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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CYB561D1 Gene

protein-coding   GIFtS: 46
GCID: GC01P110036

Cytochrome B561 Family, Member D1

(Previous name: cytochrome b-561 domain containing 1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Cytochrome B561 Family, Member D11 2
Cytochrome B-561 Domain Containing 11 2
Cytochrome B561 Domain-Containing Protein 12

External Ids:    HGNC: 268041   Entrez Gene: 2846132   Ensembl: ENSG000001741517   UniProtKB: Q8N8Q13   

Export aliases for CYB561D1 gene to outside databases

Previous GC identifers: GC01P109336 GC01P109749 GC01P107929


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for CYB561D1 Gene: 
CYB561D1 (cytochrome b561 family, member D1) is a protein-coding gene. Diseases associated with CYB561D1 include major depressive disorder, and kidney disease. GO annotations related to this gene include metal ion binding. An important paralog of this gene is ENSG00000272104.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NT_032977.9  NC_018912.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CYB561D1 gene promoter:
         NRSF form 1   NRSF form 2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCYB561D1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CYB561D1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CYB561D1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p13.3   Ensembl cytogenetic band:  1p13.3   HGNC cytogenetic band: 1p13.2

CYB561D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CYB561D1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P110036:  view genomic region     (about GC identifiers)

Start:
110,036,658 bp from pter      End:
110,045,554 bp from pter
Size:
8,897 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: C56D1_HUMAN, Q8N8Q1 (See protein sequence)
Recommended Name: Cytochrome b561 domain-containing protein 1  
Size: 229 amino acids; 25424 Da
Cofactor: Binds 2 heme groups non-covalently (By similarity)
Subcellular location: Membrane; Multi-pass membrane protein (Probable)
Secondary accessions: B4DH97 E9PCM8 Q52M36 Q5T6C2 Q5T6C3
Alternative splicing: 5 isoforms:  Q8N8Q1-1   Q8N8Q1-2   Q8N8Q1-3   Q8N8Q1-4   Q8N8Q1-5   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for CYB561D1: NX_Q8N8Q1

Explore proteomics data for CYB561D1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8N8Q1

  • CYB561D1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CYB561D1 Protein Expression
    REFSEQ proteins (5 alternative transcripts): 
    NP_001127872.1  NP_001127874.1  NP_001127875.1  NP_001127876.1  NP_872386.1  

    ENSEMBL proteins: 
     ENSP00000377312   ENSP00000435819   ENSP00000435802   ENSP00000309324   ENSP00000433095  
     ENSP00000413530   ENSP00000434344   ENSP00000358884   ENSP00000416898  

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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for CYB561D1 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--

    CYB561D1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    CYB: Cytochrome b genes

    2 InterPro protein domains:
     IPR004877 Cyt_b561_euk
     IPR006593 Cyt_b561/ferric_Rdtase_TM

    Graphical View of Domain Structure for InterPro Entry Q8N8Q1

    ProtoNet protein and cluster: Q8N8Q1

    UniProtKB/Swiss-Prot: C56D1_HUMAN, Q8N8Q1
    Similarity: Contains 1 cytochrome b561 domain


    CYB561D1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046872metal ion binding IEA--
         
    CYB561D1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for CYB561D1:
     Decreased nuclei size in G2M  Increased G2M DNA content  Increased number of mitotic ce 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for CYB561D1 
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    hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-1224-3p hsa-miR-128 hsa-miR-4267 hsa-miR-298 hsa-miR-93
    SwitchGear 3'UTR luciferase reporter plasmidCYB561D1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CYB561D1


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CYB561D1

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0022900electron transport chain ----
    GO:0055114oxidation-reduction process IEA--

    CYB561D1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for CYB561D1 (C56D1)

    1 HMDB Compound for CYB561D1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Heme(protoporphyrinato)iron (see all 19)14875-96-8--

    Search CenterWatch for drugs/clinical trials and news about CYB561D1 / C56D1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CYB561D1 gene (5 alternative transcripts): 
    NM_001134400.1  NM_001134402.1  NM_001134403.1  NM_001134404.1  NM_182580.2  

    Unigene Cluster for CYB561D1:

    Cytochrome b561 family, member D1
    Hs.514682  [show with all ESTs]
    Unigene Representative Sequence: NM_001134404
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000393709 ENST00000496961 ENST00000533024 ENST00000310611(uc010ovl.2 uc010ovm.2 uc001dxu.3 uc010ovn.2 uc010ovo.2 uc010ovp.2)
    ENST00000527072 ENST00000420578 ENST00000528785 ENST00000369868 ENST00000430195(uc001dxw.3 uc009wfd.3)

    miRNA
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    8/84 QIAGEN miScript miRNA Assays for microRNAs that regulate CYB561D1 (see all 84):
    hsa-miR-520e hsa-miR-520f hsa-miR-106a hsa-miR-1224-3p hsa-miR-128 hsa-miR-4267 hsa-miR-298 hsa-miR-93
    SwitchGear 3'UTR luciferase reporter plasmidCYB561D1 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CYB561D1
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CYB561D1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CYB561D1

    Additional mRNA sequence: 

    AK092717.1 AK096354.1 AK126707.1 AK128798.1 AK294992.1 AK299086.1 AK303546.1 BC093683.1 
    BC111999.1 BC143308.1 BX647509.1 

    7 DOTS entries:

    DT.95226762  DT.121427200  DT.101981470  DT.101981472  DT.91965387  DT.121427204  DT.40106788 

    24/67 AceView cDNA sequences (see all 67):

    BX647509 AI193319 AI370771 BM720276 AI741940 CB150164 AI741458 AL045239 
    AI375149 AI219873 AA458471 BU624840 BQ675090 BG470191 BQ669302 BG696759 
    BQ212850 AI336387 AI963552 AI990972 BM820359 NM_182580 BG253300 BM083750 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for CYB561D1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d
    SP1:                                      -                     
    SP2:                                                            
    SP3:                    -     -     -     -                     


    ECgene alternative splicing isoforms for CYB561D1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CYB561D1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAACAGGTG
    CYB561D1 Expression
    About this image


    See CYB561D1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CYB561D1

    SOURCE GeneReport for Unigene cluster: Hs.514682
        SABiosciences Custom PCR Arrays for CYB561D1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CYB561D1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for CYB561D1 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cyb561d11 , 5 cytochrome b-561 domain containing 11, 5 90.25(n)1
    90.39(a)1
      3 (46.86 cM)5
    720231  NM_001081320.21  NP_001074789.21 
     1081956875 
    lizard
    (Anolis carolinensis)
    Reptilia CYB561D16
    cytochrome b561 family, member D1
    53(a)
    1 ↔ 1
    4(105598430-105613951)
    zebrafish
    (Danio rerio)
    Actinopterygii cyb561d11 cytochrome b-561 domain containing 1 57.75(n)
    52.11(a)
      447851  NM_001004590.1  NP_001004590.1 


    ENSEMBL Gene Tree for CYB561D1 (if available)
    TreeFam Gene Tree for CYB561D1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CYB561D1 gene
    ENSG000002721042  CYB561D22  
    1 SIMAP similar gene for CYB561D1 using alignment to 5 protein entries:     C56D1_HUMAN (see all proteins):
    CYB561D2

    CYB561D1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/178 SNPs in CYB561D1 are shown (see all 178)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2010671661,2
    --110036134(+) CTGCT-/GAGGAGGC 5 -- us2k10--------
    rs11491711,2
    F,A,H--110036462(+) GCCACA/GAAAGT 5 -- us2k17Minor allele frequency- G:0.03MN NS EA WA NA 838
    rs1847904391,2
    --110036472(+) TAATTC/TCCACA 5 -- us2k10--------
    rs1158236131,2
    F--110036634(+) GTGGGC/TCACTC 5 -- us2k11Minor allele frequency- T:0.12NA 120
    rs794712011,2
    C,F--110036836(+) AGAGGC/TAGTGG 9 G syn1 int13Minor allele frequency- T:0.02EA NA 540
    rs1383732101,2
    C--110036885(+) TTCTGA/GCAGCG 9 T A mis1 int11Minor allele frequency- G:0.00NA 3406
    rs769971021,2
    C--110036919(+) GTGTGC/GGGGGC 5 -- int14Minor allele frequency- G:0.06NA WA EA 360
    rs175752051,2
    C,F--110036998(+) GGAGGG/CACCCC 5 -- int1 trp315Minor allele frequency- C:0.14NA EA CSA WA 748
    rs741139021,2
    C,F--110037126(+) CAGACG/CGAACT 5 -- int11Minor allele frequency- C:0.50WA 2
    rs1807190611,2
    --110037223(+) GGAGGA/CCGACG 8 D A int1 mis10--------

    HapMap Linkage Disequilibrium report for CYB561D1 (110036658 - 110045554 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for CYB561D1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv872141CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for CYB561D1:    About MalaCards
    major depressive disorder    kidney disease


    CYB561D1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CYB561D1

    Export disorders for CYB561D1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for CYB561D1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CYB561D1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cytochromes b561: Ascorbate-Mediated Trans-Membrane El ectron Transport. (PubMed id 23249217)1, 3 Asard H....Berczi A. (2013)
    2. Genome-wide association study of recurrent early-onse t major depressive disorder. (PubMed id 20125088)1, 4 Shi J....Levinson D.F. (2010)
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1, 2 Kimura K.... Sugano S. (2006)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (2012)
    8. New loci associated with kidney function and chronic kidney disease. (PubMed id 20383146)1 KAPttgen A....Fox C.S. (2010)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 284613 HGNC: 26804 AceView: CYB561D1 Ensembl:ENSG00000174151 euGenes: HUgn284613
    ECgene: CYB561D1 H-InvDB: CYB561D1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CYB561D1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CYB561D1 gene:
    Search GeneIP for patents involving CYB561D1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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