LOCUS       NM_000538               2306 bp    mRNA    linear   PRI 21-SEP-2024
DEFINITION  Homo sapiens regulatory factor X associated protein (RFXAP), mRNA.
ACCESSION   NM_000538
VERSION     NM_000538.4
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 2306)
  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   2  (bases 1 to 2306)
  AUTHORS   Ding,G., Xu,X., Li,D., Chen,Y., Wang,W., Ping,D., Jia,S. and Cao,L.
  TITLE     Fisetin inhibits proliferation of pancreatic adenocarcinoma by
            inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36
            demethylation
  JOURNAL   Cell Death Dis 11 (10), 893 (2020)
   PUBMED   33093461
  REMARK    GeneRIF: Fisetin inhibits proliferation of pancreatic
            adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent
            histone H3K36 demethylation.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2306)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Paulo,J.A., Cannon,J.R., Ting,L.,
            Baltier,K., Colby,G., Gebreab,F., Gygi,M.P., Parzen,H., Szpyt,J.,
            Tam,S., Zarraga,G., Pontano-Vaites,L., Swarup,S., White,A.E.,
            Schweppe,D.K., Rad,R., Erickson,B.K., Obar,R.A., Guruharsha,K.G.,
            Li,K., Artavanis-Tsakonas,S., Gygi,S.P. and Harper,J.W.
  TITLE     Architecture of the human interactome defines protein communities
            and disease networks
  JOURNAL   Nature 545 (7655), 505-509 (2017)
   PUBMED   28514442
REFERENCE   4  (bases 1 to 2306)
  AUTHORS   Hein,M.Y., Hubner,N.C., Poser,I., Cox,J., Nagaraj,N., Toyoda,Y.,
            Gak,I.A., Weisswange,I., Mansfeld,J., Buchholz,F., Hyman,A.A. and
            Mann,M.
  TITLE     A human interactome in three quantitative dimensions organized by
            stoichiometries and abundances
  JOURNAL   Cell 163 (3), 712-723 (2015)
   PUBMED   26496610
REFERENCE   5  (bases 1 to 2306)
  AUTHORS   Ding,G., Zhou,L., Qian,Y., Fu,M., Chen,J., Chen,J., Xiang,J.,
            Wu,Z., Jiang,G. and Cao,L.
  TITLE     Pancreatic cancer-derived exosomes transfer miRNAs to dendritic
            cells and inhibit RFXAP expression via miR-212-3p
  JOURNAL   Oncotarget 6 (30), 29877-29888 (2015)
   PUBMED   26337469
  REMARK    GeneRIF: Data show a negative correlation between microRNA
            miR-212-3p and regulatory factor X-associated protein (RFXAP) in
            pancreatic cancer (PC) tissue.
REFERENCE   6  (bases 1 to 2306)
  AUTHORS   Masternak,K., Barras,E., Zufferey,M., Conrad,B., Corthals,G.,
            Aebersold,R., Sanchez,J.C., Hochstrasser,D.F., Mach,B. and Reith,W.
  TITLE     A gene encoding a novel RFX-associated transactivator is mutated in
            the majority of MHC class II deficiency patients
  JOURNAL   Nat Genet 20 (3), 273-277 (1998)
   PUBMED   9806546
REFERENCE   7  (bases 1 to 2306)
  AUTHORS   Villard,J., Lisowska-Grospierre,B., van den Elsen,P., Fischer,A.,
            Reith,W. and Mach,B.
  TITLE     Mutation of RFXAP, a regulator of MHC class II genes, in primary
            MHC class II deficiency
  JOURNAL   N Engl J Med 337 (11), 748-753 (1997)
   PUBMED   9287230
REFERENCE   8  (bases 1 to 2306)
  AUTHORS   Durand,B., Sperisen,P., Emery,P., Barras,E., Zufferey,M., Mach,B.
            and Reith,W.
  TITLE     RFXAP, a novel subunit of the RFX DNA binding complex is mutated in
            MHC class II deficiency
  JOURNAL   EMBO J 16 (5), 1045-1055 (1997)
   PUBMED   9118943
REFERENCE   9  (bases 1 to 2306)
  AUTHORS   Mach,B., Steimle,V., Martinez-Soria,E. and Reith,W.
  TITLE     Regulation of MHC class II genes: lessons from a disease
  JOURNAL   Annu Rev Immunol 14, 301-331 (1996)
   PUBMED   8717517
  REMARK    Review article
REFERENCE   10 (bases 1 to 2306)
  AUTHORS   Reith,W., Siegrist,C.A., Durand,B., Barras,E. and Mach,B.
  TITLE     Function of major histocompatibility complex class II promoters
            requires cooperative binding between factors RFX and NF-Y
  JOURNAL   Proc Natl Acad Sci U S A 91 (2), 554-558 (1994)
   PUBMED   8290561
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BI823132.1, BC026088.1 and
            AL159973.16.
            
            On Dec 4, 2019 this sequence version replaced NM_000538.3.
            
            Summary: Major histocompatibility (MHC) class II molecules are
            transmembrane proteins that have a central role in development and
            control of the immune system. The protein encoded by this gene,
            along with regulatory factor X-associated ankyrin-containing
            protein and regulatory factor-5, forms a complex that binds to the
            X box motif of certain MHC class II gene promoters and activates
            their transcription. Once bound to the promoter, this complex
            associates with the non-DNA-binding factor MHC class II
            transactivator, which controls the cell type specificity and
            inducibility of MHC class II gene expression. Mutations in this
            gene have been linked to bare lymphocyte syndrome type II,
            complementation group D. Transcript variants utilizing different
            polyA signals have been found for this gene. [provided by RefSeq,
            Jul 2008].
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because transcript sequence consistent with
            the reference genome assembly was not available for all regions of
            the RefSeq transcript. The extent of this transcript is supported
            by transcript alignments.
            
            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 :: BC026088.1, SRR11853558.6302.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000255476.3/ ENSP00000255476.3
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-247               BI823132.1         21-267
            248-987             BC026088.1         247-986
            988-2306            AL159973.16        60904-62222
FEATURES             Location/Qualifiers
     source          1..2306
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="13"
                     /map="13q13.3"
     gene            1..2306
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /note="regulatory factor X associated protein"
                     /db_xref="GeneID:5994"
                     /db_xref="HGNC:HGNC:9988"
                     /db_xref="MIM:601861"
     exon            1..736
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /inference="alignment:Splign:2.1.0"
     CDS             137..955
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /note="RFX-associated protein; RFX DNA-binding complex 36
                     kDa subunit"
                     /codon_start=1
                     /product="regulatory factor X-associated protein"
                     /protein_id="NP_000529.1"
                     /db_xref="CCDS:CCDS9359.1"
                     /db_xref="GeneID:5994"
                     /db_xref="HGNC:HGNC:9988"
                     /db_xref="MIM:601861"
                     /translation="MEAQGVAEGAGPGAASGVPHPAALAPAAAPTLAPASVAAAASQF
                     TLLVMQPCAGQDEAAAPGGSVGAGKPVRYLCEGAGDGEEEAGEDEADLLDTSDPPGGG
                     ESAASLEDLEDEETHSGGEGSSGGARRRGSGGGSMSKTCTYEGCSETTSQVAKQRKPW
                     MCKKHRNKMYKDKYKKKKSDQALNCGGTASTGSAGNVKLEESADNILSIVKQRTGSFG
                     DRPARPTLLEQVLNQKRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQFPGTSM"
     exon            737..844
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /inference="alignment:Splign:2.1.0"
     exon            845..2306
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2281..2286
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /note="hexamer: ATTAAA"
     polyA_site      2306
                     /gene="RFXAP"
                     /gene_synonym="MHC2D4"
                     /note="major polyA site"
ORIGIN      
        1 aggcgcagtc ggggcgcctt cccggtatag gcgcctttta ccccagcgtg tcctgagtct
       61 ttggttcgcg aagtgccgtt aggccaagca ggtgctaaaa gcccggggtc gtggaccccg
      121 gccaggtctt agcagcatgg aggcgcaggg tgtagcggag ggcgcggggc cgggcgccgc
      181 cagcggcgtg ccccaccccg cggccctagc cccggctgcg gctcccacct tggcgccagc
      241 ctcggtggcg gccgcggcct ctcaattcac cctgctagtg atgcaaccct gtgctgggca
      301 ggacgaggct gcggcccccg ggggcagcgt tggggcgggc aagcccgtta ggtacctgtg
      361 cgaaggggcc ggggatggcg aagaggaggc tggggaggac gaggcggacc tgttagacac
      421 ttcggaccct ccggggggag gcgagagcgc ggctagtttg gaggatctag aggacgagga
      481 gactcactcg gggggcgagg gcagcagcgg gggcgcccgg aggcggggca gcggtggggg
      541 cagcatgagc aagacctgca cctacgaagg ctgcagcgag accacgagcc aggtggccaa
      601 gcagcgcaaa ccgtggatgt gcaagaaaca ccgcaacaag atgtacaagg acaagtataa
      661 aaagaagaag agcgaccagg ccctgaactg cggtgggact gcctcgactg gcagcgcggg
      721 aaacgtcaaa ctcgaggaaa gtgcagataa catactctcc attgttaaac aaagaacagg
      781 atcttttggg gatcgtcctg caagacctac tcttttagaa caagtgttaa atcaaaaaag
      841 actgtcgtta ctaagaagtc cagaagtagt gcaattttta cagaaacagc aacagctatt
      901 aaatcagcaa gttttggagc aaagacaaca gcagtttcca ggaacatcaa tgtgagggaa
      961 cttaccaaga acatctacat ggttttttat cttattgtaa tagatgagca tattttttta
     1021 ccagacataa atggggtaat aatctatgcc tgtagaacat aaacattttc ctgtaaatgt
     1081 atgtgtgcat ttggggataa gtaagtattg cactttgtgc atctaatctt tcagattact
     1141 gtgagtttga agaagtcagc ttatctttcc aaataacatt taattataat gttttttaaa
     1201 aaatatattc ctcttcagtc attgttactg aaggtaatga agcagttact ttctgtggaa
     1261 gtcataaagt taatagatat taatcttgac tcatctagct cagtggttct catcaagggt
     1321 caatttgatt gtcatagtga ccttgaaaac cactggcttt tagtgagtgg ccaggaatgc
     1381 taaatgttct gcagtgtcag gggtagtccc acatactaaa gattgtctca cccgcagtgc
     1441 caataacact cctaagaaat gttgatggct attttgtggt gctaacatgt agttggggca
     1501 cctataattg ggttctctta ataacctttc tttgcagtta agactgaagc tgtcaaagag
     1561 gtaagcacat tttatataga cgtaaggaaa gtgattattg tttaatatct gtgaatttag
     1621 gatgtgcatc tcttttcaga ggtgtgttag taaaacctga cggattaact aagcacactg
     1681 ggatgtgtct cctacagttg gcttctctct ttgatgttac ctgttagtgc tgatctctta
     1741 aagcagacat ttcttgtttg ttgaatttgt gaacagtata gatctcagcc caccaatgcc
     1801 aagacaaaat tatttttctt atacttattt tttattaaac aaaatgaaaa agatcctttt
     1861 caaaaaggtg atcctgaaaa taaaactaac actccagtat tttgtcattg tttttcgcaa
     1921 ttgagctatc tgaaaactgt tattcctaag taatgttcaa aaatgataag taatctggat
     1981 acctttttct tatactttct cctaggaaaa ctttaaaact ttaaaaaggc aaacctacca
     2041 ataggaataa caaattaaat gtcaagagag tatatccaat attaggatat aaatgtatgt
     2101 gtctcaagtt taactctaca aaaatttgtt acttgttttt taaactctat atataaagtt
     2161 cgacttaatc atggctgttc taagaagtac ttatggagag caagaacgtt tttgttcatt
     2221 tcttaatgtg tgtgttttta cttgcatatc tgttcaaaac acttttaaca aaattaattc
     2281 attaaagtcc agttgttgac ctttga
//
