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CYB5D1 Gene

protein-coding   GIFtS: 45
GCID: GC17P007761

Cytochrome B5 Domain Containing 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NT_010718.17  NC_018928.2  
Regulatory elements:
   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 Chromatin IP Primers for CYB5D1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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


See CYB5D1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_653208.2  
ENSEMBL proteins: 
 ENSP00000459369   ENSP00000331479   ENSP00000461852   ENSP00000460105  

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antibodies-online proteins for CYB5D1 (5 products) 

 
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antibodies-online antibodies for CYB5D1 (11 products) 

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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


Find genes that share domains with CYB5D1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0020037heme binding IEA--
GO:0046872metal ion binding IEA--
     
Find genes that share ontologies with CYB5D1           About GenesLikeMe


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

Find genes that share phenotypes with CYB5D1           About GenesLikeMe

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

   genOway: Develop your customized and physiologically relevant rodent model for CYB5D1

miRNA
Products:
    
miRTarBase miRNAs that target CYB5D1:
hsa-mir-1301-3p (MIRT036057)

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Selected qRT-PCR Assays for microRNAs that regulate CYB5D1 (see all 19):
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*
SwitchGear 3'UTR luciferase reporter plasmidCYB5D1 3' UTR sequence
Inhib. RNA
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol1
golgi apparatus1
mitochondrion1
nucleus1

(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CYB5D1
Interactions:

    Search GeneGlobe Interaction Network for CYB5D1

STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

Selected Interacting proteins for CYB5D1 (ENSP000003314794) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
InteractantInteraction Details
GeneCardExternal ID(s)
PAM16ENSP000003156934STRING: ENSP00000315693
TIMM44ENSP000002705384STRING: ENSP00000270538
TIMM50ENSP000003181154STRING: ENSP00000318115
TIMM17AENSP000003562564STRING: ENSP00000356256
TIMM17BENSP000003657664STRING: ENSP00000365766
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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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--



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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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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Selected qRT-PCR Assays for microRNAs that regulate CYB5D1 (see all 19):
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*
SwitchGear 3'UTR luciferase reporter plasmidCYB5D1 3' UTR sequence
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Predesigned siRNA for gene silencing in human, mouse, rat CYB5D1
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GenScript: all cDNA clones in your preferred vector: CYB5D1 (NM_144607)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CYB5D1
Primer
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OriGene qPCR primer pairs and template standards for CYB5D1
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Pre-validated RT2 qPCR Primer Assay in human, mouse / rat CYB5D1
  QuantiTect SYBR Green Assays in human, mouse, rat CYB5D1
  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 

Selected AceView cDNA sequences (see all 255):

AU149978 CF529968 BE467057 AA991279 BM849688 AI671664 BQ013215 AW952285 
BQ438795 AA736517 AI954619 BQ649062 BQ013674 AI151324 AI394006 AA355717 
AW293774 BC035897 BE503406 C00123 BQ721168 BQ063399 AA594247 BQ012561 

GeneLoc Exon Structure

Selected 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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CYB5D1 expression in normal human tissues (normalized intensities)
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
 selected tissues (see all 2) fully expand
 
 Epithelial Cells
         Presumptive Podocytes Podocyte Layer
 
 Kidney (Urinary System)
         Presumptive Podocytes Podocyte Layer
CYB5D1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CYB5D1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.27475
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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)
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This gene was present in the common ancestor of animals.

Orthologs for CYB5D1 gene from Selected species (see all 14)    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
cytochrome b5 domain containing 1
69(a)
1 ↔ 1
GL343784.1(136667-141534)
tropical clawed frog
(Xenopus tropicalis)
Amphibia cyb5d11 cytochrome b5 domain containing 1 65.56(n)
63.98(a)
  780076  NM_001079152.1  NP_001072620.1 
zebrafish
(Danio rerio)
Actinopterygii Dr.175712 Transcribed sequences 76.13(n)    BM957802.1 
fruit fly
(Drosophila melanogaster)
Insecta CG154291 CG15429 53.4(n)
39.29(a)
  33637  NM_134979.3  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)
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  --

(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for CYB5D1 (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
----------
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--------
rs1486899201,2
--7764145(+) CCATAC/TCCCAG 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

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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(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)
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PubMed articles for CYB5D1 gene integrated from 10 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. (Nat. Genet. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 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. (Genome Res. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 124637 HGNC: 26516 AceView: FLJ32499andLOC92162andJMJD3 Ensembl:ENSG00000182224 euGenes: HUgn124637
ECgene: CYB5D1 H-InvDB: CYB5D1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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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.)
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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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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