LOCUS       NM_024165               2263 bp    mRNA    linear   PRI 10-FEB-2025
DEFINITION  Homo sapiens PHD finger protein 1 (PHF1), transcript variant 2,
            mRNA.
ACCESSION   NM_024165
VERSION     NM_024165.3
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 2263)
  AUTHORS   Sharma,A.E., Dermawan,J.K., Sherrod,A.E., Chopra,S., Maki,R.G. and
            Antonescu,C.R.
  TITLE     When molecular outsmarts morphology: Malignant ossifying
            fibromyxoid tumors masquerading as osteosarcomas, including a novel
            CREBZF::PHF1 fusion
  JOURNAL   Genes Chromosomes Cancer 63 (1), e23206 (2024)
   PUBMED   37819540
  REMARK    GeneRIF: When molecular outsmarts morphology: Malignant ossifying
            fibromyxoid tumors masquerading as osteosarcomas, including a novel
            CREBZF::PHF1 fusion.
REFERENCE   2  (bases 1 to 2263)
  AUTHORS   Zou,C., Ru,G.Q. and Zhao,M.
  TITLE     A PHF1-TFE3 fusion atypical ossifying fibromyxoid tumor with
            prominent collagenous rosettes: Case report with a brief review
  JOURNAL   Exp Mol Pathol 123, 104686 (2021)
   PUBMED   34560087
  REMARK    GeneRIF: A PHF1-TFE3 fusion atypical ossifying fibromyxoid tumor
            with prominent collagenous rosettes: Case report with a brief
            review.
REFERENCE   3  (bases 1 to 2263)
  AUTHORS   Kim,M., Park,J., Bouhaddou,M., Kim,K., Rojc,A., Modak,M.,
            Soucheray,M., McGregor,M.J., O'Leary,P., Wolf,D., Stevenson,E.,
            Foo,T.K., Mitchell,D., Herrington,K.A., Munoz,D.P., Tutuncuoglu,B.,
            Chen,K.H., Zheng,F., Kreisberg,J.F., Diolaiti,M.E., Gordan,J.D.,
            Coppe,J.P., Swaney,D.L., Xia,B., van 't Veer,L., Ashworth,A.,
            Ideker,T. and Krogan,N.J.
  TITLE     A protein interaction landscape of breast cancer
  JOURNAL   Science 374 (6563), eabf3066 (2021)
   PUBMED   34591612
REFERENCE   4  (bases 1 to 2263)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   5  (bases 1 to 2263)
  AUTHORS   Sbaraglia,M., Bellan,E., Gambarotti,M., Righi,A., Zanatta,L.,
            Toffolatti,L. and Dei Tos,A.P.
  TITLE     Primary malignant ossifying fibromyxoid tumour of the bone. A
            clinicopathologic and molecular report of two cases
  JOURNAL   Pathologica 112 (4), 184-190 (2020)
   PUBMED   33179613
  REMARK    GeneRIF: Primary malignant ossifying fibromyxoid tumour of the
            bone. A clinicopathologic and molecular report of two cases.
REFERENCE   6  (bases 1 to 2263)
  AUTHORS   Sarma,K., Margueron,R., Ivanov,A., Pirrotta,V. and Reinberg,D.
  TITLE     Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27
            trimethylation in vivo
  JOURNAL   Mol Cell Biol 28 (8), 2718-2731 (2008)
   PUBMED   18285464
  REMARK    GeneRIF: PHF1 modulates the activity of Ezh2 in favor of the
            repressive H3K27me3 mark
REFERENCE   7  (bases 1 to 2263)
  AUTHORS   Cao,R., Wang,H., He,J., Erdjument-Bromage,H., Tempst,P. and
            Zhang,Y.
  TITLE     Role of hPHF1 in H3K27 methylation and Hox gene silencing
  JOURNAL   Mol Cell Biol 28 (5), 1862-1872 (2008)
   PUBMED   18086877
  REMARK    GeneRIF: The role of PHF1 in H3K27 methylation and Hox gene
            silencing is reported.
REFERENCE   8  (bases 1 to 2263)
  AUTHORS   Mungall,A.J., Palmer,S.A., Sims,S.K., Edwards,C.A., Ashurst,J.L.,
            Wilming,L., Jones,M.C., Horton,R., Hunt,S.E., Scott,C.E.,
            Gilbert,J.G., Clamp,M.E., Bethel,G., Milne,S., Ainscough,R.,
            Almeida,J.P., Ambrose,K.D., Andrews,T.D., Ashwell,R.I.,
            Babbage,A.K., Bagguley,C.L., Bailey,J., Banerjee,R., Barker,D.J.,
            Barlow,K.F., Bates,K., Beare,D.M., Beasley,H., Beasley,O.,
            Bird,C.P., Blakey,S., Bray-Allen,S., Brook,J., Brown,A.J.,
            Brown,J.Y., Burford,D.C., Burrill,W., Burton,J., Carder,C.,
            Carter,N.P., Chapman,J.C., Clark,S.Y., Clark,G., Clee,C.M.,
            Clegg,S., Cobley,V., Collier,R.E., Collins,J.E., Colman,L.K.,
            Corby,N.R., Coville,G.J., Culley,K.M., Dhami,P., Davies,J.,
            Dunn,M., Earthrowl,M.E., Ellington,A.E., Evans,K.A., Faulkner,L.,
            Francis,M.D., Frankish,A., Frankland,J., French,L., Garner,P.,
            Garnett,J., Ghori,M.J., Gilby,L.M., Gillson,C.J., Glithero,R.J.,
            Grafham,D.V., Grant,M., Gribble,S., Griffiths,C., Griffiths,M.,
            Hall,R., Halls,K.S., Hammond,S., Harley,J.L., Hart,E.A.,
            Heath,P.D., Heathcott,R., Holmes,S.J., Howden,P.J., Howe,K.L.,
            Howell,G.R., Huckle,E., Humphray,S.J., Humphries,M.D., Hunt,A.R.,
            Johnson,C.M., Joy,A.A., Kay,M., Keenan,S.J., Kimberley,A.M.,
            King,A., Laird,G.K., Langford,C., Lawlor,S., Leongamornlert,D.A.,
            Leversha,M., Lloyd,C.R., Lloyd,D.M., Loveland,J.E., Lovell,J.,
            Martin,S., Mashreghi-Mohammadi,M., Maslen,G.L., Matthews,L.,
            McCann,O.T., McLaren,S.J., McLay,K., McMurray,A., Moore,M.J.,
            Mullikin,J.C., Niblett,D., Nickerson,T., Novik,K.L., Oliver,K.,
            Overton-Larty,E.K., Parker,A., Patel,R., Pearce,A.V., Peck,A.I.,
            Phillimore,B., Phillips,S., Plumb,R.W., Porter,K.M., Ramsey,Y.,
            Ranby,S.A., Rice,C.M., Ross,M.T., Searle,S.M., Sehra,H.K.,
            Sheridan,E., Skuce,C.D., Smith,S., Smith,M., Spraggon,L.,
            Squares,S.L., Steward,C.A., Sycamore,N., Tamlyn-Hall,G., Tester,J.,
            Theaker,A.J., Thomas,D.W., Thorpe,A., Tracey,A., Tromans,A.,
            Tubby,B., Wall,M., Wallis,J.M., West,A.P., White,S.S.,
            Whitehead,S.L., Whittaker,H., Wild,A., Willey,D.J., Wilmer,T.E.,
            Wood,J.M., Wray,P.W., Wyatt,J.C., Young,L., Younger,R.M.,
            Bentley,D.R., Coulson,A., Durbin,R., Hubbard,T., Sulston,J.E.,
            Dunham,I., Rogers,J. and Beck,S.
  TITLE     The DNA sequence and analysis of human chromosome 6
  JOURNAL   Nature 425 (6960), 805-811 (2003)
   PUBMED   14574404
REFERENCE   9  (bases 1 to 2263)
  AUTHORS   O'Connell,S., Wang,L., Robert,S., Jones,C.A., Saint,R. and
            Jones,R.S.
  TITLE     Polycomblike PHD fingers mediate conserved interaction with
            enhancer of zeste protein
  JOURNAL   J Biol Chem 276 (46), 43065-43073 (2001)
   PUBMED   11571280
REFERENCE   10 (bases 1 to 2263)
  AUTHORS   Coulson,M., Robert,S., Eyre,H.J. and Saint,R.
  TITLE     The identification and localization of a human gene with sequence
            similarity to Polycomblike of Drosophila melanogaster
  JOURNAL   Genomics 48 (3), 381-383 (1998)
   PUBMED   9545646
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL662799.16.
            
            On Jun 2, 2019 this sequence version replaced NM_024165.2.
            
            Summary: This gene encodes a Polycomb group protein. The protein is
            a component of a histone H3 lysine-27 (H3K27)-specific
            methyltransferase complex, and functions in transcriptional
            repression of homeotic genes. The protein is also recruited to
            double-strand breaks, and reduced protein levels results in X-ray
            sensitivity and increased homologous recombination. Multiple
            transcript variants encoding different isoforms have been found for
            this gene. [provided by RefSeq, May 2009].
            
            Transcript Variant: This variant (2), also called variant PHF2,
            represents the longest transcript and encodes the longer isoform
            (b).
            
            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 :: BC008834.2, AF052205.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000374516.8/ ENSP00000363640.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-202               AL662799.16        63383-63584
            203-377             AL662799.16        64617-64791
            378-459             AL662799.16        64877-64958
            460-555             AL662799.16        65067-65162
            556-656             AL662799.16        65565-65665
            657-805             AL662799.16        65778-65926
            806-901             AL662799.16        66105-66200
            902-970             AL662799.16        66410-66478
            971-1094            AL662799.16        66612-66735
            1095-1162           AL662799.16        66846-66913
            1163-1267           AL662799.16        67094-67198
            1268-1457           AL662799.16        67324-67513
            1458-1552           AL662799.16        67604-67698
            1553-1633           AL662799.16        67959-68039
            1634-2263           AL662799.16        68179-68808
FEATURES             Location/Qualifiers
     source          1..2263
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.32"
     gene            1..2263
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /note="PHD finger protein 1"
                     /db_xref="GeneID:5252"
                     /db_xref="HGNC:HGNC:8919"
                     /db_xref="MIM:602881"
     exon            1..202
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            203..377
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     CDS             219..1922
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /note="isoform b is encoded by transcript variant 2;
                     hPCl1; polycomb-like protein 1; tudor domain containing
                     19C; testicular tissue protein Li 140; polycomb-like 1"
                     /codon_start=1
                     /product="PHD finger protein 1 isoform b"
                     /protein_id="NP_077084.2"
                     /db_xref="CCDS:CCDS4777.1"
                     /db_xref="GeneID:5252"
                     /db_xref="HGNC:HGNC:8919"
                     /db_xref="MIM:602881"
                     /translation="MAQPPRLSRSGASSLWDPASPAPTSGPRPRLWEGQDVLARWTDG
                     LLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALPGEELLCCVCRSETVVPGN
                     RLVSCEKCRHAYHQDCHVPRAPAPGEGEGTSWVCRQCVFAIATKRGGALKKGPYARAM
                     LGMKLSLPYGLKGLDWDAGHLSNRQQSYCYCGGPGEWNLKMLQCRSCLQWFHEACTQC
                     LSKPLLYGDRFYEFECCVCRGGPEKVRRLQLRWVDVAHLVLYHLSVCCKKKYFDFDRE
                     ILPFTSENWDSLLLGELSDTPKGERSSRLLSALNSHKDRFISGREIKKRKCLFGLHAR
                     MPPPVEPPTGDGALTSFPSGQGPGGGVSRPLGKRRRPEPEPLRRRQKGKVEELGPPSA
                     VRNQPEPQEQRERAHLQRALQASVSPPSPSPNQSYQGSSGYNFRPTDARCLPSSPIRM
                     FASFHPSASTAGTSGDSGPPDRSPLELHIGFPTDIPKSAPHSMTASSSSVSSPSPGLP
                     RRSAPPSPLCRSLSPGTGGGVRGGVGYLSRGDPVRVLARRVRPDGSVQYLVEWGGGGI
                     F"
     exon            378..459
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            460..555
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            556..656
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            657..805
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            806..901
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            902..970
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            971..1094
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1095..1162
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1163..1267
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1268..1457
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1458..1552
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1553..1633
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     exon            1634..2263
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2244..2249
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /note="hexamer: AATAAA"
     polyA_site      2263
                     /gene="PHF1"
                     /gene_synonym="hPHF1; MTF2L2; PCL1; PHF2; TDRD19C"
                     /note="major polyA site"
ORIGIN      
        1 ctcctcctcc tgccgctgcc gctgctttgg ctgctgcgtc atacgcccca gagccgccgg
       61 gacggagggg ctgggcctgg ggaccccccg gcctccgcct gcacgccccc ccacgcccgg
      121 acgtgccctc tccgcgcggg ggactcgcct aggtctccta cgtctgcccc tgcccggctc
      181 ccggcggccc cagctgtcac cggccccccc aggatgcaat ggcgcagccc ccccggctga
      241 gccgctctgg tgcctcctca ctttgggacc cagcttctcc tgctcccacc tctggcccca
      301 ggcctcggct ttgggagggt caagatgtgc tggccagatg gactgatggg ctgctatact
      361 tgggtaccat caaaaaggtg gacagtgcta gggaggtgtg tctggtccag tttgaggatg
      421 attcgcagtt tctggttcta tggaaagaca ttagccctgc tgccctccct ggagaggaac
      481 tcctctgttg tgtctgtcgc tctgagactg tggtccctgg gaaccggctg gtcagctgtg
      541 agaagtgtcg ccatgcttat caccaggact gccatgttcc cagggctcca gcccctggag
      601 agggagaggg cacatcctgg gtatgccgcc agtgtgtctt tgcgatcgcc accaagaggg
      661 gaggtgccct gaagaagggc ccctatgccc gggccatgct gggtatgaag ctttctctgc
      721 catatggact gaaggggctg gactgggatg ctggacatct gagcaaccga cagcagagtt
      781 actgttactg tggtggccct ggggagtgga acctgaaaat gctgcagtgc cggagctgcc
      841 tgcagtggtt ccatgaggcc tgcacccagt gtctgagcaa gcccctcctc tatggggaca
      901 ggttctatga atttgaatgc tgtgtgtgtc gcgggggccc tgagaaagtc cggagactac
      961 agcttcgctg ggtggatgtg gcccatcttg tcctgtatca cctcagtgtt tgctgtaaga
     1021 agaaatactt tgattttgat cgtgagatcc tccccttcac ttctgagaat tgggacagtt
     1081 tgctcctggg ggagctttca gacaccccca aaggagaacg ttcttccagg ctcctctctg
     1141 ctcttaacag ccacaaggac cgtttcattt cagggagaga gattaagaag aggaaatgtt
     1201 tgtttggtct ccatgctcgg atgcctcccc ctgtggagcc ccctactgga gatggagcac
     1261 tcaccagctt cccttcaggg cagggccctg ggggaggggt ctcacgtccc ctggggaagc
     1321 gccggaggcc ggagccagag cccctgagga ggaggcagaa ggggaaagtg gaggagctgg
     1381 ggccaccctc agcagtgcgc aatcagcccg agccccagga gcagagggag cgggctcatc
     1441 tgcagagggc actgcaggcc tcagtgtctc caccatcccc cagccctaac cagagttacc
     1501 agggcagcag cggctacaac ttccggccca cagatgcccg ctgcctgccc agcagcccca
     1561 tccggatgtt tgcttccttc cacccttctg ccagcaccgc agggacctct ggggacagtg
     1621 gacccccaga caggtcaccc ctggaacttc acattggttt ccccacagac atccctaaaa
     1681 gtgcccccca ctcgatgact gcctcatctt cctcagtttc atccccatcc ccaggtcttc
     1741 ctagacgctc agcaccccct tctcccctgt gccgtagttt gtctcctggg actgggggag
     1801 gagtccgagg tggggttggt tacctgtccc gaggggaccc tgtccgggtc cttgctcgga
     1861 gagtacggcc tgatggctct gtgcagtacc tggttgagtg gggaggaggg ggcatcttct
     1921 gaacagcctg cctctgccca gctccccatt cacacacacc ggcactttca taccctgacc
     1981 tctgacctca cctacagctg ggatgtacct ggagagatag ggggtagttc tccctactgc
     2041 ccaggctgga atccaagagt ggggagtggg gaagaggccc tcttctctac cctccttcat
     2101 gattcctgac ccctcccatc cttcccattt cctttgatgt tattttgtta cagcttttta
     2161 aatatttttt aaaattattt aacccctggg ggcagagact gaggagggag gatgataagg
     2221 gatcccggac tctgtatgat tgaaataaag agaaataaac aaa
//
