Human Gene SEL1L (uc010tvv.2) Description and Page Index
  Description: Homo sapiens sel-1 suppressor of lin-12-like (C. elegans) (SEL1L), transcript variant 1, mRNA.
RefSeq Summary (NM_005065): The protein encoded by this gene is part of a protein complex required for the retrotranslocation or dislocation of misfolded proteins from the endoplasmic reticulum lumen to the cytosol, where they are degraded by the proteasome in a ubiquitin-dependent manner. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011].
Transcript (Including UTRs)
   Position: hg19 chr14:81,937,891-82,000,205 Size: 62,315 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr14:81,943,316-82,000,088 Size: 56,773 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:81,937,891-82,000,205)mRNA (may differ from genome)Protein (794 aa)
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SE1L1_HUMAN
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 (By similarity). 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.
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.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Highly expressed in pancreas.
PTM: N-glycosylated.
SIMILARITY: Belongs to the sel-1 family.
SIMILARITY: Contains 1 fibronectin type-II domain.
SIMILARITY: Contains 11 Sel1-like repeats.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SEL1LID42246ch14q24.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SEL1L
CDC HuGE Published Literature: SEL1L
Positive Disease Associations: Platelet Aggregation
Related Studies:
  1. Platelet Aggregation
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.

-  MalaCards Disease Associations
  MalaCards Gene Search: SEL1L
Diseases sorted by gene-association score: diabetes mellitus, insulin-dependent, 11 (13), good syndrome (11), diabetes mellitus, insulin-dependent (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: 88.36 RPKM in Pancreas
Total median expression: 666.76 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 -42.50117-0.363 Picture PostScript Text
3' UTR -1392.275425-0.257 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
57440 - Kringle-like

ModBase Predicted Comparative 3D Structure on Q9UBV2
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  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:0030433 ER-associated ubiquitin-dependent protein catabolic process
GO:0030970 retrograde protein transport, ER to cytosol
GO:0034976 response to endoplasmic reticulum stress
GO:0036503 ERAD pathway
GO:0050821 protein stabilization
GO:0055085 transmembrane transport
GO:1904380 endoplasmic reticulum mannose trimming

Cellular Component:
GO:0000836 Hrd1p ubiquitin ligase complex
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
GO:0044322 endoplasmic reticulum quality control compartment


-  Descriptions from all associated GenBank mRNAs
  AK075511 - Homo sapiens cDNA PSEC0209 fis, clone HEMBA1003280, highly similar to Sel-1 homolog precursor.
AB020335 - Homo sapiens TSA305 mRNA, complete cds.
LP895304 - Sequence 168 from Patent EP3253886.
JD486160 - Sequence 467184 from Patent EP1572962.
JD563485 - Sequence 544509 from Patent EP1572962.
JD178010 - Sequence 159034 from Patent EP1572962.
JD166758 - Sequence 147782 from Patent EP1572962.
JD315491 - Sequence 296515 from Patent EP1572962.
BC040498 - Homo sapiens sel-1 suppressor of lin-12-like (C. elegans), mRNA (cDNA clone IMAGE:5287167), partial cds.
JD516119 - Sequence 497143 from Patent EP1572962.
JD114524 - Sequence 95548 from Patent EP1572962.
JD301836 - Sequence 282860 from Patent EP1572962.
JD249362 - Sequence 230386 from Patent EP1572962.
JD036491 - Sequence 17515 from Patent EP1572962.
JD139617 - Sequence 120641 from Patent EP1572962.
JD245472 - Sequence 226496 from Patent EP1572962.
JD498993 - Sequence 480017 from Patent EP1572962.
JD284998 - Sequence 266022 from Patent EP1572962.
JD357335 - Sequence 338359 from Patent EP1572962.
JD566726 - Sequence 547750 from Patent EP1572962.
JD288701 - Sequence 269725 from Patent EP1572962.
JD284355 - Sequence 265379 from Patent EP1572962.
JD562735 - Sequence 543759 from Patent EP1572962.
JD093309 - Sequence 74333 from Patent EP1572962.
JD563438 - Sequence 544462 from Patent EP1572962.
JD101603 - Sequence 82627 from Patent EP1572962.
JD260137 - Sequence 241161 from Patent EP1572962.
JD099332 - Sequence 80356 from Patent EP1572962.
JD510469 - Sequence 491493 from Patent EP1572962.
JD260848 - Sequence 241872 from Patent EP1572962.
JD371033 - Sequence 352057 from Patent EP1572962.
JD516546 - Sequence 497570 from Patent EP1572962.
JD516336 - Sequence 497360 from Patent EP1572962.
JD279302 - Sequence 260326 from Patent EP1572962.
JD506717 - Sequence 487741 from Patent EP1572962.
JD564726 - Sequence 545750 from Patent EP1572962.
JD089866 - Sequence 70890 from Patent EP1572962.
JD528361 - Sequence 509385 from Patent EP1572962.
JD561816 - Sequence 542840 from Patent EP1572962.
JD404274 - Sequence 385298 from Patent EP1572962.
JD279425 - Sequence 260449 from Patent EP1572962.
JD503918 - Sequence 484942 from Patent EP1572962.
JD383311 - Sequence 364335 from Patent EP1572962.
JD110984 - Sequence 92008 from Patent EP1572962.
AF052059 - Homo sapiens SEL1L (SEL1L) mRNA, complete cds.
JD085522 - Sequence 66546 from Patent EP1572962.
JD291987 - Sequence 273011 from Patent EP1572962.
JD349622 - Sequence 330646 from Patent EP1572962.
JD435641 - Sequence 416665 from Patent EP1572962.
BC054336 - Homo sapiens cDNA clone IMAGE:5528072, containing frame-shift errors.
JD237652 - Sequence 218676 from Patent EP1572962.
JD129996 - Sequence 111020 from Patent EP1572962.
U11037 - Homo sapiens sel-1-like protein (SEL1L) mRNA, complete cds.
JD426502 - Sequence 407526 from Patent EP1572962.
JD509579 - Sequence 490603 from Patent EP1572962.
JD225992 - Sequence 207016 from Patent EP1572962.
JD345930 - Sequence 326954 from Patent EP1572962.
BC172577 - Synthetic construct Homo sapiens clone IMAGE:100069271, MGC:199282 sel-1 suppressor of lin-12-like (C. elegans) (SEL1L) mRNA, encodes complete protein.
BC172282 - Synthetic construct Homo sapiens clone IMAGE:100068976, MGC:198987 sel-1 suppressor of lin-12-like (C. elegans) (SEL1L) mRNA, encodes complete protein.
AK130629 - Homo sapiens cDNA FLJ27119 fis, clone SPL06503.
AY358651 - Homo sapiens clone DNA49820 SEL1L (UNQ128) mRNA, complete cds.
JD394925 - Sequence 375949 from Patent EP1572962.

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

Protein Q9UBV2 (Reactome details) participates in the following event(s):

R-HSA-5362441 C-terminal Hh fragments are recruited to SEL1:SYVN1 at the ER membrane
R-HSA-5387386 Hh processing variants are recruited to SEL1:SYVN at the ER membrane
R-HSA-5362459 VCP-catalyzed ATP hydrolysis promotes the translocation of Hh-C into the cytosol
R-HSA-5387389 Hh processing variants are translocated to the cytosol in a VCP-dependent manner
R-HSA-8866551 CFTR binds components of the ERAD machinery for ubiquitination and degradation
R-HSA-8866857 CFTR F508del binds components of the ERAD machinery for ubiquitination and degradation
R-HSA-8866542 VCP-catalyzed ATP hydrolysis promotes the translocation of misfolded CFTR into the cytosol
R-HSA-8866854 VCP-catalyzed ATP hydrolysis promotes the translocation of CFTR F508del into the cytosol
R-HSA-5362412 SYVN1 ubiquitinates Hh C-terminal fragments
R-HSA-5483238 Hh processing variants are ubiquitinated
R-HSA-8866546 RNF5 and RNF185 ubiquitinate misfolded CFTR
R-HSA-8866856 RNF5 and RNF185 ubiquitinate CFTR F508del
R-HSA-8867288 OS9:SEL1:ERAD E3 ligase:DERL2 ubiquitinates unfolded protein:(GlcNAc)2 (Man)9-5
R-HSA-1022127 OS9:SEL1:ERAD E3 ligase:DERL2 transports Ub-unfolded protein:(GlcNAc)2 (Man)9-5 from ERQC to cytosol
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-5362768 Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-5678895 Defective CFTR causes cystic fibrosis
R-HSA-5358351 Signaling by Hedgehog
R-HSA-5387390 Hh mutants abrogate ligand secretion
R-HSA-382551 Transport of small molecules
R-HSA-5619084 ABC transporter disorders
R-HSA-901032 ER Quality Control Compartment (ERQC)
R-HSA-162582 Signal Transduction
R-HSA-5663202 Diseases of signal transduction
R-HSA-5619115 Disorders of transmembrane transporters
R-HSA-901042 Calnexin/calreticulin cycle
R-HSA-1643685 Disease
R-HSA-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_005065, NP_005056, Q6UWT6, Q9P1T9, Q9UBV2, Q9UHK7, SE1L1_HUMAN, TSA305, UNQ128/PRO1063
UCSC ID: uc010tvv.2
RefSeq Accession: NM_005065
Protein: Q9UBV2 (aka SE1L1_HUMAN)
CCDS: CCDS9876.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005065.5
exon count: 21CDS single in 3' UTR: no RNA size: 7943
ORF size: 2385CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4970.00frame shift in genome: no % Coverage: 99.80
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.