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

CYB5D1 Gene

protein-coding   GIFtS: 43
GCID: GC17P007761

Cytochrome B5 Domain Containing 1

  Search for CYB5D1
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 B5 Domain Containing 11 2
Cytochrome B5 Domain-Containing Protein 12

External Ids:    HGNC: 265161   Entrez Gene: 1246372   Ensembl: ENSG000001822247   UniProtKB: Q6P9G03   

Export aliases for CYB5D1 gene to outside databases

Previous GC identifer: GC17P007704


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

GeneCards Summary for CYB5D1 Gene: 
CYB5D1 (cytochrome b5 domain containing 1) is a protein-coding gene. GO annotations related to this gene include heme binding and metal ion binding.


(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_000017.10  NT_010718.16  NC_018928.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CYB5D1 gene promoter:
         Pax-6   Lmo2   Olf-1   Nkx2-5   NF-kappaB   LCR-F1   c-Ets-1   NF-kappaB1   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCYB5D1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CYB5D1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CYB5D1


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

Entrez Gene cytogenetic band: 17p13.1   Ensembl cytogenetic band:  17p13.1   HGNC cytogenetic band: 17p13.1

CYB5D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CYB5D1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P007761:  view genomic region     (about GC identifiers)

Start:
7,761,064 bp from pter      End:
7,765,600 bp from pter
Size:
4,537 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: CB5D1_HUMAN, Q6P9G0 (See protein sequence)
Recommended Name: Cytochrome b5 domain-containing protein 1  
Size: 228 amino acids; 26689 Da
Secondary accessions: D3DTQ8 Q96DM7
Alternative splicing: 2 isoforms:  Q6P9G0-1   Q6P9G0-2   

Explore the universe of human proteins at neXtProt for CYB5D1: NX_Q6P9G0

Explore proteomics data for CYB5D1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q6P9G0

  • CYB5D1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CYB5D1 Protein Expression
    REFSEQ proteins: NP_653208.2  
    ENSEMBL proteins: 
     ENSP00000459369   ENSP00000331479   ENSP00000461852   ENSP00000460105  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR001199 Cyt_B5-like_heme/steroid-bd

    Graphical View of Domain Structure for InterPro Entry Q6P9G0

    ProtoNet protein and cluster: Q6P9G0

    1 Blocks protein domain: IPB001199 Cytochrome b5

    UniProtKB/Swiss-Prot: CB5D1_HUMAN, Q6P9G0
    Similarity: Belongs to the cytochrome b5 family
    Similarity: Contains 1 cytochrome b5 heme-binding domain


    CYB5D1 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): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0020037heme binding IEA--
    GO:0046872metal ion binding IEA--
         
    CYB5D1 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI phenotypic allele for Cyb5d1 (no phenotypes)

    CYB5D1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Cyb5d1tm1(KOMP)Vlcg for CYB5D1

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    (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 CYB5D1

    (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 CYB5D1 (CB5D1)

    1 HMDB Compound for CYB5D1    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 CYB5D1 / CB5D1

    (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,
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    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 CYB5D1 gene: 
    NM_144607.4  

    Unigene Cluster for CYB5D1:

    Cytochrome b5 domain containing 1
    Hs.27475  [show with all ESTs]
    Unigene Representative Sequence: NM_144607
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000571846 ENST00000332439(uc002gjb.4) ENST00000574357 ENST00000570446
    ENST00000573940 ENST00000574196
    miRNA
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    hsa-miR-3194-5p hsa-miR-125a-5p hsa-miR-3614-3p hsa-miR-1258 hsa-miR-605 hsa-miR-181a-2* hsa-miR-27b* hsa-miR-141*
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    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CYB5D1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CYB5D1

    Additional mRNA sequence: 

    AK022811.1 AK057061.1 AK124743.1 AK125598.1 AK289520.1 BC060779.1 

    8 DOTS entries:

    DT.455686  DT.100693757  DT.120935814  DT.95094182  DT.75169263  DT.120935816  DT.120935850  DT.92070137 

    24/255 AceView cDNA sequences (see all 255):

    W56526 BE219729 CB154770 BM849688 BM696116 AI151324 AW952285 BC057812 
    NM_203411 BM968430 CD365458 AA991279 BQ012561 CR597798 AA594247 BE467057 
    CF529968 BQ438795 AU149978 BI092918 AA736517 BQ013626 AI671664 BU734395 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for CYB5D1 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d
    SP1:                          -                       -                           
    SP2:                          -                                                   
    SP3:                                                  -                           
    SP4:                          -                                                   
    SP5:                    -     -     -     -     -     -                           


    ECgene alternative splicing isoforms for CYB5D1

    (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

    CYB5D1 expression in normal human tissues (normalized intensities)      CYB5D1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CATTTTCCAG
    CYB5D1 Expression
    About this image


    CYB5D1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Lung (Respiratory System)
             trachea   
     
     Kidney (Urinary System)
             Presumptive Podocytes Podocyte Layer
     
     Skeletal Muscle (Muscoskeletal System)
             gastrocnemius muscle   

    See CYB5D1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CYB5D1

    SOURCE GeneReport for Unigene cluster: Hs.27475
        SABiosciences Custom PCR Arrays for CYB5D1
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    In Situ
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    (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 animals.

    Orthologs for CYB5D1 gene from 4/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cyb5d11 , 5 cytochrome b5 domain containing 11, 5 81.87(n)1
    83.33(a)1
      11 (42.59 cM)5
    3279511  NM_001045525.11  NP_001038990.11 
     693919255 
    lizard
    (Anolis carolinensis)
    Reptilia CYB5D16
    Uncharacterized protein
    69(a)
    1 ↔ 1
    GL343784.1(136667-141534)
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.175712 Transcribed sequences 76.13(n)    BM957802.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG154291 CG15429 53.95(n)
    39.69(a)
      33637  NM_134979.2  NP_608823.2 


    ENSEMBL Gene Tree for CYB5D1 (if available)
    TreeFam Gene Tree for CYB5D1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/54 SNPs in CYB5D1 are shown (see all 54)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0374864
    ----see VAR_0374862 F L mis40--------
    rs1870062861,2
    --7763227(+) TTAAGA/GGAGAG 1 -- ut310--------
    rs1901547491,2
    --7763238(+) TAGTTC/GTACAG 1 -- ut310--------
    rs1395207241,2
    --7763278(+) ATGATA/GGAAAT 1 -- ut310--------
    rs1495525031,2
    --7763323(+) ATAGGA/TAATGT 1 -- ut310--------
    rs745782371,2
    C,F--7763413(+) AGTGCG/TTCATT 1 -- ut311Minor allele frequency- T:0.19EA 120
    rs577360141,2
    C--7763466(+) CCCTC-/TTTTTT 1 -- ut310--------
    rs1818722841,2
    --7763578(+) GTGATC/TCTCCC 1 -- ut310--------
    rs1858063881,2
    --7763631(+) TGCCTA/GATTTT 1 -- ut310--------
    rs1441875541,2
    C--7763847(+) CTAGAA/GCCAGA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for CYB5D1 (7761064 - 7765600 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CYB5D1:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv907653CNV Loss21882294
    nsv833351CNV Loss17160897
    dgv510n67CNV Gain20364138

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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
      --

    (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 CYB5D1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CYB5D1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    3. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (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: 124637 HGNC: 26516 AceView: FLJ32499andLOC92162andJMJD3 Ensembl:ENSG00000182224 euGenes: HUgn124637
    ECgene: CYB5D1 H-InvDB: CYB5D1

    (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 CYB5D1 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 CYB5D1 gene:
    Search GeneIP for patents involving CYB5D1

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    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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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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