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Protein

Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein

Gene

HMCES

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity1 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
Short name:
ES cell-specific 5hmC-binding protein
Alternative name(s):
Putative peptidase SRAPD1 (EC:3.4.-.-)
SRAP domain-containing protein 1
Gene namesi
Name:HMCES
Synonyms:C3orf37, DC12, SRAPD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:24446. HMCES.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142672398.

Polymorphism and mutation databases

BioMutaiC3orf37.
DMDMi74731769.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 354354Embryonic stem cell-specific 5-hydroxymethylcytosine-binding proteinPRO_0000164394Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei160 – 1601PhosphoserineCombined sources
Modified residuei295 – 2951PhosphoserineCombined sources
Modified residuei322 – 3221PhosphoserineCombined sources
Cross-linki339 – 339Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96FZ2.
MaxQBiQ96FZ2.
PaxDbiQ96FZ2.
PeptideAtlasiQ96FZ2.
PRIDEiQ96FZ2.

PTM databases

iPTMnetiQ96FZ2.
PhosphoSiteiQ96FZ2.
SwissPalmiQ96FZ2.

Expressioni

Gene expression databases

BgeeiQ96FZ2.
CleanExiHS_C3orf37.
ExpressionAtlasiQ96FZ2. baseline and differential.
GenevisibleiQ96FZ2. HS.

Organism-specific databases

HPAiHPA044968.
HPA050337.

Interactioni

Protein-protein interaction databases

BioGridi121265. 21 interactions.
IntActiQ96FZ2. 13 interactions.
STRINGi9606.ENSP00000372955.

Structurei

3D structure databases

ProteinModelPortaliQ96FZ2.
SMRiQ96FZ2. Positions 72-270.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2618. Eukaryota.
COG2135. LUCA.
GeneTreeiENSGT00390000018439.
HOGENOMiHOG000104694.
HOVERGENiHBG081414.
InParanoidiQ96FZ2.
OMAiDPDKYCP.
PhylomeDBiQ96FZ2.
TreeFamiTF324343.

Family and domain databases

Gene3Di3.90.1680.10. 1 hit.
InterProiIPR003738. SRAP.
[Graphical view]
PANTHERiPTHR13604. PTHR13604. 2 hits.
PfamiPF02586. SRAP. 1 hit.
[Graphical view]
SUPFAMiSSF143081. SSF143081. 1 hit.

Sequencei

Sequence statusi: Complete.

Q96FZ2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MCGRTSCHLP RDVLTRACAY QDRRGQQRLP EWRDPDKYCP SYNKSPQSNS
60 70 80 90 100
PVLLSRLHFE KDADSSERII APMRWGLVPS WFKESDPSKL QFNTTNCRSD
110 120 130 140 150
TVMEKRSFKV PLGKGRRCVV LADGFYEWQR CQGTNQRQPY FIYFPQIKTE
160 170 180 190 200
KSGSIGAADS PENWEKVWDN WRLLTMAGIF DCWEPPEGGD VLYSYTIITV
210 220 230 240 250
DSCKGLSDIH HRMPAILDGE EAVSKWLDFG EVSTQEALKL IHPTENITFH
260 270 280 290 300
AVSSVVNNSR NNTPECLAPV DLVVKKELRA SGSSQRMLQW LATKSPKKED
310 320 330 340 350
SKTPQKEESD VPQWSSQFLQ KSPLPTKRGT AGLLEQWLKR EKEEEPVAKR

PYSQ
Length:354
Mass (Da):40,575
Last modified:December 1, 2001 - v1
Checksum:i209496BB7E331785
GO

Sequence cautioni

The sequence AAF86870.1 differs from that shown. Reason: Frameshift at positions 285, 326 and 344. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti60 – 601E → D in AAH09993 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF201934 mRNA. Translation: AAF86870.1. Frameshift.
AC137695 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW79266.1.
BC009993 mRNA. Translation: AAH09993.1.
BC010125 mRNA. Translation: AAH10125.1.
BC050686 mRNA. Translation: AAH50686.1.
BC088363 mRNA. Translation: AAH88363.1.
CCDSiCCDS33852.1.
RefSeqiNP_001006109.1. NM_001006109.1.
NP_064572.2. NM_020187.2.
XP_005247693.1. XM_005247636.2.
XP_011511296.1. XM_011512994.1.
UniGeneiHs.458320.

Genome annotation databases

EnsembliENST00000383463; ENSP00000372955; ENSG00000183624.
ENST00000389735; ENSP00000374385; ENSG00000183624.
ENST00000502878; ENSP00000426215; ENSG00000183624.
GeneIDi56941.
KEGGihsa:56941.
UCSCiuc003elt.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF201934 mRNA. Translation: AAF86870.1. Frameshift.
AC137695 Genomic DNA. No translation available.
CH471052 Genomic DNA. Translation: EAW79266.1.
BC009993 mRNA. Translation: AAH09993.1.
BC010125 mRNA. Translation: AAH10125.1.
BC050686 mRNA. Translation: AAH50686.1.
BC088363 mRNA. Translation: AAH88363.1.
CCDSiCCDS33852.1.
RefSeqiNP_001006109.1. NM_001006109.1.
NP_064572.2. NM_020187.2.
XP_005247693.1. XM_005247636.2.
XP_011511296.1. XM_011512994.1.
UniGeneiHs.458320.

3D structure databases

ProteinModelPortaliQ96FZ2.
SMRiQ96FZ2. Positions 72-270.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121265. 21 interactions.
IntActiQ96FZ2. 13 interactions.
STRINGi9606.ENSP00000372955.

PTM databases

iPTMnetiQ96FZ2.
PhosphoSiteiQ96FZ2.
SwissPalmiQ96FZ2.

Polymorphism and mutation databases

BioMutaiC3orf37.
DMDMi74731769.

Proteomic databases

EPDiQ96FZ2.
MaxQBiQ96FZ2.
PaxDbiQ96FZ2.
PeptideAtlasiQ96FZ2.
PRIDEiQ96FZ2.

Protocols and materials databases

DNASUi56941.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000383463; ENSP00000372955; ENSG00000183624.
ENST00000389735; ENSP00000374385; ENSG00000183624.
ENST00000502878; ENSP00000426215; ENSG00000183624.
GeneIDi56941.
KEGGihsa:56941.
UCSCiuc003elt.4. human.

Organism-specific databases

CTDi56941.
GeneCardsiHMCES.
H-InvDBHIX0022529.
HGNCiHGNC:24446. HMCES.
HPAiHPA044968.
HPA050337.
neXtProtiNX_Q96FZ2.
PharmGKBiPA142672398.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2618. Eukaryota.
COG2135. LUCA.
GeneTreeiENSGT00390000018439.
HOGENOMiHOG000104694.
HOVERGENiHBG081414.
InParanoidiQ96FZ2.
OMAiDPDKYCP.
PhylomeDBiQ96FZ2.
TreeFamiTF324343.

Miscellaneous databases

ChiTaRSiHMCES. human.
GenomeRNAii56941.
PROiQ96FZ2.

Gene expression databases

BgeeiQ96FZ2.
CleanExiHS_C3orf37.
ExpressionAtlasiQ96FZ2. baseline and differential.
GenevisibleiQ96FZ2. HS.

Family and domain databases

Gene3Di3.90.1680.10. 1 hit.
InterProiIPR003738. SRAP.
[Graphical view]
PANTHERiPTHR13604. PTHR13604. 2 hits.
PfamiPF02586. SRAP. 1 hit.
[Graphical view]
SUPFAMiSSF143081. SSF143081. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Novel genes expressed in human dendritic cells."
    Peng Y., Li Y., Tu Y., Gu Y., Han Z., Fu G., Chen Z.
    Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Dendritic cell.
  2. "The DNA sequence, annotation and analysis of human chromosome 3."
    Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
    , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
    Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain, Lung and Uterus.
  5. "Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems."
    Aravind L., Anand S., Iyer L.M.
    Biol. Direct 8:20-20(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  6. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Toward a comprehensive characterization of a human cancer cell phosphoproteome."
    Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., Mohammed S.
    J. Proteome Res. 12:260-271(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-160; SER-295 AND SER-322, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma and Erythroleukemia.
  9. "System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability."
    Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V., Vertegaal A.C.
    Mol. Cell. Proteomics 14:1419-1434(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-339, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiHMCES_HUMAN
AccessioniPrimary (citable) accession number: Q96FZ2
Secondary accession number(s): A6NJR9, Q96G34, Q9NRP3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: December 1, 2001
Last modified: July 6, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.