LOCUS       NM_001024918            3940 bp    mRNA    linear   ROD 31-MAY-2024
DEFINITION  Mus musculus regulatory factor X, 4 (influences HLA class II
            expression) (Rfx4), transcript variant 1, mRNA.
ACCESSION   NM_001024918
VERSION     NM_001024918.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3940)
  AUTHORS   Bedogni,F. and Hevner,R.F.
  TITLE     Cell-Type-Specific Gene Expression in Developing Mouse Neocortex:
            Intermediate Progenitors Implicated in Axon Development
  JOURNAL   Front Mol Neurosci 14, 686034 (2021)
   PUBMED   34321999
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3940)
  AUTHORS   Shimada,I.S., Somatilaka,B.N., Hwang,S.H., Anderson,A.G.,
            Shelton,J.M., Rajaram,V., Konopka,G. and Mukhopadhyay,S.
  TITLE     Derepression of sonic hedgehog signaling upon Gpr161 deletion
            unravels forebrain and ventricular abnormalities
  JOURNAL   Dev Biol 450 (1), 47-62 (2019)
   PUBMED   30914320
REFERENCE   3  (bases 1 to 3940)
  AUTHORS   Xu,P., Morrison,J.P., Foley,J.F., Stumpo,D.J., Ward,T., Zeldin,D.C.
            and Blackshear,P.J.
  TITLE     Conditional ablation of the RFX4 isoform 1 transcription factor:
            Allele dosage effects on brain phenotype
  JOURNAL   PLoS One 13 (1), e0190561 (2018)
   PUBMED   29298325
  REMARK    GeneRIF: provide a novel conditional KO animal model in which to
            investigate the downstream genes directly and/or indirectly
            regulated by RFX4 isoform 1. This model could provide new insights
            into the pathogenesis of obstructive hydrocephalus and
            holoprosencephaly in humans, both relatively common and disabling
            birth defects
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3940)
  AUTHORS   Bae,B.I., Tietjen,I., Atabay,K.D., Evrony,G.D., Johnson,M.B.,
            Asare,E., Wang,P.P., Murayama,A.Y., Im,K., Lisgo,S.N., Overman,L.,
            Sestan,N., Chang,B.S., Barkovich,A.J., Grant,P.E., Topcu,M.,
            Politsky,J., Okano,H., Piao,X. and Walsh,C.A.
  TITLE     Evolutionarily dynamic alternative splicing of GPR56 regulates
            regional cerebral cortical patterning
  JOURNAL   Science 343 (6172), 764-768 (2014)
   PUBMED   24531968
REFERENCE   5  (bases 1 to 3940)
  AUTHORS   Feenstra,J.M., Kanaya,K., Pira,C.U., Hoffman,S.E., Eppey,R.J. and
            Oberg,K.C.
  TITLE     Detection of genes regulated by Lmx1b during limb dorsalization
  JOURNAL   Dev Growth Differ 54 (4), 451-462 (2012)
   PUBMED   22417325
REFERENCE   6  (bases 1 to 3940)
  AUTHORS   Kenney-Hunt,J.P., Vaughn,T.T., Pletscher,L.S., Peripato,A.,
            Routman,E., Cothran,K., Durand,D., Norgard,E., Perel,C. and
            Cheverud,J.M.
  TITLE     Quantitative trait loci for body size components in mice
  JOURNAL   Mamm Genome 17 (6), 526-537 (2006)
   PUBMED   16783635
REFERENCE   7  (bases 1 to 3940)
  AUTHORS   Seubert,J., Yang,B., Bradbury,J.A., Graves,J., Degraff,L.M.,
            Gabel,S., Gooch,R., Foley,J., Newman,J., Mao,L., Rockman,H.A.,
            Hammock,B.D., Murphy,E. and Zeldin,D.C.
  TITLE     Enhanced postischemic functional recovery in CYP2J2 transgenic
            hearts involves mitochondrial ATP-sensitive K+ channels and p42/p44
            MAPK pathway
  JOURNAL   Circ Res 95 (5), 506-514 (2004)
   PUBMED   15256482
REFERENCE   8  (bases 1 to 3940)
  AUTHORS   Zarbalis,K., May,S.R., Shen,Y., Ekker,M., Rubenstein,J.L. and
            Peterson,A.S.
  TITLE     A focused and efficient genetic screening strategy in the mouse:
            identification of mutations that disrupt cortical development
  JOURNAL   PLoS Biol 2 (8), E219 (2004)
   PUBMED   15314648
REFERENCE   9  (bases 1 to 3940)
  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
  REMARK    GeneRIF: mouse regulatory factor X4 transcript is expressed in the
            suprachiasmatic nucleus and regulated by light
REFERENCE   10 (bases 1 to 3940)
  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
  REMARK    GeneRIF: Data implicate the RFX4_v3 variant transcript as being
            crucial for early brain development, as well as for the genesis of
            the subcommissural organ.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BB595996.2 and AB086957.1.
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (1).
            
            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 :: AB086957.1, SRR1660821.37106.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131, SAMN01164132
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-146               BB595996.2         1-146
            147-3940            AB086957.1         1-3794
FEATURES             Location/Qualifiers
     source          1..3940
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="10"
                     /map="10 41.63 cM"
     gene            1..3940
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /note="regulatory factor X, 4 (influences HLA class II
                     expression)"
                     /db_xref="GeneID:71137"
                     /db_xref="MGI:MGI:1918387"
     exon            1..466
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     CDS             424..2631
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /note="isoform 1 is encoded by transcript variant 1;
                     transcription factor RFX4; winged-helix transcription
                     factor RFX4; regulatory factor X 4 protein"
                     /codon_start=1
                     /product="transcription factor RFX4 isoform 1"
                     /protein_id="NP_001020089.1"
                     /db_xref="CCDS:CCDS24082.1"
                     /db_xref="GeneID:71137"
                     /db_xref="MGI:MGI:1918387"
                     /translation="MHCGLLEEPDMDSTESWIERCLNESENKRYSSHTSLGNVSNDEN
                     EEKENNRASKPHSTPATLQWLEENYEIAEGVCIPRSALYMHYLDFCEKNDTQPVNAAS
                     FGKIIRQQFPQLTTRRLGTRGQSKYHYYGIAVKESSQYYDVMYSKKGAAWVSETGKRE
                     VTKQTVAYSPRSKLGTLLPDFPNVKDLNLPASLPEEKVSTFIMMYRTHCQRILDTVIR
                     ANFDEVQSFLLHFWQGMPPHMLPVLGSSTVVNIVGVCDSILYKAISGVLMPTVLQALP
                     DSLTQVIRKFAKQLDEWLKVALHDLPENLRNIKFELSRRFSQILRRQTSLNHLCQASR
                     TVIHSADITFQMLEDWRNVDLSSITKQTLYTMEDSRDEHRRLIIQLYQEFDHLLEEQS
                     PIESYIEWLDTMVDRCVVKVAAKRQGSLKKVAQQFLLMWSCFGTRVIRDMTLHSAPSF
                     GSFHLIHLMFDDYVLYLLESLHCQERANELMRAMKGEGSTAEAQEEIILTEATPPTPS
                     PGPSFSPAKSATSVEVPPPSSPVSNPSPEYTGLSTAGAMQSYTWSLTYTVTTAAGSPA
                     ENSQQLPCMRSTHMPSSSVTHRIPVYSHREEHGYTGSYNYGSYGNQHPHPLQNQYPAL
                     PHDTAISGPLHYSPYHRSSAQYPFNSPTSRMEPCLMSSTPRLHPTPVTPRWPEVPTAN
                     ACYTSPSVHSTRYGNSSDMYTPLTTRRNSEYEHMQHFPGFAYINGEASTGWAK"
     exon            467..553
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            554..614
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            615..738
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            739..800
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            801..1014
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1015..1092
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1093..1256
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1257..1357
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1358..1416
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1417..1561
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1562..1656
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1657..1774
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1775..1894
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            1895..2056
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            2057..2219
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            2220..2358
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     exon            2359..3940
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3920..3925
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /note="hexamer: AATAAA"
     polyA_site      3939
                     /gene="Rfx4"
                     /gene_synonym="4933412G19Rik; NYD-sp10"
                     /note="major polyA site"
ORIGIN      
        1 tcgccacggc cccatctgac gagcggccat tcatcaggcc cgctggccta tcaatgacat
       61 tgctcccatc ggggctccta taaaatgatg ttttttccca tgaaacatcc gcaaacattt
      121 tgacgggttt ggctttgccc gactggatta ctgagtgtcc cctcgctcgc tcgctcgctc
      181 tctcgctctc tccttcagct ctagcttcct tccttccctc gcttcttcgc ctcttttctt
      241 tccactagtt ctttcttttc cccttttatc cttttgccct ctcacccacc gtctccccct
      301 ctctctctcg ctatcccttc cttccttatt tcttccctcc cttcctccct gggcatctct
      361 agcacagggg atccccaaat atcaggactt ttggggggcg tctgtgctgt ccatgggaag
      421 agcatgcatt gtgggttact ggaggaaccc gacatggatt ccacagagag ctggattgaa
      481 agatgtctca atgaaagcga gaataaacgc tattccagtc acacatctct ggggaatgtg
      541 tctaatgatg aaaatgagga aaaagaaaat aacagagcat ccaagcccca ctccacgccg
      601 gccaccctgc aatggctgga ggaaaactat gagattgctg agggcgtctg catcccccgc
      661 agcgccctct acatgcacta cctggatttc tgtgagaaga acgacactca gcctgtcaat
      721 gctgccagct ttgggaagat cataaggcag cagtttcctc agctaaccac cagaagactc
      781 gggacccgag gacagtcaaa gtaccattac tatggcatag cggtgaagga gagctcccag
      841 tattatgatg tgatgtactc aaagaaagga gctgcctggg tgagcgagac gggcaagaga
      901 gaagtcacca agcagacggt ggcatattct ccccggtcca agcttgggac attgctgcca
      961 gactttccaa acgtcaaaga cctaaatctg ccagccagtc ttcctgagga gaaggtgtct
     1021 acctttatta tgatgtacag aacacactgt cagagaatac tggacactgt aataagagcc
     1081 aactttgatg aggttcaaag tttccttctg cacttttggc aagggatgcc gccccacatg
     1141 ctgcccgtgc taggctcctc cacggtggtg aacatcgtgg gtgtgtgtga ctccatcctc
     1201 tacaaagcca tctccggtgt gttgatgccc acggtgctgc aggcgttgcc ggacagctta
     1261 actcaggtga tccgaaagtt tgccaagcag ctggacgagt ggctgaaagt ggctctccac
     1321 gatctcccgg aaaacctgag aaacatcaaa tttgaattat caaggaggtt ttcccaaatc
     1381 ctaaggaggc aaacatcgct gaaccatctg tgccaggcat ctcgaacggt gatccacagt
     1441 gcagacatca cgttccagat gctggaggac tggaggaatg tggacctgag tagcatcacc
     1501 aagcagactc tgtataccat ggaggactct cgggatgagc accgcagact catcatccag
     1561 ttgtaccagg agtttgacca cctgctggag gaacagtccc ccatcgagtc ttacatagaa
     1621 tggctggata ccatggtaga ccgatgcgtt gtaaaggtgg ctgccaagag acaagggtct
     1681 ctgaagaaag tagcccaaca gttcctgctg atgtggtctt gctttggtac gagggtgatc
     1741 cgggacatga ccttgcacag tgcccccagc ttcgggtctt ttcacctgat tcacctgatg
     1801 ttcgacgact acgtgctcta cttgctagaa tctctgcatt gtcaggagcg ggccaacgag
     1861 ctcatgcgag ccatgaaagg agaaggaagc actgcagaag cccaggaaga gattatcttg
     1921 acagaggcta ccccaccaac cccttcacct ggtccatcat tttctccagc aaagtctgcc
     1981 acatctgtgg aggtgccacc tccctcctcc cctgtcagca acccatcccc cgaatacact
     2041 ggccttagca cagcaggagc gatgcagtca tatacgtggt cgctaacata tacagtaaca
     2101 acggctgcag ggtcaccggc tgagaactcc caacaactac cctgtatgag gagcacccat
     2161 atgccttctt cctccgtcac acacaggata ccagtctact cccacagaga ggagcatggg
     2221 tacacgggaa gctataacta cgggagctat ggcaaccagc atcctcaccc actgcagaac
     2281 cagtatccag ccttgcctca tgacacagcc atctctgggc ctctccacta ttccccttac
     2341 cacaggagct ctgcccagta ccctttcaat agccccactt ccaggatgga accttgtttg
     2401 atgagcagta ctcccaggct gcatcctacc ccagtgactc cccgatggcc agaggtgccg
     2461 actgccaacg catgctacac aagcccatct gtgcattcca cgaggtatgg aaactctagt
     2521 gacatgtaca ccccgctgac cacgcgcagg aattctgagt atgagcacat gcaacacttt
     2581 cctggctttg cttacatcaa cggagaggcc tccactggat gggctaagtg actgctttca
     2641 tagaaatcca tatttaatat taataattaa taataataat aaacccagta cccaccctcc
     2701 agaagacttt atttcaatac atcataactt gcgggctgac ctaagcatcc attctcctaa
     2761 tgaacaagag gatgttcaat gtggagtgaa tagactttag ttcagaaaca ggagtcacta
     2821 aaagtcagtg ggattgggtt tctgtagcca agccagactt gactgtttct atagagcact
     2881 atcttgggca ggccaatctg tgcctttccc ctctgttcca tgaccttgca tggcaactac
     2941 tccttgtata gggtacttat tttcttgttg acaaagctct ttagtcttga aggatggata
     3001 ctggagccag aatctggttt gtgttcttgg acgggcacat aatttaccaa gagcattcac
     3061 cttgccacct gtctgtctgt cacctcgctg tacggttacc agccctcaga catgtaatcc
     3121 acatcccgac ttcctggtga tgtcattcct acttcctgga gtccctggaa gtttttgaaa
     3181 atgctaagct ccctgctaag ttccattcgt acctgccata ttacctgcat tgtcctggac
     3241 tgtaagcact gttgttgagg gacagaagag gcctgttata tattgccttt cgttgattga
     3301 tgtctgtagg gaccagttct tctctgtaca aggatttgtc ctaagtttgc acaatggcta
     3361 gcatcagcaa aaggcaggag agggttttct taagttctgt gagaaatgtg gatttatggc
     3421 actaaacact gtcctccact gtgttacttt gcgaagctgg atggagcaga ctttcactta
     3481 gcaagcacca agtgtgaaaa caactgtctg gtttcttcat aagactagaa tactttctga
     3541 cactttgcta gaaaaaaaaa attcaaagct gtgcctttga gtctatacta tactgtgtat
     3601 gtgtggaaat aaaaaaaatg tattgtactt tgggaaaatt ttttcttagg tattttttgt
     3661 cagatttgta gctatttgtg aggtttgtta gagattaaca taggttttct ttctgtatta
     3721 taagatgcac caagcaatta tggtggacct attaccctat gggtaagaaa taaatggaaa
     3781 tatgacatcg gatgttttag caaatgttct gtaaataaaa tgtttgatca caccacccag
     3841 tgtgataatc atgtctacag ctaaaatgga aatagtttta tctgtacagt tgtgcaagat
     3901 atggatggtt tcacactcaa ataaaaagta ttgaaatgac
//
