Human Gene SZT2 (uc001cjk.3) Description and Page Index
  Description: Homo sapiens seizure threshold 2 homolog (mouse) (SZT2), mRNA.
RefSeq Summary (NM_015284): The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia. It is localized to the peroxisome, and is implicated in resistance to oxidative stress. It likely functions by increasing superoxide dismutase (SOD) activity, but itself has no direct SOD activity. Studies in mice show that this gene confers low seizure threshold, and may also enhance epileptogenesis. [provided by RefSeq, Jun 2011]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignment to same-species transcripts and to orthologous mouse transcript (NM_198170.3). The encoded protein is supported by similar sized ortholog in mouse (NP_937813.3), and model proteins in bovine (XP_613325.4), rat (XP_001069457.2) and rabbit (XP_002715736.1). ##Evidence-Data-START## RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2148874 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## inferred exon combination :: based on alignments, homology ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:43,855,556-43,919,918 Size: 64,363 Total Exon Count: 71 Strand: +
Coding Region
   Position: hg19 chr1:43,855,640-43,916,151 Size: 60,512 Coding Exon Count: 71 

Page IndexSequence and LinksMalaCardsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:43,855,556-43,919,918)mRNA (may differ from genome)Protein (3375 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: SZT2
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 18* (1330), early infantile epileptic encephalopathy without suppression burst* (400), undetermined early-onset epileptic encephalopathy* (124), non-syndromic intellectual disability (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.54 RPKM in Testis
Total median expression: 249.06 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.2084-0.407 Picture PostScript Text
3' UTR -1515.143767-0.402 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
  ModBase Predicted Comparative 3D Structure on Q5T011-5
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 orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Descriptions from all associated GenBank mRNAs
  AB007936 - Homo sapiens mRNA for KIAA0467 protein, partial cds.
BC151232 - Homo sapiens KIAA0467, mRNA (cDNA clone MGC:166922 IMAGE:8860124), complete cds.
BC082968 - Homo sapiens KIAA0467, mRNA (cDNA clone IMAGE:6537453), partial cds.
BC052802 - Homo sapiens KIAA0467, mRNA (cDNA clone IMAGE:6538086), complete cds.
BC041069 - Homo sapiens KIAA0467, mRNA (cDNA clone IMAGE:5479965), partial cds.
AK027078 - Homo sapiens cDNA: FLJ23425 fis, clone HEP22862.
BC017576 - Homo sapiens chromosome 1 open reading frame 84, mRNA (cDNA clone IMAGE:4092807), complete cds.
JD216894 - Sequence 197918 from Patent EP1572962.
JD461878 - Sequence 442902 from Patent EP1572962.
BC051343 - Homo sapiens chromosome 1 open reading frame 84, mRNA (cDNA clone IMAGE:6371787).
AK091821 - Homo sapiens cDNA FLJ34502 fis, clone HLUNG2005656.
AX747203 - Sequence 728 from Patent EP1308459.
AB527118 - Synthetic construct DNA, clone: pF1KB7335, Homo sapiens C1orf84 gene for chromosome 1 open reading frame 84, without stop codon, in Flexi system.
BC148353 - Synthetic construct Homo sapiens clone IMAGE:100015328, MGC:182991 C1orf84 protein (C1orf84) mRNA, encodes complete protein.
JD085628 - Sequence 66652 from Patent EP1572962.
AK131107 - Homo sapiens mRNA for FLJ00408 protein.
JD550570 - Sequence 531594 from Patent EP1572962.
AK126972 - Homo sapiens cDNA FLJ45025 fis, clone BRAWH3017260.
AK001249 - Homo sapiens cDNA FLJ10387 fis, clone NT2RM2002178, highly similar to Homo sapiens mRNA; cDNA DKFZp434E0335.
AL117402 - Homo sapiens mRNA; cDNA DKFZp434E0335 (from clone DKFZp434E0335).
JD246302 - Sequence 227326 from Patent EP1572962.
JD171485 - Sequence 152509 from Patent EP1572962.
JD261775 - Sequence 242799 from Patent EP1572962.
JD219793 - Sequence 200817 from Patent EP1572962.
JD415713 - Sequence 396737 from Patent EP1572962.
JD085595 - Sequence 66619 from Patent EP1572962.
JD339310 - Sequence 320334 from Patent EP1572962.
JD149096 - Sequence 130120 from Patent EP1572962.
JD130581 - Sequence 111605 from Patent EP1572962.
JD545270 - Sequence 526294 from Patent EP1572962.
JD252425 - Sequence 233449 from Patent EP1572962.
JD117686 - Sequence 98710 from Patent EP1572962.
CU675268 - Synthetic construct Homo sapiens gateway clone IMAGE:100022419 3' read HYI mRNA.
MP014968 - Sequence 171 from Patent WO2019016252.

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf84, KIAA0467, NM_015284, NP_056099, Q5T011-5, uc001cjk.2
UCSC ID: uc001cjk.3
RefSeq Accession: NM_015284
Protein: Q5T011-5, splice isoform of Q5T011 CCDS: CCDS30694.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015284.3
exon count: 71CDS single in 3' UTR: no RNA size: 13996
ORF size: 10128CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 17730.00frame shift in genome: no % Coverage: 99.88
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.