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CYB561D2 Gene(Protein Coding)

Cytochrome B561 Family Member D2

GCID:
GC03P050350
GIFtS:
45
Genes Participants
UDN Logo

Aliases for CYB561D2 Gene

Aliases for CYB561D2 Gene

  • Cytochrome B561 Family Member D2 2 3 5
  • Putative Tumor Suppressor Protein 101F6 3 4
  • 101F6 3 4
  • Cytochrome B561 Domain-Containing Protein 2 3
  • Cytochrome B-561 Domain Containing 2 2
  • Cytochrome B561 Family, Member D2 2
  • Putative Tumor Suppressor 101F6 2
  • XXcos-LUCA11.4 3
  • TSP10 3

External Ids for CYB561D2 Gene

Previous GeneCards Identifiers for CYB561D2 Gene

  • GC03P050348
  • GC03P050363
  • GC03P050388

Summaries for CYB561D2 Gene

GeneCards Summary for CYB561D2 Gene

CYB561D2 (Cytochrome B561 Family Member D2) is a Protein Coding gene. An important paralog of this gene is CYB561D1.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CYB561D2 Gene

Genomics for CYB561D2 Gene

Products:

  1. Regulatory Element

Regulatory Elements for CYB561D2 Gene

Enhancers for CYB561D2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G050332 1.7 FANTOM5 ENCODE dbSUPER 21.6 -13.0 -13024 9.4 HDGF HNRNPUL1 PKNOX1 CREB3L1 AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 HYAL3 CYB561D2 IFRD2 LSMEM2 HYAL1 RBM6 SEMA3F ENSG00000230454 RASSF1 SEMA3B
GH03G050234 2.1 FANTOM5 Ensembl ENCODE dbSUPER 15.1 -105.4 -105440 21.3 CREB3L1 AGO1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 MEF2D HYAL3 GNAI2 HYAL1 CYB561D2 SEMA3B-AS1 SEMA3B LSMEM2 NAT6 IFRD2 SEMA3F-AS1
GH03G050257 2 FANTOM5 Ensembl ENCODE dbSUPER 15 -83.2 -83194 19.3 CREB3L1 AGO1 DMAP1 FEZF1 YY1 ZNF416 ZNF143 SP3 MEF2D SSRP1 HYAL3 CYB561D2 NICN1 IFRD2 GNAI2 SEMA3F-AS1 HEMK1 AMT HYAL1 AMIGO3
GH03G050349 1.1 ENCODE 21.9 +0.1 122 2.5 HDGF PKNOX1 MLX CREB3L1 AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 CYB561D2 NICN1 HYAL1 HYAL3 ENSG00000272104
GH03G050201 1.8 FANTOM5 Ensembl ENCODE dbSUPER 12 -146.6 -146605 4.8 HDGF FOXA2 ARID4B DMAP1 ZNF48 YY1 FOS SP3 SP5 MXD4 RBM6 GNAI2 SEMA3B SEMA3B-AS1 LSMEM2 CYB561D2 HYAL3 SEMA3F SEMA3F-AS1 RBM5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CYB561D2 on UCSC Golden Path with GeneCards custom track

Promoters for CYB561D2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152349 105 1201 HDGF PKNOX1 MLX CREB3L1 AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1

Transcription factor binding sites by QIAGEN in the CYB561D2 gene promoter:

Genomic Location for CYB561D2 Gene

Chromosome:
3
Start:
50,350,695 bp from pter
End:
50,368,197 bp from pter
Size:
17,503 bases
Orientation:
Plus strand

Genomic View for CYB561D2 Gene

Genes around CYB561D2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CYB561D2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CYB561D2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CYB561D2 Gene

Proteins for CYB561D2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CYB561D2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14569-C56D2_HUMAN
    Recommended name:
    Cytochrome b561 domain-containing protein 2
    Protein Accession:
    O14569
    Secondary Accessions:
    • A8K552

    Protein attributes for CYB561D2 Gene

    Size:
    222 amino acids
    Molecular mass:
    23974 Da
    Cofactor:
    Name=heme; Xref=ChEBI:CHEBI:30413;
    Quaternary structure:
    No Data Available

neXtProt entry for CYB561D2 Gene

Protein Expression for CYB561D2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CYB561D2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CYB561D2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CYB561D2 Gene

Domains & Families for CYB561D2 Gene

Gene Families for CYB561D2 Gene

HGNC:

Protein Domains for CYB561D2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CYB561D2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CYB561D2: view

No data available for UniProtKB/Swiss-Prot for CYB561D2 Gene

Function for CYB561D2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Gene Ontology (GO) - Molecular Function for CYB561D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CYB561D2: view
genes like me logo Genes that share phenotypes with CYB561D2: view

Animal Model Products

CRISPR Products

miRNA for CYB561D2 Gene

miRTarBase miRNAs that target CYB561D2

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CYB561D2 Gene

Localization for CYB561D2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CYB561D2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CYB561D2 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for CYB561D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CYB561D2: view

Pathways & Interactions for CYB561D2 Gene

SuperPathways for CYB561D2 Gene

PathCards logo More details on SuperPathways for CYB561D2
No Data Available

Interacting Proteins for CYB561D2 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000232508%0d%0a9606.ENSP00000226951%0d%0a
Selected Interacting proteins: O14569-C56D2_HUMAN ENSP00000232508 for CYB561D2 Gene via IID STRING

Gene Ontology (GO) - Biological Process for CYB561D2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with CYB561D2: view

No data available for Pathways by source and SIGNOR curated interactions for CYB561D2 Gene

Drugs & Compounds for CYB561D2 Gene

Products:

  1. Drug

(1) Drugs for CYB561D2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
heme Pharma Agonist 0
genes like me logo Genes that share compounds with CYB561D2: view

Transcripts for CYB561D2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for CYB561D2 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(177) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CYB561D2 Gene

Cytochrome b561 family, member D2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CYB561D2 Gene

No ASD Table

Relevant External Links for CYB561D2 Gene

GeneLoc Exon Structure for
CYB561D2
ECgene alternative splicing isoforms for
CYB561D2

Expression for CYB561D2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CYB561D2 Gene

mRNA expression in normal human tissues for CYB561D2 Gene
mRNA expression by BioGPS for CYB561D2 GenemRNA expression by GTEx for CYB561D2 Gene

Protein differential expression in normal tissues from HIPED for CYB561D2 Gene

This gene is overexpressed in NK cells (8.1), Islet of Langerhans (7.8), CD8 Tcells (7.0), and Monocytes (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CYB561D2 Gene



Protein tissue co-expression partners for CYB561D2 Gene

NURSA nuclear receptor signaling pathways regulating expression of CYB561D2 Gene:

CYB561D2

SOURCE GeneReport for Unigene cluster for CYB561D2 Gene:

Hs.149443

Evidence on tissue expression from TISSUES for CYB561D2 Gene

  • Pancreas(4.2)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with CYB561D2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CYB561D2 Gene

Orthologs for CYB561D2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CYB561D2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia CYB561D2 34
  • 99.55 (n)
dog
(Canis familiaris)
 Mammalia -- 35
  • 91 (a)
 OneToMany
CYB561D2 34
  • 89.49 (n)
cow
(Bos Taurus)
 Mammalia CYB561D2 34 35
  • 89.94 (n)
mouse
(Mus musculus)
 Mammalia Cyb561d2 34 16 35
  • 89.19 (n)
rat
(Rattus norvegicus)
 Mammalia Cyb561d2 34
  • 87.84 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 80 (a)
 OneToMany
oppossum
(Monodelphis domestica)
 Mammalia -- 35
  • 77 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves CYB561D2 34
  • 75.17 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 35
  • 76 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia cyb561d2 34
  • 64.1 (n)
Str.791 34
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32424 34
zebrafish
(Danio rerio)
 Actinopterygii cyb561d2 34 35
  • 53.39 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.3475 35
  • 40 (a)
 OneToMany
Species where no ortholog for CYB561D2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CYB561D2 Gene

ENSEMBL:
Gene Tree for CYB561D2 (if available)
TreeFam:
Gene Tree for CYB561D2 (if available)

Paralogs for CYB561D2 Gene

Paralogs for CYB561D2 Gene

(1) SIMAP similar genes for CYB561D2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CYB561D2: view

Variants for CYB561D2 Gene

Sequence variations from dbSNP and Humsavar for CYB561D2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs886037963 Pathogenic 50,350,001(-) TCTCC(C/T)GAGAG nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon, stop-gained, utr-variant-5-prime
rs886037965 Pathogenic 50,349,690(-) AAAGC(C/T)GGCTG nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs886037966 Pathogenic 50,350,584(-) CAAGA(-/TC)ACCTA nc-transcript-variant, upstream-variant-2KB, reference, frameshift-variant, utr-variant-5-prime
rs150832847 Likely benign 50,364,700(+) CTTGA(A/G)GCTGC intron-variant, upstream-variant-2KB, reference, missense
rs191208192 Uncertain significance 50,366,072(+) CTGCC(C/T)GATAG intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for CYB561D2 Gene

Variant ID Type Subtype PubMed ID
dgv8317n54 CNV loss 21841781
esv3584502 CNV gain 24956385
nsv1072688 CNV deletion 25765185
nsv460531 CNV loss 19166990
nsv470561 CNV loss 18288195
nsv523662 CNV loss 19592680
nsv590255 CNV loss 21841781
nsv834692 CNV loss 17160897
nsv834693 CNV loss 17160897
nsv954855 CNV deletion 24416366

Variation tolerance for CYB561D2 Gene

Residual Variation Intolerance Score: 73.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.13; 22.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CYB561D2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CYB561D2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CYB561D2 Gene

Disorders for CYB561D2 Gene

Relevant External Links for CYB561D2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CYB561D2

No disorders were found for CYB561D2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CYB561D2 Gene

Publications for CYB561D2 Gene

  1. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. (PMID: 11085536) Lerman M.I. … Minna J.D. (Cancer Res. 2000) 2 3 4 64
  2. Cytochromes b561: ascorbate-mediated trans-membrane electron transport. (PMID: 23249217) Asard H. … BAcrczi A. (Antioxid. Redox Signal. 2013) 2 3 64
  3. Functional expression and characterization of human 101F6 protein, a homologue of cytochrome b561 and a candidate tumor suppressor gene product. (PMID: 19734123) Recuenco M.C. … Tsubaki M. (Biofactors 2008) 3 22 64
  4. The DNA sequence, annotation and analysis of human chromosome 3. (PMID: 16641997) Muzny D.M. … Gibbs R.A. (Nature 2006) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for CYB561D2 Gene

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