Mouse Gene Sel1l (ENSMUST00000021347.11) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus sel-1 suppressor of lin-12-like (C. elegans) (Sel1l), transcript variant 1, mRNA. (from RefSeq NM_001039089)
Gencode Transcript: ENSMUST00000021347.11
Gencode Gene: ENSMUSG00000020964.14
Transcript (Including UTRs)
   Position: mm10 chr12:91,806,043-91,849,157 Size: 43,115 Total Exon Count: 21 Strand: -
Coding Region
   Position: mm10 chr12:91,809,844-91,849,031 Size: 39,188 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:91,806,043-91,849,157)mRNA (may differ from genome)Protein (790 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SE1L1_MOUSE
DESCRIPTION: RecName: Full=Protein sel-1 homolog 1; AltName: Full=Suppressor of lin-12-like protein 1; Short=Sel-1L; Flags: Precursor;
FUNCTION: May play a role in Notch signaling. May be involved in the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin- dependent degradation of misfolded endoplasmic reticulum proteins (By similarity).
SUBUNIT: Part of a complex containing SEL1L, SYVN1 and DERL2. May form a complex with ERLEC1, HSPA5, OS9, and SYVN1. Interacts with FOXRED2 and EDEM1 (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein (By similarity).
PTM: N-glycosylated (By similarity).
SIMILARITY: Belongs to the sel-1 family.
SIMILARITY: Contains 1 fibronectin type-II domain.
SIMILARITY: Contains 11 Sel1-like repeats.

-  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


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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.80126-0.363 Picture PostScript Text
3' UTR -1136.603801-0.299 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
IPR000562 - FN_type2_col-bd
IPR013806 - Kringle-like
IPR006597 - Sel1-like
IPR011990 - TPR-like_helical

Pfam Domains:
PF00040 - Fibronectin type II domain
PF08238 - Sel1 repeat

SCOP Domains:
81901 - HCP-like
48452 - TPR-like
143469 - ImmE5-like
57440 - Kringle-like

ModBase Predicted Comparative 3D Structure on Q9Z2G6
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details    Gene Details
Gene Sorter    Gene Sorter
GenBankRGDEnsembl  SGD
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006641 triglyceride metabolic process
GO:0007219 Notch signaling pathway
GO:0009306 protein secretion
GO:0030970 retrograde protein transport, ER to cytosol
GO:0034976 response to endoplasmic reticulum stress
GO:0036503 ERAD pathway

Cellular Component:
GO:0000839 Hrd1p ubiquitin ligase ERAD-L complex
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0036513 Derlin-1 retrotranslocation complex


-  Descriptions from all associated GenBank mRNAs
  AK220502 - Mus musculus mRNA for mKIAA4137 protein.
AK160936 - Mus musculus 15 days embryo head cDNA, RIKEN full-length enriched library, clone:4021401G01 product:Sel1 (suppressor of lin-12) 1 homolog (C. elegans), full insert sequence.
BC049959 - Mus musculus sel-1 suppressor of lin-12-like (C. elegans), mRNA (cDNA clone IMAGE:4923124), partial cds.
AK008076 - Mus musculus adult male small intestine cDNA, RIKEN full-length enriched library, clone:2010003M20 product:unclassifiable, full insert sequence.
AF063095 - Mus musculus SELlL (Sel1l) mRNA, complete cds.
BC057452 - Mus musculus sel-1 suppressor of lin-12-like (C. elegans), mRNA (cDNA clone IMAGE:3965128), partial cds.
BC026816 - Mus musculus sel-1 suppressor of lin-12-like (C. elegans), mRNA (cDNA clone MGC:25250 IMAGE:4457637), complete cds.
AK146022 - Mus musculus 14 days pregnant adult female placenta cDNA, RIKEN full-length enriched library, clone:I530024L02 product:Sel1 (suppressor of lin-12) 1 homolog (C. elegans), full insert sequence.
AK005023 - Mus musculus adult male liver cDNA, RIKEN full-length enriched library, clone:1300016D21 product:Sel1 (suppressor of lin-12) 1 homolog (C. elegans), full insert sequence.
AK161546 - Mus musculus adult male pituitary gland cDNA, RIKEN full-length enriched library, clone:5330403H04 product:Sel-1 homolog precursor (Suppressor of lin-12-like protein) (Sel-1L) homolog [Mus musculus], full insert sequence.
AK160420 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:1700080G14 product:Sel1 (suppressor of lin-12) 1 homolog (C. elegans), full insert sequence.
AK005544 - Mus musculus adult female placenta cDNA, RIKEN full-length enriched library, clone:1600026C08 product:Sel1 (suppressor of lin-12) 1 homolog (C. elegans), full insert sequence.
AK158190 - Mus musculus adult inner ear cDNA, RIKEN full-length enriched library, clone:F930039K02 product:unclassifiable, full insert sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04141 - Protein processing in endoplasmic reticulum

Reactome (by CSHL, EBI, and GO)

Protein Q9Z2G6 (Reactome details) participates in the following event(s):

R-MMU-5362441 C-terminal Hh fragments are recruited to SEL1:SYVN1 at the ER membrane
R-MMU-5362459 VCP-catalyzed ATP hydrolysis promotes the translocation of Hh-C into the cytosol
R-MMU-8866551 CFTR binds components of the ERAD machinery for ubiquitination and degradation
R-MMU-8866542 VCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol
R-MMU-1022127 OS9:SEL1:ERAD E3 ligase:DERL2 transports Ub-unfolded protein:(GlcNAc)2 (Man)9-5 from ERQC to cytosol
R-MMU-8867288 OS9:SEL1:ERAD E3 ligase:DERL2 ubiquitinates unfolded protein:(GlcNAc)2 (Man)9-5
R-MMU-5362412 SYVN1 ubiquitinates Hh C-terminal fragments
R-MMU-8866546 RNF5 and RNF185 ubiquitinate misfolded CFTR
R-MMU-5358346 Hedgehog ligand biogenesis
R-MMU-382556 ABC-family proteins mediated transport
R-MMU-901032 ER Quality Control Compartment (ERQC)
R-MMU-5358351 Signaling by Hedgehog
R-MMU-382551 Transport of small molecules
R-MMU-901042 Calnexin/calreticulin cycle
R-MMU-162582 Signal Transduction
R-MMU-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-MMU-446203 Asparagine N-linked glycosylation
R-MMU-597592 Post-translational protein modification
R-MMU-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001039089, Q9DBD8, Q9Z2G6, SE1L1_MOUSE, Sel1h, uc007oky.1
UCSC ID: uc007oky.1
RefSeq Accession: NM_001039089
Protein: Q9Z2G6 (aka SE1L1_MOUSE)
CCDS: CCDS26091.1

-  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.