Human Gene CYBA (uc002fld.2) Description and Page Index
  Description: Homo sapiens cytochrome b-245, alpha polypeptide (CYBA), mRNA.
RefSeq Summary (NM_000101): Cytochrome b is comprised of a light chain (alpha) and a heavy chain (beta). This gene encodes the light, alpha subunit which has been proposed as a primary component of the microbicidal oxidase system of phagocytes. Mutations in this gene are associated with autosomal recessive chronic granulomatous disease (CGD), that is characterized by the failure of activated phagocytes to generate superoxide, which is important for the microbicidal activity of these cells. [provided by RefSeq, Jul 2008]. 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 transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: CA311054.1, CA311071.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1970526 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000261623.8/ ENSP00000261623.3 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:88,711,495-88,717,492 Size: 5,998 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr16:88,712,506-88,717,421 Size: 4,916 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,711,495-88,717,492)mRNA (may differ from genome)Protein (128 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: H3BR52_HUMAN
DESCRIPTION: SubName: Full=Cytochrome b-245 light chain;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CYBA
CDC HuGE Published Literature: CYBA
Positive Disease Associations: atherosclerosis , atherosclerosis, coronary , cardiac death cardiovascular disease oxidative stress , cardiovascular , Cell Adhesion Molecules , cerebrovascular disease , cervical intraepithelial neoplasia grade 3 , cholesterol , coronary artery disease , coronary endothelial vasodilator function , coronary heart disease in younger individuals. , hypertension , hypertension NADPH oxidase activity , hypertension vascular aging , Insulin Resistance|Obesity , kidney failure, acute , NADPH Oxidase , oxidative stress , periodontitis , vascular NAD(P)H oxidase activity , vasodilation, flow-mediated
Related Studies:
  1. atherosclerosis
    Hayaishi-Okano, R. et al. 2003, Association of NAD(P)H Oxidase p22 phox Gene Variation With Advanced Carotid Atherosclerosis in Japanese Type 2 Diabetes, Diabetes care. 2003 Feb;26(2):458-63. [PubMed 12547880]
    These results show that the C242T mutation in the p22 phox gene is associated with progression of asymptomatic atherosclerosis in the subjects with type 2 diabetes and is also associated with insulin resistance in nondiabetic subjects.
  2. atherosclerosis, coronary
    He, M. et al. 2004, [Study on the relationship between the polymorphism of P22phox C242T, vitamin E and coronary heart disease], Wei sheng yan jiu. 2004 Jul;33(4):443-6. [PubMed 15461271]
    The polymorphism of P22phox C242T is associated with CHD in Chinese. Vitamin E is protective against CHD and there is effect on the progress of CHD in the interaction of the polymorphism of P22phox C242T and vitamin E.
  3. atherosclerosis, coronary
    Nasti, S. et al. 2006, C242T Polymorphism in CYBA gene (p22;{phox}) and risk of coronary artery disease in a population of Caucasian Italians, Dis Markers 2006 22(3) 167-73. [PubMed 16788250]
    these results support the increased risk of developing early CAD and of having rapid progression of coronary stenosis in subjects carrying the C242T nucleotide transition among the Italian population.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CYBA
Diseases sorted by gene-association score: chronic granulomatous disease, autosomal, due to deficiency of cyba* (1300), chronic granulomatous disease* (467), phagocyte bactericidal dysfunction (9), diabetic polyneuropathy (7), atherosclerosis (6), tetralogy of fallot (1)
* = Manually curated disease association

-  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: 187.27 RPKM in Whole Blood
Total median expression: 1115.53 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 -36.8071-0.518 Picture PostScript Text
3' UTR -426.241011-0.422 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
IPR007732 - Cyt_b558_asu

Pfam Domains:
PF05038 - Cytochrome Cytochrome b558 alpha-subunit

ModBase Predicted Comparative 3D Structure on H3BR52
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0020037 heme binding

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC006465 - Homo sapiens cytochrome b-245, alpha polypeptide, mRNA (cDNA clone MGC:2279 IMAGE:3502788), complete cds.
M21186 - Human neutrophil cytochrome b light chain p22 phagocyte b-cytochrome mRNA, complete cds.
HH837079 - Sequence 6 from Patent EP2231168.
HI214720 - Sequence 6 from Patent EP2076526.
HV601522 - JP 2011500003-A/6: Novel siRNA Structures.
HV708913 - JP 2012506450-A/11: Methods for treating eye disorders.
HV856595 - JP 2010507387-A/6: Novel siRNAs and Methods of Use Thereof.
HW061133 - JP 2012529430-A/8: METHODS FOR TREATING CHRONIC KIDNEY DISEASE.
HW165082 - JP 2013102767-A/6: Novel siRNA's and Use Thereof.
HW675590 - JP 2014210789-A/6: Novel siRNA Structures.
HW835278 - JP 2015051004-A/6: Novel siRNA's and Use Thereof.
JA482091 - Sequence 74 from Patent WO2011072091.
JA538121 - Sequence 6 from Patent EP2371958.
JB251941 - Sequence 8 from Patent EP2440214.
JE980383 - Sequence 74 from Patent EP2862929.
LF384486 - JP 2014500723-A/191989: Polycomb-Associated Non-Coding RNAs.
LP764840 - Sequence 8 from Patent EP3276004.
MS836043 - Sequence 7 from Patent EP3112469.
AK097127 - Homo sapiens cDNA FLJ39808 fis, clone SPLEN2009081.
AK300049 - Homo sapiens cDNA FLJ57889 complete cds, highly similar to Cytochrome b-245 light chain.
BT006861 - Homo sapiens cytochrome b-245, alpha polypeptide mRNA, complete cds.
DQ893235 - Synthetic construct clone IMAGE:100005865; FLH195484.01X; RZPDo839C12152D cytochrome b-245, alpha polypeptide (CYBA) gene, encodes complete protein.
DQ896565 - Synthetic construct Homo sapiens clone IMAGE:100011025; FLH195480.01L; RZPDo839C12151D cytochrome b-245, alpha polypeptide (CYBA) gene, encodes complete protein.
AB590173 - Synthetic construct DNA, clone: pFN21AE1371, Homo sapiens CYBA gene for cytochrome b-245, alpha polypeptide, without stop codon, in Flexi system.
BC033739 - Homo sapiens cytochrome b-245, alpha polypeptide, mRNA (cDNA clone IMAGE:5179916), with apparent retained intron.
BC028224 - Homo sapiens cytochrome b-245, alpha polypeptide, mRNA (cDNA clone IMAGE:5217162), with apparent retained intron.
BC048338 - Homo sapiens mRNA similar to cytochrome b-245, alpha polypeptide (cDNA clone IMAGE:5212219).
AK309030 - Homo sapiens cDNA, FLJ99071.
BC011565 - Homo sapiens cytochrome b-245, alpha polypeptide, mRNA (cDNA clone IMAGE:4563468), with apparent retained intron.
AK125578 - Homo sapiens cDNA FLJ43590 fis, clone SMINT2001818.
KJ901368 - Synthetic construct Homo sapiens clone ccsbBroadEn_10762 CYBA gene, encodes complete protein.
LF375076 - JP 2014500723-A/182579: Polycomb-Associated Non-Coding RNAs.
MA421964 - JP 2018519830-A/7: UTRs increasing the translation efficiency of RNA molecules.
MA620063 - JP 2018138019-A/191989: Polycomb-Associated Non-Coding RNAs.
MA610653 - JP 2018138019-A/182579: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04670 - Leukocyte transendothelial migration
hsa05140 - Leishmaniasis

-  Other Names for This Gene
  Alternate Gene Symbols: AK097127, H3BR52, H3BR52_HUMAN, NM_000101, NP_000092, uc002fld.1
UCSC ID: uc002fld.2
RefSeq Accession: NM_000101
Protein: H3BR52

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CYBA:
cgd (Chronic Granulomatous Disease)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK097127.1
exon count: 5CDS single in 3' UTR: no RNA size: 3061
ORF size: 387CDS single in intron: no Alignment % ID: 99.80
txCdsPredict score: 974.00frame shift in genome: no % Coverage: 41.33
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: 1029# 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.