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Aliases for SIL1 Gene

Aliases for SIL1 Gene

  • SIL1 Nucleotide Exchange Factor 2 3 5
  • BiP-Associated Protein 3 4
  • BAP 3 4
  • SIL1 Homolog, Endoplasmic Reticulum Chaperone (S. Cerevisiae) 2
  • SIL1-Like Protein Endoplasmic Reticulum Chaperone 3
  • SIL1 Homolog, Endoplasmic Reticulum Chaperone 3
  • Nucleotide Exchange Factor SIL1 3
  • Marinesco-Sjogren Syndrome 2
  • ULG5 3
  • MSS 3

External Ids for SIL1 Gene

Previous HGNC Symbols for SIL1 Gene

  • MSS

Previous GeneCards Identifiers for SIL1 Gene

  • GC05M138157
  • GC05M138313
  • GC05M138358
  • GC05M138310
  • GC05M133472
  • GC05M138282

Summaries for SIL1 Gene

Entrez Gene Summary for SIL1 Gene

  • This gene encodes a resident endoplasmic reticulum (ER), N-linked glycoprotein with an N-terminal ER targeting sequence, 2 putative N-glycosylation sites, and a C-terminal ER retention signal. This protein functions as a nucleotide exchange factor for another unfolded protein response protein. Mutations in this gene have been associated with Marinesco-Sjogren syndrome. Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for SIL1 Gene

SIL1 (SIL1 Nucleotide Exchange Factor) is a Protein Coding gene. Diseases associated with SIL1 include Marinesco-Sjogren Syndrome and Sjogren's Syndrome. Among its related pathways are Protein processing in endoplasmic reticulum. GO annotations related to this gene include binding and unfolded protein binding.

UniProtKB/Swiss-Prot for SIL1 Gene

  • Required for protein translocation and folding in the endoplasmic reticulum (ER). Functions as a nucleotide exchange factor for the ER lumenal chaperone HSPA5.

Gene Wiki entry for SIL1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SIL1 Gene

Genomics for SIL1 Gene

Regulatory Elements for SIL1 Gene

Enhancers for SIL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G139381 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11 -96.2 -96161 15.5 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 WRNIP1 ARID4B SIN3A DMAP1 DNAJC18 PURA SLC23A1 PAIP2 SIL1 MATR3 PROB1 MZB1
GH05G139131 1.5 Ensembl ENCODE dbSUPER 10 +161.1 161076 2.7 HNRNPUL1 AGO1 SIN3A TAF15 KAT8 SMARCA4 HNF4A KDM1A SP7 LEF1 LOC105379194 CDC23 KDM3B MATR3 SIL1 GC05P139106 GC05P139105 GC05P139104 GC05P139103 GC05P139102
GH05G139147 1.4 Ensembl ENCODE dbSUPER 10.2 +144.5 144466 4.0 HDAC1 PKNOX1 FOXA2 CBX3 TBL1XR1 RAD21 TCF12 GATA2 FOS ZNF548 LOC105379194 CDC23 KDM3B CTNNA1 MATR3 SIL1 GC05P139163 GC05P139162 GC05P139106 GC05P139105
GH05G139413 1.4 Ensembl ENCODE 9.9 -123.5 -123493 6.6 FOXA2 CREB3L1 ARNT ARID4B SIN3A DMAP1 FEZF1 ZNF2 ZBTB7B YY1 DNAJC18 IGIP RNU5B-4P ECSCR PROB1 MZB1 SLC23A1 PAIP2 LRRTM2 SIL1
GH05G139341 1.2 ENCODE 10.6 -48.8 -48758 2.6 MLX CREB3L1 AGO1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZNF610 KDM3B PURA RPL7P19 SLC23A1 MZB1 PROB1 MATR3 SNORA74A SIL1 SNORD63
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SIL1 on UCSC Golden Path with GeneCards custom track

Promoters for SIL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187620 -943 2601 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 ZNF610 ZNF585B

Genomic Location for SIL1 Gene

Chromosome:
5
Start:
138,946,720 bp from pter
End:
139,293,557 bp from pter
Size:
346,838 bases
Orientation:
Minus strand

Genomic View for SIL1 Gene

Genes around SIL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SIL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SIL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SIL1 Gene

Proteins for SIL1 Gene

  • Protein details for SIL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H173-SIL1_HUMAN
    Recommended name:
    Nucleotide exchange factor SIL1
    Protein Accession:
    Q9H173
    Secondary Accessions:
    • D3DQC2
    • Q8N2L3

    Protein attributes for SIL1 Gene

    Size:
    461 amino acids
    Molecular mass:
    52085 Da
    Quaternary structure:
    • Interacts with HSPA5.

neXtProt entry for SIL1 Gene

Post-translational modifications for SIL1 Gene

No data available for DME Specific Peptides for SIL1 Gene

Domains & Families for SIL1 Gene

Protein Domains for SIL1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SIL1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9H173

UniProtKB/Swiss-Prot:

SIL1_HUMAN :
  • Belongs to the SIL1 family.
Family:
  • Belongs to the SIL1 family.
genes like me logo Genes that share domains with SIL1: view

No data available for Gene Families for SIL1 Gene

Function for SIL1 Gene

Molecular function for SIL1 Gene

UniProtKB/Swiss-Prot Function:
Required for protein translocation and folding in the endoplasmic reticulum (ER). Functions as a nucleotide exchange factor for the ER lumenal chaperone HSPA5.

Gene Ontology (GO) - Molecular Function for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0051082 unfolded protein binding NAS 11101517
genes like me logo Genes that share ontologies with SIL1: view

Phenotypes for SIL1 Gene

genes like me logo Genes that share phenotypes with SIL1: view

Human Phenotype Ontology for SIL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for SIL1 Gene

miRTarBase miRNAs that target SIL1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SIL1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SIL1 Gene

Localization for SIL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SIL1 Gene

Endoplasmic reticulum lumen.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SIL1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
nucleus 2
mitochondrion 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 16502470
GO:0005783 endoplasmic reticulum NAS 11101517
GO:0005788 endoplasmic reticulum lumen IEA --
genes like me logo Genes that share ontologies with SIL1: view

Pathways & Interactions for SIL1 Gene

genes like me logo Genes that share pathways with SIL1: view

Pathways by source for SIL1 Gene

1 KEGG pathway for SIL1 Gene

Gene Ontology (GO) - Biological Process for SIL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006457 protein folding NAS 11101517
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport NAS 11101517
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with SIL1: view

No data available for SIGNOR curated interactions for SIL1 Gene

Drugs & Compounds for SIL1 Gene

(1) Drugs for SIL1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SIL1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SIL1: view

Transcripts for SIL1 Gene

Unigene Clusters for SIL1 Gene

SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SIL1

Alternative Splicing Database (ASD) splice patterns (SP) for SIL1 Gene

No ASD Table

Relevant External Links for SIL1 Gene

GeneLoc Exon Structure for
SIL1
ECgene alternative splicing isoforms for
SIL1

Expression for SIL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SIL1 Gene

Protein differential expression in normal tissues from HIPED for SIL1 Gene

This gene is overexpressed in Milk (29.5) and Testis (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SIL1 Gene



NURSA nuclear receptor signaling pathways regulating expression of SIL1 Gene:

SIL1

SOURCE GeneReport for Unigene cluster for SIL1 Gene:

Hs.483521

mRNA Expression by UniProt/SwissProt for SIL1 Gene:

Q9H173-SIL1_HUMAN
Tissue specificity: Highly expressed in tissues which produce large amounts of secreted proteins such as kidney, liver and placenta. Also expressed in colon, heart, lung, ovary, pancreas, peripheral leukocyte, prostate, spleen and thymus. Expressed at low levels throughout the brain.

Evidence on tissue expression from TISSUES for SIL1 Gene

  • Skin(4.5)
  • Liver(4.4)
  • Intestine(3.4)
  • Lung(3.1)
  • Nervous system(2.7)
  • Lymph node(2.5)
  • Muscle(2.4)
  • Thyroid gland(2.3)
  • Blood(2.2)
  • Stomach(2.2)
  • Heart(2.1)
  • Gall bladder(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SIL1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • head
  • pituitary gland
  • skull
Thorax:
  • breast
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
Pelvis:
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shoulder
  • thigh
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SIL1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for SIL1 Gene

Orthologs for SIL1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SIL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SIL1 34 35
  • 99.19 (n)
dog
(Canis familiaris)
Mammalia SIL1 34 35
  • 89.57 (n)
cow
(Bos Taurus)
Mammalia SIL1 34 35
  • 87.26 (n)
rat
(Rattus norvegicus)
Mammalia Sil1 34
  • 85.39 (n)
mouse
(Mus musculus)
Mammalia Sil1 34 16 35
  • 84.96 (n)
oppossum
(Monodelphis domestica)
Mammalia SIL1 35
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SIL1 35
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves SIL1 34 35
  • 67.61 (n)
lizard
(Anolis carolinensis)
Reptilia SIL1 35
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sil1 34
  • 56.95 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC568308 34
  • 58.25 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003488 34
  • 48.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10420 36 34 35
  • 45.71 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SIL1 37
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 35 (a)
OneToOne
Species where no ortholog for SIL1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SIL1 Gene

ENSEMBL:
Gene Tree for SIL1 (if available)
TreeFam:
Gene Tree for SIL1 (if available)

Paralogs for SIL1 Gene

No data available for Paralogs for SIL1 Gene

Variants for SIL1 Gene

Sequence variations from dbSNP and Humsavar for SIL1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs119456965 Pathogenic 139,050,960(-) AGTTC(C/T)GAAAT reference, stop-gained
rs119456966 Pathogenic 138,947,191(-) AGCTG(C/T)AGGAT reference, stop-gained
rs119456967 Pathogenic 138,947,133(-) CTTGC(C/T)GAAGG reference, missense
rs370290043 Pathogenic 138,947,482(+) CCATC(C/T)GCCAC intron-variant
rs548535414 Pathogenic 139,026,799(+) ACAGT(A/G)CCTGA splice-donor-variant

Structural Variations from Database of Genomic Variants (DGV) for SIL1 Gene

Variant ID Type Subtype PubMed ID
esv2666199 CNV deletion 23128226
esv2672987 CNV deletion 23128226
esv3408136 CNV insertion 20981092
esv3447133 CNV duplication 20981092
esv3566707 CNV deletion 23714750
esv3566709 CNV deletion 23714750
esv3606932 CNV loss 21293372
esv3606933 CNV loss 21293372
esv3606935 CNV gain 21293372
esv3606936 CNV loss 21293372
nsv1017883 CNV gain 25217958
nsv1029030 CNV gain 25217958
nsv1137028 CNV deletion 24896259
nsv1140572 CNV deletion 24896259
nsv436490 CNV deletion 17901297
nsv5027 CNV insertion 18451855
nsv950408 CNV deletion 24416366
nsv968249 CNV duplication 23825009

Variation tolerance for SIL1 Gene

Residual Variation Intolerance Score: 74.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.99; 60.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SIL1 Gene

Human Gene Mutation Database (HGMD)
SIL1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SIL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SIL1 Gene

Disorders for SIL1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SIL1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
marinesco-sjogren syndrome
  • marinesco-sjögren syndrome
sjogren's syndrome
  • sicca syndrome
spindle cell synovial sarcoma
  • synovial sarcoma with spindle cell components
short-rib thoracic dysplasia 9 with or without polydactyly
  • renal dysplasia, retinal pigmentary dystrophy, cerebellar ataxia and skeletal dysplasia
marchiafava bignami disease
  • acute marchiafava-bignami disease
- elite association - COSMIC cancer census association via MalaCards
Search SIL1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SIL1_HUMAN
  • Marinesco-Sjoegren syndrome (MSS) [MIM:248800]: Autosomal recessive multisystem disorder which is characterized by cerebellar ataxia due to cerebellar atrophy, with Purkinje and granule cell loss and myopathy featuring marked muscle replacement with fat and connective tissue. Other cardinal features include bilateral cataracts, hypergonadotrophic hypogonadism and mild to severe mental retardation. Skeletal abnormalities, short stature, dysarthria, strabismus and nystagmus are also frequent findings. Mutational inactivation of this protein may result in ER stress-induced cell death signaling or malfunctioning chaperone machineries that mishandle client proteins which are critical for the organs targeted in MSS. {ECO:0000269 PubMed:16282977, ECO:0000269 PubMed:16282978}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SIL1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SIL1
genes like me logo Genes that share disorders with SIL1: view

No data available for Genatlas for SIL1 Gene

Publications for SIL1 Gene

  1. Mutations in SIL1 cause Marinesco-Sjoegren syndrome, a cerebellar ataxia with cataract and myopathy. (PMID: 16282977) Senderek J. … Zerres K. (Nat. Genet. 2005) 2 3 4 22 64
  2. The gene disrupted in Marinesco-Sjoegren syndrome encodes SIL1, an HSPA5 cochaperone. (PMID: 16282978) Anttonen A.-K. … Lehesjoki A.-E. (Nat. Genet. 2005) 3 4 22 64
  3. BAP, a mammalian BiP-associated protein, is a nucleotide exchange factor that regulates the ATPase activity of BiP. (PMID: 12356756) Chung K.T. … Hendershot L.M. (J. Biol. Chem. 2002) 2 3 4 64
  4. LHS1 and SIL1 provide a lumenal function that is essential for protein translocation into the endoplasmic reticulum. (PMID: 11101517) Tyson J.R. … Stirling C.J. (EMBO J. 2000) 2 3 4 64
  5. Novel mutations in the SIL1 gene in a Japanese pedigree with the Marinesco-SjAPgren syndrome. (PMID: 20111056) Takahata T. … Kitaoka T. (J. Hum. Genet. 2010) 3 22 64

Products for SIL1 Gene

Sources for SIL1 Gene

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