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MYCBP2 Gene(Protein Coding)

MYC Binding Protein 2, E3 Ubiquitin Protein Ligase

GCID:
GC13M077044
GIFtS:
46
Genes Participants
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Aliases for MYCBP2 Gene

Aliases for MYCBP2 Gene

  • MYC Binding Protein 2, E3 Ubiquitin Protein Ligase 2 3 5
  • RING-Type E3 Ubiquitin Transferase MYCBP2 3 4
  • Protein Associated With Myc 3 4
  • Pam/Highwire/Rpm-1 Protein 3 4
  • Myc-Binding Protein 2 3 4
  • PAM 3 4
  • E3 Ubiquitin-Protein Ligase MYCBP2 3
  • MYC Binding Protein 2 2
  • EC 2.3.2.27 4
  • Highwire 3
  • KIAA0916 4
  • Myc-Bp2 3
  • Phr 3

External Ids for MYCBP2 Gene

Previous GeneCards Identifiers for MYCBP2 Gene

  • GC13M075417
  • GC13M076517
  • GC13M077618
  • GC13M058316

Summaries for MYCBP2 Gene

Entrez Gene Summary for MYCBP2 Gene

  • This gene encodes an E3 ubiquitin-protein ligase and member of the PHR (Phr1/MYCBP2, highwire and RPM-1) family of proteins. The encoded protein plays a role in axon guidance and synapse formation in the developing nervous system. In mammalian cells, this protein regulates the cAMP and mTOR signaling pathways, and may additionally regulate autophagy. Reduced expression of this gene has been observed in acute lymphoblastic leukemia patients and a mutation in this gene has been identified in patients with a rare inherited vision defect. [provided by RefSeq, Mar 2017]

GeneCards Summary for MYCBP2 Gene

MYCBP2 (MYC Binding Protein 2, E3 Ubiquitin Protein Ligase) is a Protein Coding gene. Diseases associated with MYCBP2 include Ecthyma and Reticulate Acropigmentation Of Kitamura. Among its related pathways are Integrated Breast Cancer Pathway. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and ligase activity.

UniProtKB/Swiss-Prot for MYCBP2 Gene

  • E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of TSC2/tuberin. Interacts with the E2 enzymes UBE2D1, UBE2D3 and UBE2L3 (in vitro). May function as a facilitator or regulator of transcriptional activation by MYC. May have a role during synaptogenesis.

Gene Wiki entry for MYCBP2 Gene

Additional gene information for MYCBP2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MYCBP2 Gene

Genomics for MYCBP2 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for MYCBP2 Gene

Promoters and enhancers for MYCBP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH13I077324 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 556.4 +0.7 746 3.1 HDGF FOXA2 PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 MYCBP2 CLN5 FBXL3 KCTD12 GC13P077273
GH13I077429 Enhancer 1.1 FANTOM5 ENCODE 12.7 -102.8 -102841 1.6 PKNOX1 SMAD1 BMI1 BATF KLF5 IRF4 ZNF207 ZNF143 ATF7 ETV6 MYCBP2 LOC105370271
GH13I077477 Enhancer 1.1 Ensembl ENCODE 12.2 -151.3 -151279 1.6 HDGF PKNOX1 ATF1 SIN3A ZNF2 YY1 GTF3C2 ZNF207 ZNF143 ATF7 MYCBP2 LOC105370271 SCEL
GH13I077299 Enhancer 0.9 Ensembl ENCODE dbSUPER 13.8 +26.5 26487 1.7 ZNF316 CEBPB FOSL2 FOS SPI1 MYCBP2 CLN5 GC13P077273
GH13I077297 Enhancer 0.8 Ensembl ENCODE dbSUPER 13.3 +28.7 28708 1.6 IKZF2 SPI1 MYCBP2 CLN5 MYCBP2-AS1 GC13P077273
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around MYCBP2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MYCBP2 gene promoter:

Genomic Locations for MYCBP2 Gene

Genomic Locations for MYCBP2 Gene
chr13:77,044,655-77,327,050
(GRCh38/hg38)
Size:
282,396 bases
Orientation:
Minus strand
chr13:77,618,792-77,901,185
(GRCh37/hg19)

Genomic View for MYCBP2 Gene

Genes around MYCBP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MYCBP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MYCBP2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for MYCBP2 Gene

Proteins for MYCBP2 Gene

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  • Protein details for MYCBP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75592-MYCB2_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase MYCBP2
    Protein Accession:
    O75592
    Secondary Accessions:
    • A6NJC6
    • Q5JSX8
    • Q5VZN6
    • Q6PIB6
    • Q9UQ11
    • Q9Y6E4

    Protein attributes for MYCBP2 Gene

    Size:
    4640 amino acids
    Molecular mass:
    510084 Da
    Quaternary structure:
    • Interacts with MYC (PubMed:9689053). Interacts with TSC2 (tuberin) when TSC2 is in complex with TSC1 (hamartin) (PubMed:14559897). Interacts with FBXO45 (PubMed:19398581). Interacts with RAE1 (PubMed:22357847). Interacts with CPNE1 (via VWFA domain) and CPNE4 (via VWFA domain) (By similarity).
    SequenceCaution:
    • Sequence=AAD39842.1; Type=Frameshift; Positions=4636; Evidence={ECO:0000305}; Sequence=AAH37971.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI39758.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for MYCBP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MYCBP2 Gene

Protein Expression for MYCBP2 Gene

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

Post-translational modifications for MYCBP2 Gene

Other Protein References for MYCBP2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for MYCBP2 Gene

Domains & Families for MYCBP2 Gene

Gene Families for MYCBP2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for MYCBP2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for MYCBP2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O75592

UniProtKB/Swiss-Prot:

MYCB2_HUMAN :
  • The PHR domains are compact beta-sandwich folds composed of 11 antiparallel strands and decorated with conserved apical loops. They are likely to play a structural role and mediate interactions with substrates or partners (By similarity).
  • Belongs to the highwire family.
Domain:
  • The PHR domains are compact beta-sandwich folds composed of 11 antiparallel strands and decorated with conserved apical loops. They are likely to play a structural role and mediate interactions with substrates or partners (By similarity).
Family:
  • Belongs to the highwire family.
genes like me logo Genes that share domains with MYCBP2: view

Function for MYCBP2 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
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Molecular function for MYCBP2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase which mediates ubiquitination and subsequent proteasomal degradation of TSC2/tuberin. Interacts with the E2 enzymes UBE2D1, UBE2D3 and UBE2L3 (in vitro). May function as a facilitator or regulator of transcriptional activation by MYC. May have a role during synaptogenesis.

Enzyme Numbers (IUBMB) for MYCBP2 Gene

Phenotypes From GWAS Catalog for MYCBP2 Gene

Gene Ontology (GO) - Molecular Function for MYCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15161933
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with MYCBP2: view
genes like me logo Genes that share phenotypes with MYCBP2: view

Animal Models for MYCBP2 Gene

MGI Knock Outs for MYCBP2:

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MYCBP2 Gene

Localization for MYCBP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MYCBP2 Gene

Nucleus.

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 MYCBP2 gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MYCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA --
GO:0016020 membrane HDA,IDA 19946888
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with MYCBP2: view

Pathways & Interactions for MYCBP2 Gene

genes like me logo Genes that share pathways with MYCBP2: view

Pathways by source for MYCBP2 Gene

1 BioSystems pathway for MYCBP2 Gene

UniProtKB/Swiss-Prot O75592-MYCB2_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for MYCBP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with MYCBP2: view

No data available for SIGNOR curated interactions for MYCBP2 Gene

Drugs & Compounds for MYCBP2 Gene

Products:

  1. Drug

(3) Drugs for MYCBP2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for MYCBP2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
 14000-31-8
genes like me logo Genes that share compounds with MYCBP2: view

Transcripts for MYCBP2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for MYCBP2 Gene

(30) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(270) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for MYCBP2 Gene

MYC binding protein 2, E3 ubiquitin protein ligase:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MYCBP2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2:
SP3:
SP4: -
SP5:
SP6:

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for MYCBP2 Gene

GeneLoc Exon Structure for
MYCBP2
ECgene alternative splicing isoforms for
MYCBP2

Expression for MYCBP2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MYCBP2 Gene

mRNA expression in normal human tissues for MYCBP2 Gene
mRNA expression by GTEx for MYCBP2 GenemRNA expression by BioGPS for MYCBP2 Gene

Protein differential expression in normal tissues from HIPED for MYCBP2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (35.4) and Testis (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MYCBP2 Gene



Protein tissue co-expression partners for MYCBP2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of MYCBP2 Gene:

MYCBP2

SOURCE GeneReport for Unigene cluster for MYCBP2 Gene:

Hs.591221

mRNA Expression by UniProt/SwissProt for MYCBP2 Gene:

O75592-MYCB2_HUMAN
Tissue specificity: Expressed in all tissues examined, expression is exceptionally abundant in brain and thymus. Colocalizes with TSC1 and TSC2 along the neurites and in the growth cones. Colocalized with TSC1 in one of the filopodial extensions at the tip of a growth cone.

Evidence on tissue expression from TISSUES for MYCBP2 Gene

  • Nervous system(4.7)
  • Liver(4.4)
  • Lung(2.1)
  • Heart(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with MYCBP2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for MYCBP2 Gene

Orthologs for MYCBP2 Gene

This gene was present in the common ancestor of animals.

Orthologs for MYCBP2 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 100 (a)
 OneToMany
-- 34
  • 92 (a)
 OneToMany
-- 34
  • 92 (a)
 OneToMany
-- 34
  • 91 (a)
 OneToMany
-- 34
  • 90 (a)
 OneToMany
-- 34
  • 75 (a)
 OneToMany
-- 34
OneToMany
chimpanzee
(Pan troglodytes)
 Mammalia MYCBP2 33 34
  • 99.73 (n)
dog
(Canis familiaris)
 Mammalia MYCBP2 33 34
  • 94.03 (n)
oppossum
(Monodelphis domestica)
 Mammalia MYCBP2 34
  • 93 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia MYCBP2 33 34
  • 92.23 (n)
mouse
(Mus musculus)
 Mammalia Mycbp2 33 16 34
  • 89.94 (n)
rat
(Rattus norvegicus)
 Mammalia Mycbp2 33
  • 88.97 (n)
chicken
(Gallus gallus)
 Aves MYCBP2 33 34
  • 83.9 (n)
lizard
(Anolis carolinensis)
 Reptilia MYCBP2 34
  • 90 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.3526 33
zebrafish
(Danio rerio)
 Actinopterygii mycbp2 33 34
  • 72.88 (n)
Dr.17163 33
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.12300 33
fruit fly
(Drosophila melanogaster)
 Insecta hiw 33 34
  • 50.09 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011177 33
  • 29.1 (n)
worm
(Caenorhabditis elegans)
 Secernentea rpm-1 34 33
  • 45.62 (n)
 OneToMany
F07B7.12 34
  • 26 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 41 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4977 33
Species where no ortholog for MYCBP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • 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)

Evolution for MYCBP2 Gene

ENSEMBL:
Gene Tree for MYCBP2 (if available)
TreeFam:
Gene Tree for MYCBP2 (if available)

Paralogs for MYCBP2 Gene

(3) SIMAP similar genes for MYCBP2 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for MYCBP2 Gene

genes like me logo Genes that share paralogs with MYCBP2: view

No data available for Paralogs for MYCBP2 Gene

Variants for MYCBP2 Gene

Sequence variations from dbSNP and Humsavar for MYCBP2 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs193920951 uncertain-significance, Malignant tumor of prostate 77,126,432(-) C/G/T coding_sequence_variant, intron_variant, missense_variant
rs386352333 uncertain-significance, not provided 77,051,078(-) T/C coding_sequence_variant, missense_variant
rs1000003742 -- 77,199,934(-) G/C intron_variant
rs1000004973 -- 77,201,890(-) A/C intron_variant
rs1000009677 -- 77,288,743(-) A/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for MYCBP2 Gene

Variant ID Type Subtype PubMed ID
esv1226195 CNV insertion 17803354
esv2515250 CNV insertion 19546169
esv2759951 CNV loss 17122850
esv3550737 CNV deletion 23714750
nsv1037653 CNV loss 25217958
nsv1039620 CNV gain 25217958
nsv1148797 CNV duplication 26484159
nsv528143 CNV loss 19592680
nsv832653 CNV loss 17160897

Variation tolerance for MYCBP2 Gene

Gene Damage Index Score: 4.67; 65.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MYCBP2 Gene

Human Gene Mutation Database (HGMD)
MYCBP2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MYCBP2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MYCBP2 Gene

Disorders for MYCBP2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for MYCBP2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
ecthyma
reticulate acropigmentation of kitamura
  • rak
brunner syndrome
  • brnrs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MYCBP2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MYCBP2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MYCBP2 Gene

Publications for MYCBP2 Gene

  1. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 2 3 4 58
  2. Identification of a large Myc-binding protein that contains RCC1-like repeats. (PMID: 9689053) Guo Q … Bishop JM (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 58
  3. RAE-1, a novel PHR binding protein, is required for axon termination and synapse formation in Caenorhabditis elegans. (PMID: 22357847) Grill B … Garner CC (The Journal of neuroscience : the official journal of the Society for Neuroscience 2012) 3 4 58
  4. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 44 58
  5. Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development. (PMID: 19398581) Saiga T … Nakayama KI (Molecular and cellular biology 2009) 3 4 58

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