LOCUS       NM_001206691            3698 bp    mRNA    linear   PRI 04-AUG-2024
DEFINITION  Homo sapiens regulatory factor X4 (RFX4), transcript variant 4,
            mRNA.
ACCESSION   NM_001206691
VERSION     NM_001206691.2
KEYWORDS    RefSeq.
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 3698)
  AUTHORS   Choi,W., Choe,M.S., Kim,S.M., Kim,S.J., Lee,J., Lee,Y., Lee,S.M.,
            Dho,S.H., Lee,M.Y. and Kim,L.K.
  TITLE     RFX4 is an intrinsic factor for neuronal differentiation through
            induction of proneural genes POU3F2 and NEUROD1
  JOURNAL   Cell Mol Life Sci 81 (1), 99 (2024)
   PUBMED   38386071
  REMARK    GeneRIF: RFX4 is an intrinsic factor for neuronal differentiation
            through induction of proneural genes POU3F2 and NEUROD1.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3698)
  AUTHORS   Jeong,H.Y., Kim,H.J., Kim,C.E., Lee,S., Choi,M.C. and Kim,S.H.
  TITLE     High expression of RFX4 is associated with tumor progression and
            poor prognosis in patients with glioblastoma
  JOURNAL   Int J Neurosci 131 (1), 7-14 (2021)
   PUBMED   32075484
  REMARK    GeneRIF: High expression of RFX4 is associated with tumor
            progression and poor prognosis in patients with glioblastoma.
REFERENCE   3  (bases 1 to 3698)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   4  (bases 1 to 3698)
  AUTHORS   Cobb,J., Cule,E., Moncrieffe,H., Hinks,A., Ursu,S., Patrick,F.,
            Kassoumeri,L., Flynn,E., Bulatovic,M., Wulffraat,N., van Zelst,B.,
            de Jonge,R., Bohm,M., Dolezalova,P., Hirani,S., Newman,S.,
            Whitworth,P., Southwood,T.R., De Iorio,M., Wedderburn,L.R. and
            Thomson,W.
  CONSRTM   Childhood Arthritis Response to Medication Study (CHARMS);
            Childhood Arthritis Prospective Study (CAPS); BSPAR study group
  TITLE     Genome-wide data reveal novel genes for methotrexate response in a
            large cohort of juvenile idiopathic arthritis cases
  JOURNAL   Pharmacogenomics J 14 (4), 356-364 (2014)
   PUBMED   24709693
REFERENCE   5  (bases 1 to 3698)
  AUTHORS   Zhang,D., Zeldin,D.C. and Blackshear,P.J.
  TITLE     Regulatory factor X4 variant 3: a transcription factor involved in
            brain development and disease
  JOURNAL   J Neurosci Res 85 (16), 3515-3522 (2007)
   PUBMED   17510980
  REMARK    Review article
REFERENCE   6  (bases 1 to 3698)
  AUTHORS   Matsushita,H., Uenaka,A., Ono,T., Hasegawa,K., Sato,S., Koizumi,F.,
            Nakagawa,K., Toda,M., Shingo,T., Ichikawa,T., Noguchi,Y.,
            Tamiya,T., Furuta,T., Kawase,T., Date,I. and Nakayama,E.
  TITLE     Identification of glioma-specific RFX4-E and -F isoforms and
            humoral immune response in patients
  JOURNAL   Cancer Sci 96 (11), 801-809 (2005)
   PUBMED   16271074
REFERENCE   7  (bases 1 to 3698)
  AUTHORS   Araki,R., Takahashi,H., Fukumura,R., Sun,F., Umeda,N., Sujino,M.,
            Inouye,S.T., Saito,T. and Abe,M.
  TITLE     Restricted expression and photic induction of a novel mouse
            regulatory factor X4 transcript in the suprachiasmatic nucleus
  JOURNAL   J Biol Chem 279 (11), 10237-10242 (2004)
   PUBMED   14701801
REFERENCE   8  (bases 1 to 3698)
  AUTHORS   Blackshear,P.J., Graves,J.P., Stumpo,D.J., Cobos,I.,
            Rubenstein,J.L. and Zeldin,D.C.
  TITLE     Graded phenotypic response to partial and complete deficiency of a
            brain-specific transcript variant of the winged helix transcription
            factor RFX4
  JOURNAL   Development 130 (19), 4539-4552 (2003)
   PUBMED   12925582
REFERENCE   9  (bases 1 to 3698)
  AUTHORS   Morotomi-Yano,K., Yano,K., Saito,H., Sun,Z., Iwama,A. and Miki,Y.
  TITLE     Human regulatory factor X 4 (RFX4) is a testis-specific dimeric
            DNA-binding protein that cooperates with other human RFX members
  JOURNAL   J Biol Chem 277 (1), 836-842 (2002)
   PUBMED   11682486
REFERENCE   10 (bases 1 to 3698)
  AUTHORS   Emery,P., Durand,B., Mach,B. and Reith,W.
  TITLE     RFX proteins, a novel family of DNA binding proteins conserved in
            the eukaryotic kingdom
  JOURNAL   Nucleic Acids Res 24 (5), 803-807 (1996)
   PUBMED   8600444
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AB095365.1, AK074913.1,
            AY102009.1 and AI002078.1.
            
            On Jun 2, 2019 this sequence version replaced NM_001206691.1.
            
            Summary: This gene is a member of the regulatory factor X gene
            family, which encodes transcription factors that contain a
            highly-conserved winged helix DNA binding domain. The protein
            encoded by this gene is structurally related to regulatory factors
            X1, X2, X3, and X5. It has been shown to interact with itself as
            well as with regulatory factors X2 and X3, but it does not interact
            with regulatory factor X1. Alternative splicing results in multiple
            transcript variants. [provided by RefSeq, May 2011].
            
            Transcript Variant: This variant (4, also known as RFX4_v4) uses an
            alternate 5' exon and thus differs in the 5' UTR and 5' coding
            region, compared to variant 3. The encoded isoform (d, also known
            as RFX4-C) has a distinct N-terminus and is longer than isoform c.
            
            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 :: AB095365.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1800              AB095365.1         7-1806
            1801-3100           AK074913.1         1390-2689
            3101-3692           AY102009.1         3012-3603
            3693-3698           AI002078.1         10-15               c
FEATURES             Location/Qualifiers
     source          1..3698
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q23.3"
     gene            1..3698
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="regulatory factor X4"
                     /db_xref="GeneID:5992"
                     /db_xref="HGNC:HGNC:9985"
                     /db_xref="MIM:603958"
     exon            1..199
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     CDS             130..2364
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="isoform d is encoded by transcript variant 4;
                     winged-helix transcription factor RFX4; testis development
                     protein NYD-SP10; regulatory factor X, 4 (influences HLA
                     class II expression)"
                     /codon_start=1
                     /product="transcription factor RFX4 isoform d"
                     /protein_id="NP_001193620.1"
                     /db_xref="CCDS:CCDS55880.1"
                     /db_xref="GeneID:5992"
                     /db_xref="HGNC:HGNC:9985"
                     /db_xref="MIM:603958"
                     /translation="MIKRRAHPGAGGDRTRPRRRRSTESWIERCLNESENKRYSSHTS
                     LGNVSNDENEEKENNRASKPHSTPATLQWLEENYEIAEGVCIPRSALYMHYLDFCEKN
                     DTQPVNAASFGKIIRQQFPQLTTRRLGTRGQSKYHYYGIAVKESSQYYDVMYSKKGAA
                     WVSETGKKEVSKQTVAYSPRSKLGTLLPEFPNVKDLNLPASLPEEKVSTFIMMYRTHC
                     QRILDTVIRANFDEVQSFLLHFWQGMPPHMLPVLGSSTVVNIVGVCDSILYKAISGVL
                     MPTVLQALPDSLTQVIRKFAKQLDEWLKVALHDLPENLRNIKFELSRRFSQILRRQTS
                     LNHLCQASRTVIHSADITFQMLEDWRNVDLNSITKQTLYTMEDSRDEHRKLITQLYQE
                     FDHLLEEQSPIESYIEWLDTMVDRCVVKVAAKRQGSLKKVAQQFLLMWSCFGTRVIRD
                     MTLHSAPSFGSFHLIHLMFDDYVLYLLESLHCQERANELMRAMKGEGSTAEVREEIIL
                     TEAAAPTPSPVPSFSPAKSATSVEVPPPSSPVSNPSPEYTGLSTTGAMQSYTWSLTYT
                     VTTAAGSPAENSQQLPCMRNTHVPSSSVTHRIPVYPHREEHGYTGSYNYGSYGNQHPH
                     PMQSQYPALPHDTAISGPLHYAPYHRSSAQYPFNSPTSRMEPCLMSSTPRLHPTPVTP
                     RWPEVPSANTCYTSPSVHSARYGNSSDMYTPLTTRRNSEYEHMQHFPGFAYINGEAST
                     GWAK"
     exon            200..286
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            287..347
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            348..471
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            472..533
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            534..747
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            748..825
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            826..989
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            990..1090
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1091..1149
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1150..1294
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1295..1389
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1390..1507
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1508..1627
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1628..1789
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1790..1952
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1953..2091
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            2092..3698
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3679..3684
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="hexamer: AATAAA"
     polyA_site      3698
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="major polyA site"
ORIGIN      
        1 aacccactga cctgagccac cccctggaga ggccacagct gctggcttcc tgggcttctc
       61 caaactcctg tgtgtcgcca ctgccaccgg cagggagcca ggagagagac agaaaggggc
      121 tgagacagaa tgatcaaaag gagagcccac cctggtgcgg gaggcgacag gaccaggcct
      181 cgacggcgcc gttccactga gagctggatt gaaagatgtc tcaacgaaag tgaaaacaaa
      241 cgttattcca gccacacatc tctggggaat gtttctaatg atgaaaatga ggaaaaagaa
      301 aataatagag catccaagcc ccactccact cctgctactc tgcaatggct ggaggagaac
      361 tatgagattg cagagggggt ctgcatccct cgcagtgccc tctatatgca ttacctggat
      421 ttctgcgaga agaatgatac ccaacctgtc aatgctgcca gctttggaaa gatcataagg
      481 cagcagtttc ctcagttaac caccagaaga ctcgggaccc gaggacagtc aaagtaccat
      541 tactatggca ttgcagtgaa agaaagctcc caatattatg atgtgatgta ttccaagaaa
      601 ggagctgcct gggtgagtga gacgggcaag aaagaagtga gcaaacagac agtggcatat
      661 tcaccccggt ccaaactcgg aacactgctg ccagaatttc ccaatgtcaa agatctaaat
      721 ctgccagcca gcctgcctga ggagaaggtt tctaccttta ttatgatgta cagaacacac
      781 tgtcagagaa tactggacac tgtaataaga gccaactttg atgaggttca aagtttcctt
      841 ctgcactttt ggcaaggaat gccgccccac atgctgcctg tgctgggctc ctccacggtg
      901 gtgaacattg tcggcgtgtg tgactccatc ctctacaaag ctatctccgg ggtgctgatg
      961 cccactgtgc tgcaggcatt acctgacagc ttaactcagg tgattcgaaa gtttgccaag
     1021 caactggatg agtggctaaa agtggctctc cacgacctcc cagaaaactt gcgaaacatc
     1081 aagttcgaat tgtcgagaag gttctcccaa attctgagac ggcaaacatc actaaatcat
     1141 ctctgccagg catctcgaac agtgatccac agtgcagaca tcacgttcca aatgctggaa
     1201 gactggagga acgtggacct gaacagcatc accaagcaaa ccctttacac catggaagac
     1261 tctcgcgatg agcaccggaa actcatcacc caattatatc aggagtttga ccatctcttg
     1321 gaggagcagt ctcccatcga gtcctacatt gagtggctgg ataccatggt tgaccgctgt
     1381 gttgtgaagg tggctgccaa gagacaaggg tccttgaaga aagtggccca gcagttcctc
     1441 ttgatgtggt cctgtttcgg cacaagggtg atccgggaca tgaccttgca cagcgccccc
     1501 agcttcgggt cttttcacct aattcactta atgtttgatg actacgtgct ctacctgtta
     1561 gaatctctgc actgtcagga gcgggccaat gagctcatgc gagccatgaa gggagaagga
     1621 agcactgcag aagtccgaga agagatcatc ttgacagagg ctgccgcacc aaccccttca
     1681 ccagtgccat cgttttctcc agcaaaatct gccacatctg tggaagtgcc acctccctct
     1741 tcccctgtta gcaatccttc ccctgagtac actggcctca gcactacagg agcaatgcag
     1801 tcttacacgt ggtctctaac atacacagtg acgacggctg ctgggtcccc agctgagaac
     1861 tcccaacagc tgccctgtat gaggaacact catgtgcctt cttcctccgt cacacacagg
     1921 ataccagttt atccccacag agaggaacat ggatacacgg gaagctataa ctatgggagc
     1981 tatggcaacc agcatcctca ccccatgcag agccagtatc cggccctccc tcatgacaca
     2041 gctatctctg ggccactcca ctatgcccct taccacagga gctctgcaca gtaccctttt
     2101 aatagcccca cttcccggat ggaaccttgt ttgatgagca gtactcccag actgcatcct
     2161 accccagtca ctccccgctg gccagaggtg ccctcagcca acacgtgcta cacaagcccg
     2221 tctgtgcatt ctgcgaggta cggaaactct agtgacatgt atacacctct gacaacgcgc
     2281 aggaattctg aatatgagca catgcaacac tttcctggct ttgcttacat caacggagag
     2341 gcctctacag gatgggctaa atgactgcta tcataggcat ccatatttaa tattaataat
     2401 aataattaat aataataata aacccaacac ccatccccca gaagacttta tctctataca
     2461 ttgtaactca tgggctattc ctaagtgccc attttcctaa tgaacatgag gatgggatca
     2521 atgtgggatg aataaacttt agttcagaaa caggacttac taaaagtcag tgggactggg
     2581 tttctgtagc caagccagac ttgactgttt ctgtagagca ctatctcggg caggccattc
     2641 tgtgcctttt ccctctgttc catgactttg ctttgtgttg gcaaccactt ctagtaagct
     2701 actgattttc ctgttgacaa aatctcttta gtcttgaagg atggatactg gagacagaat
     2761 ctggtttgtg ttcttggatg ggcacataat ttaccaagag cattcacctt gccatctgtc
     2821 ttgtcattgt actgtacaag gaacagccct cagacgtgtt ctgcacatcc cttcttcctg
     2881 gtggtaccat ccctatttcc tggagcacca gggctaaatg gggagctatc tggaaactct
     2941 agattttctg tcatacccac atctgtcaca gtacctgcat tgtcttggaa tgtaagcact
     3001 gtcttgaggg aaggaagagg tctgttctgt attgccttaa gttgattgag gtttgtagga
     3061 gactggttct tctacataca aggatttgtc ttaagtttgc acaatggcta gtgtcagcaa
     3121 aaggcaggag agggtttttg tttttttttt aagttctatg agaatgtgga tttatggcat
     3181 tgagtatcac actcagctct gctgtgttaa ctttgtgaaa ctggatggaa caaactttaa
     3241 cttaccaagc accaagtgtg aaagtgactt tcacggttcc ttcataaaac tataataata
     3301 tccgacactt tgatagaaaa aaattcaaag ctgtgccttt gagcctatac tatactgtgt
     3361 atgtgtggaa ataaaaatgt attgtacttt tggagaattt tttgtaggca tttttctgtc
     3421 agatttgtag taatttgtga ggtttgttag agattaatat aggttttctt tctgtattat
     3481 aaaatgcacc aagcaattat ggtggaccta ttaccctatg ggtaagaaat aaatggaaat
     3541 atgacatcgg atgtttcagc aactgttctg taaataaaat ctttgatcac accactcagt
     3601 gtgataattg tgtctacagc taaaatggaa atagttttat ctgtacagtt gtgcaagata
     3661 tgaatggttt cacactcaaa taaaaaatat tgaaacga
//
