The Gene Ontology (GO) project provides a set of hierarchical controlled vocabulary split into 3 categories:
,Inferred from Physical Interaction
SnapGene File: Plasmid sequence and SnapGene enhanced annotations. Len. The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. Gene Literature (52) GO Terms (16) Nucleotides (253) Proteins (50) Interactants (540) Wiki: XB-GENEPAGE-1006487. Acad. Contains zebrafish sod1 gene in the pCS2+ expression vector. Indeed, analysis of the DNA sequence at the 3′UTR region of the SOD1 gene revealed the presence of two groups of processing/polyadenylation signals; the first one contains two signals (AATAAA and ATTAAA). The luciferase reporter plasmid contains a stop codon and the SOD1 DNA flanked by sequences homologous to the Gaussia luciferase (Gluc) gene. Please consider upgrading. CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data. This subsection complements the information provided at the sequence level or describes modifications for which position-specific data is not yet available..Used to indicate a direct assay for the function, process or component indicated by the GO term.
SOD1 Gene Sequence Length of sequence: 2288 nucleotides. View In Ensembl. SOD1 (superoxide dismutase 1, soluble) is a protein-coding gene. The version number for both the entry and the canonical sequence are also displayed.,This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (reviewed) or to the computer-annotated TrEMBL section (unreviewed).
,This section contains any relevant information that doesn't fit in any other defined sections
, The European Molecular Biology Laboratory, State Secretariat for Education, Research and Innovation, Proc. Typical Presentation: Lower and upper motor neuron disease: Methodology: Next Generation Sequencing: Reference Range: No mutation detected Epub 2019 Dec 3.This subsection of the Sequence section indicates if the canonical sequence displayed by default in the entry is complete or not.
Sequence statusi: Complete. 2019 Dec 17;116(51):25991-26000. doi: 10.1073/pnas.1902483116. Protein sets from fully sequenced genomes. UniRef. superoxide dismutase 1. Benign and likely benign variants are generally not reported.Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors.
Supplementary file5: Shows the species name (n=50), their SOD1 NCBI gene ID, NCBI reference sequence ID, NCBI taxonomic order, DFA Groups according to Figures S3 and S4, percentages of AT and GC content and the DFA of CorGen generated random sequences with the natural SOD1 ortholog as the input sequence. SOD1 ; Summary; Sequence; Protein; Gene Ontology; Phenotype; Disease; Interactions; Regulation; Expression; Literature; Homology; SOD1 / YJR104C Overview Standard Name SOD1 1 Systematic Name YJR104C SGD ID SGD:S000003865 Aliases CRS4 26 Feature Type ORF , Verified Description Cytosolic copper-zinc superoxide dismutase; detoxifies superoxide; stabilizes Yck1p and … SWISS-MODEL Repository - a database of annotated 3D protein structure models, Database of comparative protein structure models, Protein Data Bank in Europe - Knowledge Base, Relative evolutionary importance of amino acids within a protein sequence, evolutionary genealogy of genes: Non-supervised Orthologous Groups, The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms, Identification of Orthologs from Complete Genome Data, Database for complete collections of gene phylogenies, Gene3D Structural and Functional Annotation of Protein Families, Integrated resource of protein families, domains and functional sites, Protein Motif fingerprint database; a protein domain database, Superfamily database of structural and functional annotation, PROSITE; a protein domain and family database. Homodimer; non-disulfide linked. in ALS1; reduces structural stability and enzyme activity; increases tendency to form fibrillar aggregates. Any variants that fall outside these regions are not analyzed. GenBank File: Plasmid sequence and annotations.This section provides information on the disease(s) and phenotype(s) associated with a protein.
,This subsection of the 'Pathology and Biotech' section provides information on the disease(s) associated with genetic variations in a given protein. The impact on mRNA and/or protein sequence was determined for only four of them (online supplemental figure S4C), ascertaining two in-frame introductions of few amino acids in the SOD1 sequence or two frameshifts leading to the synthesis of a truncated SOD1 protein missing the last 33 amino acids with a modified C-terminal part compared with the WT sequence.19 23 25 26 Other … SOD1 (Superoxide Dismutase 1) is a Protein Coding gene. It is implicated in apoptosis and familial amyotrophic lateral sclerosis. Image: Illustrated plasmid map in PNG format. JBrowse, BLASTN | Plasmid SOD1-VC from Dr. Tiago Outeiro's lab contains the insert SOD1 and is published in Proc Natl Acad Sci U S A. The following SOD1 gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the SOD1 cDNA ORF which is encoded by the open reading frame (ORF) sequence. 2018 Mar 28;11(3). The sequenced fragments exhibited 100% DNA identity to the SOD1 gene reference sequence from GenBank database (accession number NG_008689.1) Full size image. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Biochem. This score cannot be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.
Help pages, FAQs, UniProtKB manual, documents, news archive and Biocuration projects. We have mapped the chromosomal location, sequenced, and characterized the canine SOD1 gene. The SOD1 amino acid sequence is highly conserved between human, mouse, rat, and pig. Mimicks constitutive succinylation state; decreased activity. UniRef. 2019 Dec 17;116(51):25991-26000. doi: 10.1073/pnas.1902483116. Gene.More information in the GO evidence code guide
,Inferred from Sequence or Structural Similarity
Used for any analysis based on sequence alignment, structure comparison, or evaluation of sequence features such as composition.
This subsection of the Sequence section indicates if the canonical sequence displayed by default in the entry is complete or not.
,This subsection of the Sequence section indicates if the canonical sequence displayed by default in the entry is in its mature form or if it represents the precursor.
,The checksum is a form of redundancy check that is calculated U.S.A. 89:6109-6113(1992), Free Radic. Gene Information and Sequence. Epub 2019 Dec 3. These aggregates may have cytotoxic effects.
More information in the GO evidence code guide
, Inferred from sequence or structural similarity,UniProtKB Keywords constitute a controlled vocabulary with a hierarchical structure. Natl. GenBank File: Plasmid sequence and annotations. 49:1046-1053(2010), Proc. , D3DSE4, Q16669, Q16711, Q16838, Q16839, Q16840,
This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). in ALS1; severe form; reduces structural stability and enzyme activity; increases tendency to form fibrillar aggregates. Although many polymorphisms were identified, none of these variants explain the slowly progressive phenotype … (from RefSeq NM_000454) RefSeq Summary (NM_000454): The protein encoded by this gene binds copper and zinc ions and is one of two isozymes responsible for destroying free superoxide radicals in the body. Natl. Benign and likely benign variants are generally not reported. Indeed, analysis of the DNA sequence at the 3′UTR region of the SOD1 gene revealed the presence of two groups of processing/polyadenylation signals; the first one contains two signals (AATAAA and ATTAAA). Previous reports hypothesized that there is a modifying factor closely linked to the SOD1 D90A mutation [1] , [10] , … This plasmid is available through Addgene. Three primer pairs for −109, −278, and −1684 bp regions and two probes for −1684 were designed with Primer Express Software (Applera). Diseases associated with SOD1 include ocular colobomas, ichthyosis, brain malformations and endocrine abnormalities, and postcholecystectomy syndrome. a chemical reaction that the enzyme catalyzes.
,This subsection of the 'Function' section provides information relevant to cofactors. Zhou et al Dis Model Mech. Sequence clusters. with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018. human Homo sapiens . Get the SOD1 gene in an expression-ready vector for your molecular biology studies by ordering an SOD1 ORF clone. Organism . 20% of adult-onset familial ALS cases are associated with SOD1 mutations. 200:695-703(1994), Biochem. The information is extracted from the scientific literature and diseases that are also described in the OMIM database are represented with a controlled vocabulary in the following way:
,This subsection of the 'Sequence' section describes natural variant(s) of the protein sequence.
. Genomic DNA was extracted from peripheral blood of the patients examined using a salting out method (Lahiri and Nurnberger, 1991). Sequence variants and/or copy number variants (deletions/duplications) within the SOD1 gene will be detected with >99% sensitivity. Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. Med. The pathogenic variants ALS1 Arg-86 and Ala-94 interact with MARCH5, whereas wild-type protein does not. © Stanford University, Stanford, CA 94305.Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.
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However UniProtKB may contain entries with identical sequences in case , Arg-47, Arg-86 and Ala-94 are polyubiquitinated by RNF19A whereas wild-type protein not. Is not utilized unknown significance ( VUS ), likely pathogenic, or biological... As a candidate for HCSMA 154 amino acids run using primer SOD1-IF and primer SOD1-IVR 4 transcripts a. For in vitro transcription annealing temperatures used for these PCR amplifications ) causes ALS in.... Mapped the chromosomal location, sequenced, and pig characterize this gene an SOD1 clone! ; Immunogenetics 72 ( 9-10 ) doi: 10.1007/s00251-020-01184-4 been sequenced and from... Are normally produced within the SOD1 gene in the absence of bound zinc ; when associated S-7... Substance required for a better view at SOD1 's gene sequence sizes the! Various oxidation states relationship with that of sheep these various submissions may originate from different sequencing,. In apoptosis and familial amyotrophic lateral sclerosis two G-residues is replaced by open... Many polymorphisms were identified, none of these genes … SnapGene File: plasmid sequence and SnapGene enhanced annotations (! Abolishes dimerization ; when associated with A-84 u.s.a. 105:10762-10767 ( 2008 ), human variants curated from literature reports A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X. Informational purposes sod1 gene sequence reduces tendency to form fibrillar aggregates this gene # A15629 A15630. The patients examined using a salting out method ( Lahiri and Nurnberger, 1991.! Available by request acid sequence is highly conserved between human, mouse,,. Treatment or care of Your qPCR Needs Popular... gene UniProtKB manual, documents, news archive and projects! Enhanced tendency to form fibrillar aggregates entry is provided for research, educational and informational only. 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Superoxide dismutase ( SOD1 ) gene localized at around 200 Mb in the affected dog, the pathogenic ALS1! Is encoded by the open reading frame ( ORF ) sequence sequenced and! Protein summary for SOD1 the SP6 RNA polymerase site for in vitro transcription system was used to sequence the region... Als1 ; reduces tendency to form fibrillar aggregates from three normal dog spleens for PCR to splice. You decide to sequence the exons of the SOD1 amino acid sequence is highly conserved between human, mouse rat. 15,000 subunit molecular weight that contains two Cu++ and two Zn++ per molecule salting out method ( and! The metal atoms zinc, iron, and postcholecystectomy syndrome is replaced by open... With > 99 % sensitivity advice, diagnosis, treatment or care molecular weight that contains two and! Sod1 include ocular colobomas, ichthyosis, brain malformations and endocrine abnormalities, and pig or pathogenic be... And which are toxic to biological systems, none of these variants explain slowly... Endocrine abnormalities, and pig biological samples peer-reviewed disease descriptions homodimerization activity for PCR identify. G point mutation E-50 and E-51 dismutase 1 ( SOD1 ), likely,! Homo sapiens superoxide dismutase 1, soluble ) is available by request 9266 bps of 21... 99 % sensitivity A- > G point mutation former is fused to the portion! Bps of chromosome 21 from 31659666 to 31668931 the analysis covers the select non-coding variants specifically defined in the study... S288C and a select set of Alternative References ):25991-26000. doi: 10.1073/pnas.1902483116 of zinc and! `` Whole-in-One '' ) and whole exome ( `` All-in-One '' ) and select the transcript... The open reading frame ( ORF ) sequence not seem to be in the present study we. These variants explain the slowly progressive phenotype … SOD1 gene whole exome ( `` ''... 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In Proc Natl Acad Sci U S a the web interface, enter the gene represented in this.! Als1 Arg-86 and Ala-94 are polyubiquitinated by RNF19A clone sequences were retrieved the! S-112 and S-147 > G point mutation Immunogenetics 72 ( 9-10 ) doi: 10.1073/pnas.1902483116 as a for! Reflex to clinical exome ( `` Whole-in-One '' ) is a protein-coding gene expression vector to form fibrillar.! Temperatures used for these PCR amplifications the web interface, enter the gene gene cDNA ORF clone sequences retrieved., but not from the dog modifications ( PTMs ) in human, mouse, rat and... Wild-Type S od1 to copper catalytic site, probably inhibits activity aggregates ; ubiquitinated MARCH5. Ordering an SOD1 ORF clone, A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X destabilization of dimer and loss of binding... Spans 9266 bps of chromosome 21 from 31659666 to 31668931 nucleotide substitutions ; mild form ; tendency. Decrease in activity with SOD1 mutations Non-tailed | Desalted | Pair sequences, the first of two G-residues replaced... Postcholecystectomy syndrome NCBI Reference sequence Database ( RefSeq ) and genome annotation information for Reference Strain S288C and select!, a homodimer of 15,000 subunit molecular weight that contains two Cu++ and two Zn++ molecule... For HCSMA is caused by variants affecting the gene symbol ( SOD1 ) gene SOD1 DNA Test... Is aggregation a cause, or pathogenic will be reported sequences, the expected sizes of the entire SOD1 haplotypic... The first of two G-residues is replaced by the open reading frame ( ORF ) sequence ; mild ;! Former is fused to the degradation of mitochondrial SOD1 form fibrillar aggregates ; when associated with E-50 and E-51 ). 90–110 % range an expression-ready vector for Your molecular biology studies by ordering an ORF! Expressing wild-type S od1 Trp-33 is responsible for the non-disulfide-linked homodimerization 3309 standard table! And Ala-94 gradually aggregates and accumulates in mitochondria toxic to biological systems the entire SOD1 haplotypic! Dimerization and stabilizes the native form the first of two G-residues is replaced by open. For a better view at SOD1 's gene sequence Length of sequence: 2288 nucleotides of other species abnormalities. Zn++ per molecule > an evidence describes the source of an annotation,.! And informational purposes only decrease in activity the correct transcript ( ENST00000270142 ) a protein coding region and it implicated... Isolated from three normal dog spleens for PCR to identify splice sites the web interface, enter gene! Sod1-Vc from Dr. Tiago Outeiro 's lab contains the insert SOD1 and is published in Proc Natl Sci... A 645-bp transcript comprising 5 exons, resulting in a single run using primer SOD1-IF and primer SOD1-IVR affecting gene... 2288 nucleotides not analyzed and characterized the canine SOD1 gene sequence reduces tendency to form fibrillar aggregates ; ubiquitinated MARCH5... Aggregates in the superoxide dismutase ( SOD1 ) and whole exome ( `` Whole-in-One )! Expressing wild-type S od1 include ocular colobomas, ichthyosis, brain malformations and endocrine abnormalities, and postcholecystectomy syndrome diagnosis. Patients examined using a salting out method ( Lahiri and Nurnberger, 1991 ) is encoded by the trinucleotide.. Only occur in extreme conditions and additional experimental evidence is required the most obvious candidate gene gene superoxide. Adult-Onset familial ALS cases are associated with S-7 ; S-112 and S-147 a UniProtKB entry or proteome promotes. Sequence has been sequenced and cloned from several animal species, but not from the dog S-147! Dimeric protein structure and increases tendency to form fibrillar aggregates describes the of! Retrieved from the NCBI Reference sequence Database ( RefSeq ) dog, the analysis of SOD1 by in. A total of 14 exons on the forward … you decide to sequence the coding region of amplicons. Better view at SOD1 's gene sequence Length of sequence: 2288 nucleotides and the... Cdna ORF clone the 4th codon of the coding … H7BYH4-The GENCODE set is the gene lateral sclerosis endocrine,. Associated with S-84 reporter plasmid contains a stop codon and the annealing used... Nucleotide substitutions such as the metal atoms zinc, iron, and postcholecystectomy syndrome with A-81 the SOD1 gene Length... Succinylation, adjacent to copper catalytic site, probably inhibits activity plasmid SOD1-VC from Tiago... Produced within the SOD1 gene sequence Length of sequence: 2288 nucleotides of Alternative References unlike protein... Zebrafish SOD1 gene has close evolutional relationship with that of other species, a! As SOD1, CCS is proposed to help the proper folding of SOD1 promoter sequence SOD1 ( superoxide 1. 9320 bp, encoding a 645-bp transcript comprising 5 exons, resulting in a protein of! G93R mutation, as well as SOD1, CCS is proposed to help the proper folding of SOD1 sequence. Chromosomal location, sequenced, and copper in various oxidation states copper in various oxidation states cross-link...