LOCUS       NM_213594               3859 bp    mRNA    linear   PRI 03-OCT-2024
DEFINITION  Homo sapiens regulatory factor X4 (RFX4), transcript variant 3,
            mRNA.
ACCESSION   NM_213594
VERSION     NM_213594.3
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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 3859)
  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 AB095366.1, AY102009.1 and
            AI002078.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 30, 2019 this sequence version replaced NM_213594.2.
            
            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 (3, also known as RFX4_v3)
            represents the longest transcript and encodes isoform c, also known
            as RFX4-D.
            
            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 :: AB095366.1, AY102009.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145743, SAMEA2154665
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000392842.6/ ENSP00000376585.1
            RefSeq Select criteria :: based on conservation
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2053              AB095366.1         98-2150
            2054-3853           AY102009.1         1804-3603
            3854-3859           AI002078.1         10-15               c
FEATURES             Location/Qualifiers
     source          1..3859
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q23.3"
     gene            1..3859
                     /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..360
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     CDS             318..2525
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="isoform c is encoded by transcript variant 3;
                     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 c"
                     /protein_id="NP_998759.1"
                     /db_xref="CCDS:CCDS9106.1"
                     /db_xref="GeneID:5992"
                     /db_xref="HGNC:HGNC:9985"
                     /db_xref="MIM:603958"
                     /translation="MHCGLLEEPDMDSTESWIERCLNESENKRYSSHTSLGNVSNDEN
                     EEKENNRASKPHSTPATLQWLEENYEIAEGVCIPRSALYMHYLDFCEKNDTQPVNAAS
                     FGKIIRQQFPQLTTRRLGTRGQSKYHYYGIAVKESSQYYDVMYSKKGAAWVSETGKKE
                     VSKQTVAYSPRSKLGTLLPEFPNVKDLNLPASLPEEKVSTFIMMYRTHCQRILDTVIR
                     ANFDEVQSFLLHFWQGMPPHMLPVLGSSTVVNIVGVCDSILYKAISGVLMPTVLQALP
                     DSLTQVIRKFAKQLDEWLKVALHDLPENLRNIKFELSRRFSQILRRQTSLNHLCQASR
                     TVIHSADITFQMLEDWRNVDLNSITKQTLYTMEDSRDEHRKLITQLYQEFDHLLEEQS
                     PIESYIEWLDTMVDRCVVKVAAKRQGSLKKVAQQFLLMWSCFGTRVIRDMTLHSAPSF
                     GSFHLIHLMFDDYVLYLLESLHCQERANELMRAMKGEGSTAEVREEIILTEAAAPTPS
                     PVPSFSPAKSATSVEVPPPSSPVSNPSPEYTGLSTTGAMQSYTWSLTYTVTTAAGSPA
                     ENSQQLPCMRNTHVPSSSVTHRIPVYPHREEHGYTGSYNYGSYGNQHPHPMQSQYPAL
                     PHDTAISGPLHYAPYHRSSAQYPFNSPTSRMEPCLMSSTPRLHPTPVTPRWPEVPSAN
                     TCYTSPSVHSARYGNSSDMYTPLTTRRNSEYEHMQHFPGFAYINGEASTGWAK"
     exon            361..447
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            448..508
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            509..632
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            633..694
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            695..908
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            909..986
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            987..1150
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1151..1251
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1252..1310
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1311..1455
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1456..1550
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1551..1668
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1669..1788
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1789..1950
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            1951..2113
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            2114..2252
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     exon            2253..3859
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3840..3845
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="hexamer: AATAAA"
     polyA_site      3859
                     /gene="RFX4"
                     /gene_synonym="NYD-SP10"
                     /note="major polyA site"
ORIGIN      
        1 gcaaacattt tgacgggttt ggctttgccc ggctggatta ctgagtgtcc ccttgctcgc
       61 tcgctttttc tctctccccc ttctccgagc tcgctccctt ctctccctct ctctcctctt
      121 ttcttctttc tcttttcttt cctcttcttt ttcttttctt ttcctttcct cctttatcct
      181 tgtgccccct cactttctgc gtctctctct ctccccttct ccctccctcc ctcccttcct
      241 ccctgggcat ctctagcaca ggggatcccc aaacatcagg acttttgggg ggcgcctgtg
      301 ctgtccatgg gaagagcatg cattgtgggt tactggagga acccgacatg gattccacag
      361 agagctggat tgaaagatgt ctcaacgaaa gtgaaaacaa acgttattcc agccacacat
      421 ctctggggaa tgtttctaat gatgaaaatg aggaaaaaga aaataataga gcatccaagc
      481 cccactccac tcctgctact ctgcaatggc tggaggagaa ctatgagatt gcagaggggg
      541 tctgcatccc tcgcagtgcc ctctatatgc attacctgga tttctgcgag aagaatgata
      601 cccaacctgt caatgctgcc agctttggaa agatcataag gcagcagttt cctcagttaa
      661 ccaccagaag actcgggacc cgaggacagt caaagtacca ttactatggc attgcagtga
      721 aagaaagctc ccaatattat gatgtgatgt attccaagaa aggagctgcc tgggtgagtg
      781 agacgggcaa gaaagaagtg agcaaacaga cagtggcata ttcaccccgg tccaaactcg
      841 gaacactgct gccagaattt cccaatgtca aagatctaaa tctgccagcc agcctgcctg
      901 aggagaaggt ttctaccttt attatgatgt acagaacaca ctgtcagaga atactggaca
      961 ctgtaataag agccaacttt gatgaggttc aaagtttcct tctgcacttt tggcaaggaa
     1021 tgccgcccca catgctgcct gtgctgggct cctccacggt ggtgaacatt gtcggcgtgt
     1081 gtgactccat cctctacaaa gctatctccg gggtgctgat gcccactgtg ctgcaggcat
     1141 tacctgacag cttaactcag gtgattcgaa agtttgccaa gcaactggat gagtggctaa
     1201 aagtggctct ccacgacctc ccagaaaact tgcgaaacat caagttcgaa ttgtcgagaa
     1261 ggttctccca aattctgaga cggcaaacat cactaaatca tctctgccag gcatctcgaa
     1321 cagtgatcca cagtgcagac atcacgttcc aaatgctgga agactggagg aacgtggacc
     1381 tgaacagcat caccaagcaa accctttaca ccatggaaga ctctcgcgat gagcaccgga
     1441 aactcatcac ccaattatat caggagtttg accatctctt ggaggagcag tctcccatcg
     1501 agtcctacat tgagtggctg gataccatgg ttgaccgctg tgttgtgaag gtggctgcca
     1561 agagacaagg gtccttgaag aaagtggccc agcagttcct cttgatgtgg tcctgtttcg
     1621 gcacaagggt gatccgggac atgaccttgc acagcgcccc cagcttcggg tcttttcacc
     1681 taattcactt aatgtttgat gactacgtgc tctacctgtt agaatctctg cactgtcagg
     1741 agcgggccaa tgagctcatg cgagccatga agggagaagg aagcactgca gaagtccgag
     1801 aagagatcat cttgacagag gctgccgcac caaccccttc accagtgcca tcgttttctc
     1861 cagcaaaatc tgccacatct gtggaagtgc cacctccctc ttcccctgtt agcaatcctt
     1921 cccctgagta cactggcctc agcactacag gagcaatgca gtcttacacg tggtctctaa
     1981 catacacagt gacgacggct gctgggtccc cagctgagaa ctcccaacag ctgccctgta
     2041 tgaggaacac tcatgtgcct tcttcctccg tcacacacag gataccagtt tatccccaca
     2101 gagaggaaca tggatacacg ggaagctata actatgggag ctatggcaac cagcatcctc
     2161 accccatgca gagccagtat ccggccctcc ctcatgacac agctatctct gggccactcc
     2221 actatgcccc ttaccacagg agctctgcac agtacccttt taatagcccc acttcccgga
     2281 tggaaccttg tttgatgagc agtactccca gactgcatcc taccccagtc actccccgct
     2341 ggccagaggt gccctcagcc aacacgtgct acacaagccc gtctgtgcat tctgcgaggt
     2401 acggaaactc tagtgacatg tatacacctc tgacaacgcg caggaattct gaatatgagc
     2461 acatgcaaca ctttcctggc tttgcttaca tcaacggaga ggcctctaca ggatgggcta
     2521 aatgactgct atcataggca tccatattta atattaataa taataattaa taataataat
     2581 aaacccaaca cccatccccc agaagacttt atctctatac attgtaactc atgggctatt
     2641 cctaagtgcc cattttccta atgaacatga ggatgggatc aatgtgggat gaataaactt
     2701 tagttcagaa acaggactta ctaaaagtca gtgggactgg gtttctgtag ccaagccaga
     2761 cttgactgtt tctgtagagc actatctcgg gcaggccatt ctgtgccttt tccctctgtt
     2821 ccatgacttt gctttgtgtt ggcaaccact tctagtaagc tactgatttt cctgttgaca
     2881 aaatctcttt agtcttgaag gatggatact ggagacagaa tctggtttgt gttcttggat
     2941 gggcacataa tttaccaaga gcattcacct tgccatctgt cttgtcattg tactgtacaa
     3001 ggaacagccc tcagacgtgt tctgcacatc ccttcttcct ggtggtacca tccctatttc
     3061 ctggagcacc agggctaaat ggggagctat ctggaaactc tagattttct gtcataccca
     3121 catctgtcac agtacctgca ttgtcttgga atgtaagcac tgtcttgagg gaaggaagag
     3181 gtctgttctg tattgcctta agttgattga ggtttgtagg agactggttc ttctacatac
     3241 aaggatttgt cttaagtttg cacaatggct agtgtcagca aaaggcagga gagggttttt
     3301 gttttttttt taagttctat gagaatgtgg atttatggca ttgagtatca cactcagctc
     3361 tgctgtgtta actttgtgaa actggatgga acaaacttta acttaccaag caccaagtgt
     3421 gaaagtgact ttcacggttc cttcataaaa ctataataat atccgacact ttgatagaaa
     3481 aaaattcaaa gctgtgcctt tgagcctata ctatactgtg tatgtgtgga aataaaaatg
     3541 tattgtactt ttggagaatt ttttgtaggc atttttctgt cagatttgta gtaatttgtg
     3601 aggtttgtta gagattaata taggttttct ttctgtatta taaaatgcac caagcaatta
     3661 tggtggacct attaccctat gggtaagaaa taaatggaaa tatgacatcg gatgtttcag
     3721 caactgttct gtaaataaaa tctttgatca caccactcag tgtgataatt gtgtctacag
     3781 ctaaaatgga aatagtttta tctgtacagt tgtgcaagat atgaatggtt tcacactcaa
     3841 ataaaaaata ttgaaacga
//
