 8,334 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr9:101,984,646-101,992,706 Size: 8,061 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:101,984,564-101,992,897)mRNA (may differ from genome)Protein (96 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SC61B_HUMAN
DESCRIPTION: RecName: Full=Protein transport protein Sec61 subunit beta;
FUNCTION: Necessary for protein translocation in the endoplasmic reticulum.
SUBUNIT: Heterotrimeric complex composed of SEC61-alpha, SEC61- beta and SEC61-gamma. Part of a complex composed of SEC61, SEC62 and SEC63. Interacts with SEC62.
INTERACTION: P51572:BCAP31; NbExp=7; IntAct=EBI-1788819, EBI-77683;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass membrane protein.
SIMILARITY: Belongs to the SEC61-beta family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SEC61B
Diseases sorted by gene-association score: polycystic kidney disease 4, with or without hepatic disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 107.35 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1972.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.4082-0.212 Picture PostScript Text
3' UTR -33.30191-0.174 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005609 - Sec61_beta
IPR016482 - Sec61_beta_euk

Pfam Domains:
PF03911 - Sec61beta family

ModBase Predicted Comparative 3D Structure on P60468
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005086 ARF guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0048408 epidermal growth factor binding
GO:0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity

Biological Process:
GO:0000060 protein import into nucleus, translocation
GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation
GO:0006886 intracellular protein transport
GO:0015031 protein transport
GO:0030433 ER-associated ubiquitin-dependent protein catabolic process
GO:0030970 retrograde protein transport, ER to cytosol
GO:0031204 posttranslational protein targeting to membrane, translocation

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005784 Sec61 translocon complex
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031205 endoplasmic reticulum Sec complex


-  Descriptions from all associated GenBank mRNAs
  LF206457 - JP 2014500723-A/13960: Polycomb-Associated Non-Coding RNAs.
AK223384 - Homo sapiens mRNA for protein translocation complex beta variant, clone: FCC106F05.
BC001734 - Homo sapiens Sec61 beta subunit, mRNA (cDNA clone MGC:1255 IMAGE:3502133), complete cds.
L25085 - Human Sec61-complex beta-subunit mRNA, complete cds.
JD461732 - Sequence 442756 from Patent EP1572962.
CR456883 - Homo sapiens full open reading frame cDNA clone RZPDo834E0915D for gene SEC61B, Sec61 beta subunit; complete cds, incl. stopcodon.
CR542159 - Homo sapiens full open reading frame cDNA clone RZPDo834D0324D for gene SEC61B, Sec61 beta subunit; complete cds, without stopcodon.
KJ893176 - Synthetic construct Homo sapiens clone ccsbBroadEn_02570 SEC61B gene, encodes complete protein.
AJ293399 - Homo sapiens mRNA differentially expressed in malignant melanoma, clone MM I3.
LF354600 - JP 2014500723-A/162103: Polycomb-Associated Non-Coding RNAs.
LF359207 - JP 2014500723-A/166710: Polycomb-Associated Non-Coding RNAs.
JD347884 - Sequence 328908 from Patent EP1572962.
JD345932 - Sequence 326956 from Patent EP1572962.
LF354601 - JP 2014500723-A/162104: Polycomb-Associated Non-Coding RNAs.
MA442034 - JP 2018138019-A/13960: Polycomb-Associated Non-Coding RNAs.
MA590177 - JP 2018138019-A/162103: Polycomb-Associated Non-Coding RNAs.
MA594784 - JP 2018138019-A/166710: Polycomb-Associated Non-Coding RNAs.
MA590178 - JP 2018138019-A/162104: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P60468 (Reactome details) participates in the following event(s):

R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-1236947 Egress of internalized antigen to the cytosol via sec61
R-HSA-1799329 Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
R-HSA-5250579 ASNA1 transports TA proteins from cytosol to ER membrane
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-1236974 ER-Phagosome pathway
R-HSA-72766 Translation
R-HSA-381038 XBP1(S) activates chaperone genes
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-392499 Metabolism of proteins
R-HSA-381070 IRE1alpha activates chaperones
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000223641.1, ENST00000223641.2, ENST00000223641.3, ENST00000223641.4, NM_006808, P38390, P38391, P60468, Q6IBC1, SC61B_HUMAN, SEC61B , uc317dhr.1, uc317dhr.2
UCSC ID: ENST00000223641.5_4
RefSeq Accession: NM_006808.3
Protein: P60468 (aka SC61B_HUMAN or S61B_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.