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

CYB5D2 Gene

protein-coding   GIFtS: 48
GCID: GC17P004046

Cytochrome B5 Domain Containing 2

  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 B5 Domain Containing 21 2
Cytochrome B5 Domain-Containing Protein 22 3
neuferricin2

External Ids:    HGNC: 284711   Entrez Gene: 1249362   Ensembl: ENSG000001677407   UniProtKB: Q8WUJ13   

Export aliases for CYB5D2 gene to outside databases

Previous GC identifer: GC17P003994


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

GeneCards Summary for CYB5D2 Gene: 
CYB5D2 (cytochrome b5 domain containing 2) is a protein-coding gene. Diseases associated with CYB5D2 include intrahepatic cholangiocarcinoma, and cholangiocarcinoma. GO annotations related to this gene include heme binding. An important paralog of this gene is NENF.

UniProtKB/Swiss-Prot: NEUFC_HUMAN, Q8WUJ1
Function: Heme-binding protein which promotes neuronal but not astrocyte differentiation (By similarity)




(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 CYB5D2 gene promoter:
         Nkx3-1   SREBP-1c   NRSF form 1   HNF-4alpha2   NRSF form 2   HNF-4alpha1   SREBP-1b   Egr-4   SREBP-1a   ZID   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCYB5D2 promoter sequence
   Search SABiosciences Chromatin IP Primers for CYB5D2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CYB5D2


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

Entrez Gene cytogenetic band: 17p13.2   Ensembl cytogenetic band:  17p13.2   HGNC cytogenetic band: 17p13.2

CYB5D2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CYB5D2 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P004046:  view genomic region     (about GC identifiers)

Start:
4,046,462 bp from pter      End:
4,090,605 bp from pter
Size:
44,144 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: NEUFC_HUMAN, Q8WUJ1 (See protein sequence)
Recommended Name: Neuferricin precursor  
Size: 264 amino acids; 28690 Da
Subcellular location: Secreted (By similarity)
Secondary accessions: B2R7R6 D3DTJ9 I3L1K2
Alternative splicing: 2 isoforms:  Q8WUJ1-1   Q8WUJ1-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CYB5D2: NX_Q8WUJ1

Explore proteomics data for CYB5D2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8WUJ1

  • CYB5D2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CYB5D2 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001241684.1  NP_001241685.1  NP_653212.1  

    ENSEMBL proteins: 
     ENSP00000458352   ENSP00000458903   ENSP00000301391   ENSP00000461090  

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    Cloud-Clone Corp. Proteins for CYB5D2 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    CYB5D2 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
    1 InterPro protein domain:
     IPR001199 Cyt_B5-like_heme/steroid-bd

    Graphical View of Domain Structure for InterPro Entry Q8WUJ1

    ProtoNet protein and cluster: Q8WUJ1

    1 Blocks protein domain: IPB001199 Cytochrome b5

    UniProtKB/Swiss-Prot: NEUFC_HUMAN, Q8WUJ1
    Domain: The cytochrome b5 heme-binding domain was proven to bind heme, although it lacks the conserved
    iron-binding His residues at position 73 and 106 (By similarity)
    Similarity: Belongs to the cytochrome b5 family. MAPR subfamily
    Similarity: Contains 1 cytochrome b5 heme-binding domain


    CYB5D2 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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NEUFC_HUMAN, Q8WUJ1
    Function: Heme-binding protein which promotes neuronal but not astrocyte differentiation (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0020037heme binding IEA--
         
    CYB5D2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CYB5D2:
     Decreased TP53 protein express 

         1 MGI phenotypic allele for Cyb5d2 (no phenotypes)

    CYB5D2 for phenotypes           About GeneDecksing

    Animal Models:
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    Inhib. RNA
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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 CYB5D2

    1 Interacting protein for CYB5D2 (Q8WUJ13) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PAPLNO954283I2D: score=5 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007399nervous system development IEA--

    CYB5D2 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 CYB5D2 (NEUFC)

    1 HMDB Compound for CYB5D2    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 CYB5D2 / NEUFC

    (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 CYB5D2 gene (3 alternative transcripts): 
    NM_001254755.1  NM_001254756.1  NM_144611.3  

    Unigene Cluster for CYB5D2:

    Cytochrome b5 domain containing 2
    Hs.513871  [show with all ESTs]
    Unigene Representative Sequence: NM_144611
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000577075 ENST00000575251 ENST00000301391(uc002fxm.4 uc002fxl.4 uc010cko.3)
    ENST00000573984 ENST00000575411
    miRNA
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    3 QIAGEN miScript miRNA Assays for microRNAs that regulate CYB5D2:
    hsa-miR-3200-5p hsa-miR-616* hsa-miR-373*
    SwitchGear 3'UTR luciferase reporter plasmidCYB5D2 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AK172844.1 AK313088.1 BC020263.1 BC051697.1 

    13 DOTS entries:

    DT.456353  DT.100809060  DT.95268275  DT.100025700  DT.120970255  DT.120970213  DT.120970249  DT.86854704 
    DT.120970306  DT.91735132  DT.95268276  DT.91748244  DT.95335547 

    24/170 AceView cDNA sequences (see all 170):

    BP346958 AA383302 AI688288 BM782679 BM681125 BQ895942 CR592653 AA421590 
    BM455169 BM744912 AA775255 BQ887225 AA877407 AK172844 BP369658 CR600228 
    AI151098 NM_144611 AA977855 AV650263 N57057 AA724109 CB112805 AA421572 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for CYB5D2 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e · 8f
    SP1:                    -     -     -     -           -           -           -                                       
    SP2:                    -     -     -     -     -     -           -           -                                       
    SP3:                          -     -     -     -     -           -           -                                       
    SP4:                                            -     -           -           -                                       
    SP5:                                      -     -     -           -           -                                       


    ECgene alternative splicing isoforms for CYB5D2

    (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

    CYB5D2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACATTAAAGC
    CYB5D2 Expression
    About this image


    See CYB5D2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CYB5D2

    SOURCE GeneReport for Unigene cluster: Hs.513871
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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 eukaryotes.

    Orthologs for CYB5D2 gene from 8/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cyb5d21 , 5 cytochrome b5 domain containing 21, 5 80.1(n)1
    80.61(a)1
      11 (44.51 cM)5
    1929861  NM_001024926.31  NP_001020097.21 
     727772325 
    chicken
    (Gallus gallus)
    Aves CYB5D21 cytochrome b5 domain containing 2 64.63(n)
    62.04(a)
      417495  XM_415743.3  XP_415743.1 
    zebrafish
    (Danio rerio)
    Actinopterygii cyb5d21 cytochrome b5 domain containing 2 56.03(n)
    53.81(a)
      795950  NM_001102674.1  NP_001096144.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG120561 CG12056 50.76(n)
    41.28(a)
      31855  NM_132307.3  NP_572535.1 
    worm
    (Caenorhabditis elegans)
    Secernentea tag-1311 Protein TAG-131 50.59(n)
    45.58(a)
      175557  NM_065467.2  NP_497868.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DAP16
    Heme-binding protein involved in regulation of cyt...
    23(a)
    1 → many
    XVI(228314-228772)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons MAPR41 membrane-associated progesterone binding protein 4 46.97(n)
    41.41(a)
      827155  NM_117583.7  NP_567451.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g02055001 hypothetical protein 44.22(n)
    37.13(a)
      4331992  NM_001055849.2  NP_001049314.2 


    ENSEMBL Gene Tree for CYB5D2 (if available)
    TreeFam Gene Tree for CYB5D2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CYB5D2 gene
    NENF2  
    1 SIMAP similar gene for CYB5D2 using alignment to 2 protein entries:     NEUFC_HUMAN (see all proteins):
    NENF

    CYB5D2 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CYB5D2
    PGOHUM00000262360


    (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

    10/334 SNPs in CYB5D2 are shown (see all 334)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0374874
    A colorectal cancer sample4--see VAR_0374872 R G mis40--------
    VAR_0374884
    A colorectal cancer sample4--see VAR_0374882 R P mis40--------
    rs1811112421,2
    --3951040(+) GCCTGA/CCCCCG 3 -- int10--------
    rs1834960311,2
    --4048274(+) ACGGGA/GTTTCA 3 -- int10--------
    rs1878751051,2
    --4048293(+) GCCAGC/GATGGT 3 -- int10--------
    rs620721791,2
    C,F--4048312(+) CCTGAC/TCTTAT 3 -- int11Minor allele frequency- T:0.50NA 2
    rs20540411,2
    C,H--4048327(+) CGCCCG/ACCTTG 3 -- int17Minor allele frequency- A:0.07NA WA 14
    rs1416338591,2
    C--4048518(+) GTCATC/TATCTT 3 -- int10--------
    rs347676761,2
    C,F--4048572(+) CTTCCC/TTCTGT 3 -- int11Minor allele frequency- T:0.03NA 120
    rs798394331,2
    F--4048669(+) GGGAAG/AGGACT 3 -- int11Minor allele frequency- A:0.06WA 118

    HapMap Linkage Disequilibrium report for CYB5D2 (4046462 - 4090605 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for CYB5D2:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv519311CNV Loss19592680
    nsv527709CNV Loss19592680
    esv29231CNV Loss19812545
    esv2751682CNV Gain17911159
    nsv457647CNV Gain19166990
    dgv173n21CNV Gain19592680
    nsv833344CNV Gain17160897

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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
    3 diseases for CYB5D2:    About MalaCards
    intrahepatic cholangiocarcinoma    cholangiocarcinoma    neuronitis


    CYB5D2 for disorders           About GeneDecksing


    Export disorders for CYB5D2 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 CYB5D2 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with CYB5D2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (2006)
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    3. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (2006)
    5. 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)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    7. 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)
    8. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 124936 HGNC: 28471 AceView: MGC32124 Ensembl:ENSG00000167740 euGenes: HUgn124936
    ECgene: CYB5D2 H-InvDB: CYB5D2

    (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 CYB5D2 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 CYB5D2 gene:
    Search GeneIP for patents involving CYB5D2

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



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