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HMCES Gene(Protein Coding)

5-Hydroxymethylcytosine Binding, ES Cell Specific

GCID:
GC03P129278
GIFtS:
39
Genes Participants
UDN Logo

Aliases for HMCES Gene

Aliases for HMCES Gene

  • 5-Hydroxymethylcytosine Binding, ES Cell Specific 2 5
  • Embryonic Stem Cell-Specific 5-Hydroxymethylcytosine-Binding Protein 2 3
  • 5-Hydroxymethylcytosine (HmC) Binding, ES Cell-Specific 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
  • SOS Response Associated Peptidase Domain Containing 1 2
  • 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. 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).

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

Products:

  1. Regulatory Element

Regulatory Elements for HMCES Gene

Enhancers for HMCES 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
GH03G129309 1.4 ENCODE dbSUPER 29.4 +35.1 35085 8.8 HDGF PKNOX1 FOXA2 AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 HMCES ISY1 RPL32P3 H1FX ENSG00000244932 H1FX-AS1 MBD4 ENSG00000261159 GC03M129283
GH03G129303 1.4 Ensembl ENCODE dbSUPER 29.4 +26.4 26449 2.9 HDAC1 PKNOX1 ATF1 RAD21 TCF12 EGR1 FOS RELB IKZF2 EGR2 HMCES ISY1 LOC100421508 GC03M129283 H1FX-AS1
GH03G129281 1.2 Ensembl ENCODE 29.7 +3.9 3948 1.6 PKNOX1 TBL1XR1 ARID4B SIN3A BMI1 RAD21 YY1 ZNF335 GLIS2 RELB HMCES EFCAB12 GC03M129283
GH03G129277 1.1 ENCODE 29.8 +0.4 378 3.1 HDGF PKNOX1 FOXA2 AGO1 WRNIP1 ARID4B SIN3A YY1 PAF1 ZNF263 HMCES CNBP ACAD9 MBD4 RAB7A GC03M129283
GH03G129238 1.8 FANTOM5 Ensembl ENCODE dbSUPER 16.4 -39.1 -39083 3.0 TBP HDAC1 ARNT ZNF121 ZNF766 RCOR1 SMARCA5 SMAD5 CEBPB ZNF592 HMCES MBD4 H1FOO PIR44075 GC03M129230
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMCES on UCSC Golden Path with GeneCards custom track

Promoters for HMCES Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000158203 484 1401 HDGF PKNOX1 FOXA2 AGO1 ZFP64 WRNIP1 ARID4B SIN3A YY1 ZNF263

Genomic Location for HMCES Gene

Chromosome:
3
Start:
129,278,816 bp from pter
End:
129,306,186 bp from pter
Size:
27,371 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 Structure • Gene Density

RefSeq DNA sequence for HMCES Gene

Proteins for HMCES Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for HMCES Gene

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

Post-translational modifications for HMCES Gene

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

Other Protein References for HMCES Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HMCES Gene

Domains & Families for HMCES Gene

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

No data available for Gene Families for HMCES Gene

Function for HMCES Gene

Products:

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

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: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

Phenotypes for HMCES Gene

GenomeRNAi human phenotypes for HMCES:
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

Flow Cytometry Products

No data available for 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

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

PathCards logo More details on SuperPathways for HMCES
No Data Available

Gene Ontology (GO) - Biological Process for HMCES Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HMCES Gene

Products:

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

mRNA/cDNA for HMCES Gene

(5) REFSEQ mRNAs :
(424) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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

Products:

  1. Primer

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

mRNA expression in normal human tissues for HMCES Gene
mRNA expression by BioGPS for HMCES GenemRNA expression by GTEx 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, PaxDb, 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

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 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 34
  • 99.44 (n)
HMCES 35
  • 99 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia C20H3orf37 34
  • 87.35 (n)
HMCES 35
  • 87 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Hmces 34 16 35
  • 84.85 (n)
rat
(Rattus norvegicus)
 Mammalia Hmces 34
  • 84.56 (n)
cow
(Bos Taurus)
 Mammalia HMCES 35
  • 81 (a)
 OneToOne
C22H3orf37 34
  • 80.7 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia HMCES 35
  • 79 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia HMCES 35
  • 69 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves C12H3ORF37 34 35
  • 65.54 (n)
lizard
(Anolis carolinensis)
 Reptilia HMCES 35
  • 62 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hmces 34
  • 64.44 (n)
MGC75607 34
African clawed frog
(Xenopus laevis)
 Amphibia Xl.5297 34
zebrafish
(Danio rerio)
 Actinopterygii hmces 34 35
  • 58.93 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG11986 34 35
  • 49.49 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP003544 34
  • 46.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes -- 35
  • 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)

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 Sequence Context AA Info Type
rs1000000572 -- 129,299,963(+) GGTCA(A/C/T)TTTTT intron-variant
rs1000055403 -- 129,292,258(+) GGGAA(C/T)TGTTT intron-variant
rs1000093345 -- 129,299,661(+) TTTTT(C/T)TTTTT intron-variant
rs1000251625 -- 129,293,988(+) TGGGT(C/T)AAAAT intron-variant
rs1000315681 -- 129,284,063(+) AACCC(C/T)TAAAT 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)

Relevant External Links for HMCES Gene

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

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

Disorders for HMCES Gene

Relevant External Links for HMCES

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 L.M. (Biol. Direct 2013) 2 3 4 64
  2. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. (PMID: 23434322) Spruijt C.G. … Vermeulen M. (Cell 2013) 2 3 64
  3. 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
  4. 5-Hydroxymethylcytosine, the "Sixth Base", during brain development and ageing. (PMID: 25471351) Kraus T.F. … Kretzschmar H.A. (J Neural Transm (Vienna) 2015) 3 64
  5. Prognostic values of 5-hmC, 5-mC and TET2 in epithelial ovarian cancer. (PMID: 25827305) Zhang L.Y. … Zhang X.C. (Arch. Gynecol. Obstet. 2015) 3 64

Products for HMCES Gene

Sources for HMCES Gene

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