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Aliases for HMCES Gene

Aliases for HMCES Gene

  • 5-Hydroxymethylcytosine Binding, ES Cell Specific 2 3 5
  • Embryonic Stem Cell-Specific 5-Hydroxymethylcytosine-Binding Protein 2 3
  • 5-Hydroxymethylcytosine (HmC) Binding, ES Cell-Specific 2 3
  • SOS Response Associated Peptidase Domain Containing 1 2 3
  • ES Cell-Specific 5hmC-Binding Protein 3 4
  • SRAP Domain-Containing Protein 1 3 4
  • Putative Peptidase SRAPD1 3 4
  • C3orf37 3 4
  • SRAPD1 3 4
  • DC12 3 4
  • Chromosome 3 Open Reading Frame 37 2
  • UPF0361 Protein C3orf37 3
  • EC 3.4.-.- 4

External Ids for HMCES Gene

Previous HGNC Symbols for HMCES Gene

  • C3orf37

Previous GeneCards Identifiers for HMCES Gene

  • GC03P128998
  • GC03P129074

Summaries for HMCES Gene

GeneCards Summary for HMCES Gene

HMCES (5-Hydroxymethylcytosine Binding, ES Cell Specific) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include peptidase activity.

UniProtKB/Swiss-Prot for HMCES Gene

  • Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).

Additional gene information for HMCES Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMCES Gene

Genomics for HMCES Gene

GeneHancer (GH) Regulatory Elements for HMCES Gene

Promoters and enhancers for HMCES 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
GH03J129277 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 679.8 +0.4 378 3.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A YY1 POLR2B E2F8 PAF1 SP3 HMCES RPL32P3 ENSG00000244932 ISY1 MBD4 H1FX RPS15AP16 H1FX-AS1 CNBP COPG1
GH03J129309 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 29.4 +35.1 35084 8.8 HDGF PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 H1FX-AS1 HMCES ISY1 ENSG00000248659 MARK2P6 MARK3P3 OR7E129P DNAJB8-AS1 OR7E21P MARK2P17
GH03J129303 Enhancer 1.2 Ensembl ENCODE dbSUPER 29.4 +26.4 26449 2.9 HDAC1 PKNOX1 ATF1 BACH1 SIN3A E4F1 CCNT2 CC2D1A ZFHX2 CTBP1 HMCES ISY1 LOC100421508 GC03M129283 H1FX-AS1
GH03J129248 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 15.1 -29.2 -29229 2.6 HDGF ATF1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF48 YY1 ETS1 PIR44075 COPG1 HMCES CNBP ISY1 RAB43 GP9 H1FX-AS1 MBD4 MIR6826
GH03J129281 Enhancer 1 Ensembl ENCODE 29.8 +3.9 3947 1.6 PKNOX1 SMAD1 ARID4B STAT5A BMI1 BATF KLF5 IRF4 RAD21 YY1 HMCES EFCAB12 GC03M129283
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMCES on UCSC Golden Path with GeneCards custom track

Genomic Locations for HMCES Gene

Genomic Locations for HMCES Gene
chr3:129,278,816-129,306,186
(GRCh38/hg38)
Size:
27,371 bases
Orientation:
Plus strand
chr3:128,997,671-129,025,029
(GRCh37/hg19)
Size:
27,359 bases
Orientation:
Plus strand

Genomic View for HMCES Gene

Genes around HMCES on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HMCES Gene

Proteins for HMCES Gene

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

    Protein Symbol:
    Q96FZ2-HMCES_HUMAN
    Recommended name:
    Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
    Protein Accession:
    Q96FZ2
    Secondary Accessions:
    • A6NJR9
    • Q96G34
    • Q9NRP3

    Protein attributes for HMCES Gene

    Size:
    354 amino acids
    Molecular mass:
    40575 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF86870.1; Type=Frameshift; Positions=285, 326, 344; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HMCES Gene

neXtProt entry for HMCES Gene

Post-translational modifications for HMCES Gene

  • Ubiquitination at isoforms=89 and isoforms=44
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Boster Bio Antibodies for HMCES
  • Santa Cruz Biotechnology (SCBT) Antibodies for HMCES

No data available for DME Specific Peptides for HMCES Gene

Domains & Families for HMCES Gene

Gene Families for HMCES Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HMCES Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMCES Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96FZ2

UniProtKB/Swiss-Prot:

HMCES_HUMAN :
  • Belongs to the SOS response-associated peptidase family.
Family:
  • Belongs to the SOS response-associated peptidase family.
genes like me logo Genes that share domains with HMCES: view

Function for HMCES Gene

Molecular function for HMCES Gene

UniProtKB/Swiss-Prot Function:
Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).

Enzyme Numbers (IUBMB) for HMCES Gene

Gene Ontology (GO) - Molecular Function for HMCES Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IEA --
GO:0008233 peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with HMCES: view
genes like me logo Genes that share phenotypes with HMCES: view

Animal Model Products

CRISPR Products

miRNA for HMCES Gene

miRTarBase miRNAs that target HMCES

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMCES

Clone Products

  • Addgene plasmids for HMCES

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HMCES Gene

Localization for HMCES Gene

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 HMCES gene
Compartment Confidence
nucleus 4
peroxisome 2
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HMCES Gene

Pathways & Interactions for HMCES Gene

SuperPathways for HMCES Gene

No Data Available

Gene Ontology (GO) - Biological Process for HMCES Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with HMCES: view

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

Drugs & Compounds for HMCES Gene

No Compound Related Data Available

Transcripts for HMCES Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMCES

Clone Products

  • Addgene plasmids for HMCES

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

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b
SP1: - - - - - -
SP2: -
SP3: - -
SP4: - - - - - - -
SP5: - - -
SP6: - -
SP7: - - - - -
SP8:
SP9: - - -

Relevant External Links for HMCES Gene

GeneLoc Exon Structure for
HMCES
ECgene alternative splicing isoforms for
HMCES

Expression for HMCES Gene

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

Protein differential expression in normal tissues from HIPED for HMCES Gene

This gene is overexpressed in Testis (22.9), Ovary (9.4), CD8 Tcells (9.1), and Fetal ovary (6.0).

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



Protein tissue co-expression partners for HMCES Gene

NURSA nuclear receptor signaling pathways regulating expression of HMCES Gene:

HMCES

Evidence on tissue expression from TISSUES for HMCES Gene

  • Nervous system(4.7)
  • Lung(4.3)
  • Lymph node(4.3)
  • Spleen(4.2)
  • Blood(4.1)
genes like me logo Genes that share expression patterns with HMCES: view

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 HMCES Gene

Orthologs for HMCES Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HMCES Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C3H3orf37 33
  • 99.44 (n)
HMCES 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C20H3orf37 33
  • 87.35 (n)
HMCES 34
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hmces 16 34 33
  • 84.85 (n)
rat
(Rattus norvegicus)
Mammalia Hmces 33
  • 84.56 (n)
cow
(Bos Taurus)
Mammalia HMCES 34
  • 81 (a)
OneToOne
C22H3orf37 33
  • 80.7 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HMCES 34
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HMCES 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves C12H3ORF37 34 33
  • 65.54 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HMCES 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hmces 33
  • 64.44 (n)
MGC75607 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5297 33
zebrafish
(Danio rerio)
Actinopterygii hmces 34 33
  • 58.93 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG11986 34 33
  • 49.49 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003544 33
  • 46.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 24 (a)
OneToOne
Species where no ortholog for HMCES was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 HMCES Gene

ENSEMBL:
Gene Tree for HMCES (if available)
TreeFam:
Gene Tree for HMCES (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMCES: view image

Paralogs for HMCES Gene

No data available for Paralogs for HMCES Gene

Variants for HMCES Gene

Sequence variations from dbSNP and Humsavar for HMCES Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000000572 -- 129,299,963(+) T/A/C intron_variant
rs1000055403 -- 129,292,258(+) T/C intron_variant
rs1000093345 -- 129,299,661(+) T/C intron_variant
rs1000251625 -- 129,293,988(+) T/C intron_variant
rs1000315681 -- 129,284,063(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
nsv1123689 CNV deletion 24896259
nsv1127992 CNV deletion 24896259
nsv520607 CNV gain+loss 19592680
nsv829722 CNV gain 17160897

Variation tolerance for HMCES Gene

Residual Variation Intolerance Score: 25.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.28; 62.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMCES Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for HMCES Gene

Additional Disease Information for HMCES

No disorders were found for HMCES Gene.

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

Publications for HMCES Gene

  1. Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems. (PMID: 23945014) Aravind L … Iyer LM (Biology direct 2013) 2 3 4 58
  2. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. (PMID: 23434322) Spruijt CG … Vermeulen M (Cell 2013) 2 3 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 58

Products for HMCES Gene

Sources for HMCES Gene

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