LOCUS       NM_020187               2485 bp    mRNA    linear   PRI 03-APR-2024
DEFINITION  Homo sapiens 5-hydroxymethylcytosine binding, ES cell specific
            (HMCES), transcript variant 2, mRNA.
ACCESSION   NM_020187
VERSION     NM_020187.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2485)
  AUTHORS   Rua-Fernandez,J., Lovejoy,C.A., Mehta,K.P.M., Paulin,K.A.,
            Toudji,Y.T., Giansanti,C., Eichman,B.F. and Cortez,D.
  TITLE     Self-reversal facilitates the resolution of HMCES DNA-protein
            crosslinks in cells
  JOURNAL   Cell Rep 42 (11), 113427 (2023)
   PUBMED   37950866
REFERENCE   2  (bases 1 to 2485)
  AUTHORS   Donsbach,M., Durauer,S., Grunert,F., Nguyen,K.T., Nigam,R.,
            Yaneva,D., Weickert,P., Bezalel-Buch,R., Semlow,D.R. and
            Stingele,J.
  TITLE     A non-proteolytic release mechanism for HMCES-DNA-protein
            crosslinks
  JOURNAL   EMBO J 42 (18), e113360 (2023)
   PUBMED   37519246
REFERENCE   3  (bases 1 to 2485)
  AUTHORS   Yaneva,D., Sparks,J.L., Donsbach,M., Zhao,S., Weickert,P.,
            Bezalel-Buch,R., Stingele,J. and Walter,J.C.
  TITLE     The FANCJ helicase unfolds DNA-protein crosslinks to promote their
            repair
  JOURNAL   Mol Cell 83 (1), 43-56 (2023)
   PUBMED   36608669
REFERENCE   4  (bases 1 to 2485)
  AUTHORS   Wu,L., Shukla,V., Yadavalli,A.D., Dinesh,R.K., Xu,D., Rao,A. and
            Schatz,D.G.
  TITLE     HMCES protects immunoglobulin genes specifically from deletions
            during somatic hypermutation
  JOURNAL   Genes Dev 36 (7-8), 433-450 (2022)
   PUBMED   35450882
REFERENCE   5  (bases 1 to 2485)
  AUTHORS   Biayna,J., Garcia-Cao,I., Alvarez,M.M., Salvadores,M.,
            Espinosa-Carrasco,J., McCullough,M., Supek,F. and Stracker,T.H.
  TITLE     Loss of the abasic site sensor HMCES is synthetic lethal with the
            activity of the APOBEC3A cytosine deaminase in cancer cells
  JOURNAL   PLoS Biol 19 (3), e3001176 (2021)
   PUBMED   33788831
  REMARK    GeneRIF: Loss of the abasic site sensor HMCES is synthetic lethal
            with the activity of the APOBEC3A cytosine deaminase in cancer
            cells.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2485)
  AUTHORS   Kraus,T.F., Guibourt,V. and Kretzschmar,H.A.
  TITLE     5-Hydroxymethylcytosine, the 'Sixth Base', during brain development
            and ageing
  JOURNAL   J Neural Transm (Vienna) 122 (7), 1035-1043 (2015)
   PUBMED   25471351
  REMARK    GeneRIF: The findings of this study described in this study
            emphasise the importance of 5hmC in brain development and ageing
            and will help to better understand the complexity and plasticity of
            the brain.
REFERENCE   7  (bases 1 to 2485)
  AUTHORS   Condliffe,D., Wong,A., Troakes,C., Proitsi,P., Patel,Y.,
            Chouliaras,L., Fernandes,C., Cooper,J., Lovestone,S., Schalkwyk,L.,
            Mill,J. and Lunnon,K.
  TITLE     Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's
            disease brain
  JOURNAL   Neurobiol Aging 35 (8), 1850-1854 (2014)
   PUBMED   24679604
  REMARK    GeneRIF: Its reduction in brain is associate with neuropathology of
            Alzheimer disease.
REFERENCE   8  (bases 1 to 2485)
  AUTHORS   Coppieters,N., Dieriks,B.V., Lill,C., Faull,R.L., Curtis,M.A. and
            Dragunow,M.
  TITLE     Global changes in DNA methylation and hydroxymethylation in
            Alzheimer's disease human brain
  JOURNAL   Neurobiol Aging 35 (6), 1334-1344 (2014)
   PUBMED   24387984
  REMARK    GeneRIF: It involves in epigenetic changes during the progression
            of Alzheimer disease pathology.
REFERENCE   9  (bases 1 to 2485)
  AUTHORS   Aravind,L., Anand,S. and Iyer,L.M.
  TITLE     Novel autoproteolytic and DNA-damage sensing components in the
            bacterial SOS response and oxidized methylcytosine-induced
            eukaryotic DNA demethylation systems
  JOURNAL   Biol Direct 8, 20 (2013)
   PUBMED   23945014
  REMARK    Publication Status: Online-Only
REFERENCE   10 (bases 1 to 2485)
  AUTHORS   Spruijt,C.G., Gnerlich,F., Smits,A.H., Pfaffeneder,T., Jansen,P.W.,
            Bauer,C., Munzel,M., Wagner,M., Muller,M., Khan,F., Eberl,H.C.,
            Mensinga,A., Brinkman,A.B., Lephikov,K., Muller,U., Walter,J.,
            Boelens,R., van Ingen,H., Leonhardt,H., Carell,T. and Vermeulen,M.
  TITLE     Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized
            derivatives
  JOURNAL   Cell 152 (5), 1146-1159 (2013)
   PUBMED   23434322
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AF201934.1, BC010125.2 and AC137695.3.
            
            On Nov 22, 2018 this sequence version replaced NM_020187.2.
            
            Transcript Variant: This variant (2) differs in the 5' UTR compared
            to variant 1. Variants 1 and 2 both encode the same isoform (a).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1660803.3572.1,
                                           SRR3476690.986214.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000383463.9/ ENSP00000372955.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-887               AF201934.1         43-929
            888-1557            BC010125.2         880-1549
            1558-1592           AF201934.1         1601-1635
            1593-2485           AC137695.3         61600-62492
FEATURES             Location/Qualifiers
     source          1..2485
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q21.3"
     gene            1..2485
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /note="5-hydroxymethylcytosine binding, ES cell specific"
                     /db_xref="GeneID:56941"
                     /db_xref="HGNC:HGNC:24446"
                     /db_xref="MIM:618288"
     exon            1..36
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     exon            37..242
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             60..1124
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /note="isoform a is encoded by transcript variant 2;
                     UPF0361 protein C3orf37; putative peptidase SRAPD1; SRAP
                     domain-containing protein 1; ES cell-specific 5hmC-binding
                     protein; embryonic stem cell-specific
                     5-hydroxymethylcytosine-binding protein;
                     5-hydroxymethylcytosine (hmC) binding, ES cell-specific;
                     SOS response associated peptidase domain containing 1;
                     peptidase HMCES; putative endonuclease HMCES; abasic site
                     processing protein HMCES"
                     /codon_start=1
                     /product="abasic site processing protein HMCES isoform a"
                     /protein_id="NP_064572.2"
                     /db_xref="CCDS:CCDS33852.1"
                     /db_xref="GeneID:56941"
                     /db_xref="HGNC:HGNC:24446"
                     /db_xref="MIM:618288"
                     /translation="MCGRTSCHLPRDVLTRACAYQDRRGQQRLPEWRDPDKYCPSYNK
                     SPQSNSPVLLSRLHFEKDADSSERIIAPMRWGLVPSWFKESDPSKLQFNTTNCRSDTV
                     MEKRSFKVPLGKGRRCVVLADGFYEWQRCQGTNQRQPYFIYFPQIKTEKSGSIGAADS
                     PENWEKVWDNWRLLTMAGIFDCWEPPEGGDVLYSYTIITVDSCKGLSDIHHRMPAILD
                     GEEAVSKWLDFGEVSTQEALKLIHPTENITFHAVSSVVNNSRNNTPECLAPVDLVVKK
                     ELRASGSSQRMLQWLATKSPKKEDSKTPQKEESDVPQWSSQFLQKSPLPTKRGTAGLL
                     EQWLKREKEEEPVAKRPYSQ"
     exon            243..386
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     exon            387..512
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     exon            513..694
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     exon            695..887
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     exon            888..2485
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2466..2471
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /note="hexamer: AATAAA"
     polyA_site      2485
                     /gene="HMCES"
                     /gene_synonym="C3orf37; DC12; SRAPD1"
                     /note="major polyA site"
ORIGIN      
        1 agagtcgagg gaggtgacgc gcgctgccgg ggcgaggttg cgaggggcgg tgttgaagaa
       61 tgtgtgggcg aacatcctgt cacttaccta gagatgttct cacgagagct tgcgcctacc
      121 aggatcggcg gggccagcag cggctcccgg agtggaggga ccctgataag tactgcccct
      181 cttacaacaa gagtcctcaa tccaacagcc cagtgcttct gtctcgactg cactttgaga
      241 aggatgcaga ctcatctgag cgtatcattg ctcccatgcg ctggggcttg gtcccttctt
      301 ggttcaaaga aagtgatcct tccaagctgc agttcaatac taccaactgt cgtagtgata
      361 ccgtaatgga gaaacggtca tttaaggtgc ctctgggaaa gggaagacgc tgtgtcgttt
      421 tagcagatgg attctatgag tggcagcgat gtcagggaac aaaccagagg cagccatact
      481 tcatctattt tcctcaaatc aagacagaga agtcaggtag cattggtgct gcagatagtc
      541 ctgagaactg ggagaaagtc tgggacaact ggaggctgct gacaatggcc gggatctttg
      601 actgctggga gcccccagag ggaggagatg tcctgtattc ctataccatc atcacagtgg
      661 attcctgcaa aggcttgagt gacatccacc acaggatgcc tgccatatta gatggagagg
      721 aggcagtttc taaatggctt gactttggtg aagtctcaac tcaggaagct ctgaaattaa
      781 tccacccaac agagaacatc accttccatg cagtctcttc tgtggtgaac aactcgcgaa
      841 acaacactcc tgagtgtctg gctcctgtcg acttggtggt caaaaaggag ctcagggcaa
      901 gtggcagtag ccagaggatg ttgcagtggt tggccacaaa gtcacccaaa aaggaagact
      961 caaaaacacc tcaaaaggaa gagtcagatg ttccccagtg gtccagtcag ttcctgcaga
     1021 agagtccact ccccaccaag agaggcactg caggactcct agagcaatgg ctgaagcggg
     1081 agaaggagga ggaacctgtg gccaagcgtc cttacagcca gtgacacagg actttcagag
     1141 accaaggcca gggtctgctg cactgctgtt ctgataatag gttcttaaca ttgtatgtat
     1201 atgtgtttgc tttgggagga ggtggcactg tgttagttga cagttgtggg ctcatgtagt
     1261 cttttttgcc atgagtagga gcccctagtg gggctggtgg acagctttgg aagaggtgtc
     1321 ctgctgctgt taccagccat gtgggcccca taggggcact gcgcctgctg ccctttcctg
     1381 gcagggctgg tggagtcttc cctcaaagca tgccttaccc agctgggaag tctctgccct
     1441 gatctggtac tccttgtagt aagctgtttt ctgctcagcc actgggctct ttcacttttt
     1501 tagttcttaa aaatttattt ttaagttcta aaataaaata aaaataagtt cttaaaattt
     1561 atttttttcc tgaataaatt gtatttggta aacttctgcc tacattttgg aaagtgatgc
     1621 tggtggggaa agttctagat cttacttggt ttcttctaga atcagtcttc aggaatggat
     1681 tttgtcacaa atggggcatg ggggctttct gaggaaataa ctacaagtct tggtggtggg
     1741 ctccttatta tgtttctttt tctttcattc ttgatacttg gaagtcgtct gaatccttta
     1801 gcttcaaacc agcctgagtt tgagtgcttg ccgtagcaga aactatcctt accacaggtg
     1861 ggaaggaaag gaccagtttc tagcagtgtc gggccactcc tctttcgaac atccctaagg
     1921 gaggcattca caaaagctgt cccaagcagc tggaagaaaa cagcttccga gatgaccagg
     1981 aggactgggc ggcgccgagc ccagaacgct cctggcgcag caccgttggc gttggccgat
     2041 tgctgctggt ggggggcggg ggtgcaggcc ccagtctcta tgcaaatcag ggatcagaag
     2101 atcggaattt ccaccaatca gcgggaagcc tcggccctgt aactgctaat gggagacagc
     2161 agcgccacgc cacaggcttt tcccctggtt tcgggagggg tggggagcca ggtggggctc
     2221 ccgcccagac cctttcccga ggtccgccct ctccgccttt tctctaaatt cctcttttga
     2281 gtgccctccc ttccggttga gaggcggggg ttggcccgta gttgtacact cagtcaccct
     2341 gcactgtgga ggcgggggcc tcccttgtgg actgatttgc gtgggatttg gttgttttat
     2401 taagagattt aaaaaattca gatgacttac tagtatgact gttttgtcat atttgcttcc
     2461 aggttaataa atgacaaaaa tgaaa
//
