H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000099596 Accession number: BT006676 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Superoxide dismutase [Cu-Zn].
 
 

Transcript original information
Accession number BT006676.1
CAGE tag ID NA
EST ID NA
Clone Number GH00635X1.0
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (SOD1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (SOD1);
Sequence data provider NA
Annotation project NA
Length of cDNA 465[bp] (No. of exon:5)[A:132 T:102 G:145 C:86]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0016056
Genomic location  G-integra Help Chromosome 21
Location 21q22.11
Position 33032083- 33040890
Strand +
Possible duplicated location(s) NA
Gene structure 5 exon(s)
Database links RefSeq NM_000454; 
Ensembl ENST00000270142;  ENST00000389995;  ENST00000470944;  ENST00000476106;  ENST00000535823; 
Entrez Gene Entrez Gene ID:6647; 
KEGG GENES KEGG GENES(6647); 
GeneCard GeneCardSOD1;  *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS;  G-integraG-integra;  cDNA-genome alignmentcDNA-genome alignment; 

Predicted CDS information
HIP ID HIP000035561
Predicted CDS 1..465;  154[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.768
Database links RefSeq NP_000445; 
UniProt P00441;  P60052; 
CCDS CCDS33536; 

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000099596
H-Inv cluster ID Locus viewHIX0016056
Accession number BT006676.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Superoxide dismutase [Cu-Zn].
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_000445)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol SOD1
HGNC aliases "amyotrophic lateral sclerosis 1 (adult)"
HGNC name superoxide dismutase 1, soluble
DDBJ NA
UniProt NA
EC number NA
GGDB
(GlycoGene Database)
 Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000035561
No. of interaction 10
Interaction partner(s) HIP000001508;  HIP000001508;  HIP000055862;  HIP000055862;  HIP000061088;  HIP000061088;  HIP000090398;  HIP000090398;  HIP000111805;  HIP000144654; 
BIND 185633; 
DIP NA
MINT MINT-67538;  MINT-67763;  MINT-68106;  MINT-68388; 
HPRD 00743; 
IntAct EBI-758140;  EBI-757387;  EBI-759274;  EBI-760159; 
Database links RefSeq NM_000454; 
Ensembl ENST00000270142;  ENST00000389995;  ENST00000470944;  ENST00000476106;  ENST00000535823; 
Entrez Gene Entrez Gene ID:6647; 
KEGG GENES KEGG GENES(6647); 
GeneCard GeneCardSOD1;  *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT; 
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA


Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT cytosol;  nuclear;  extracellular; 
Target P Other
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:20-Apr-2012
Start End PDB_ID E-value Identity Coverage SCOP_ID
2 154 1azvA 5e-57 99.3 153/153 b.1.8.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsA130311; 
Affymetrix
GeneChip		 HG-Focus 200642_at; 
HG-U133 200642_at; 
HG-U133A 200642_at; 
HG-U133A_2 200642_at; 
HG-U133B NA
HG-U133_Plus_2 200642_at; 
HG-U95 36620_at; 
HG-U95A 36620_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3917874;  3917882;  3917888;  3917890;  3917892;  3928859; 
HuGeneFL X02317_at; 
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P151464; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name: Amyotrophic lateral sclerosis, due to SOD1 deficiency (105400); 
Related information in OMIM OMIM ID:  147450;  Title: SUPEROXIDE DISMUTASE 1
Co-localized orphan diseases NA
Disease related mutation MutationView:  147450; 
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(6647)
Disease Entrez Gene ID:(6647)
Substance Entrez Gene ID:(6647)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
119 .. 119 C/T rs1804450 + CDS Nonsynonymous[Thr40Ile]
246 .. 246 T/C rs11556619 - CDS Synonymous[Val82Val]
260 .. 260 A/G rs11556620 + CDS Nonsynonymous[Asn87Ser]
272 .. 272 A/C rs80265967 + CDS Nonsynonymous[Asp91Ala]
291 .. 291 T/A rs111229903 + CDS Nonsynonymous[Asp97Glu]
301 .. 301 G/T rs76731700 + CDS AA-STOP[Glu101*]
338 .. 338 T/C rs74315452 + CDS Nonsynonymous[Ile113Thr]
420 .. 420 C/T rs1804449 + CDS Synonymous[Asn140Asn]
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;