LOCUS       NM_001355705            4369 bp    mRNA    linear   ROD 02-JUN-2024
DEFINITION  Mus musculus regulatory factor X, 5 (influences HLA class II
            expression) (Rfx5), transcript variant 2, mRNA.
ACCESSION   NM_001355705 XM_006501695
VERSION     NM_001355705.2
KEYWORDS    RefSeq.
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 4369)
  AUTHORS   Castro,W., Chelbi,S.T., Niogret,C., Ramon-Barros,C., Welten,S.P.M.,
            Osterheld,K., Wang,H., Rota,G., Morgado,L., Vivier,E., Raeber,M.E.,
            Boyman,O., Delorenzi,M., Barras,D., Ho,P.C., Oxenius,A. and
            Guarda,G.
  TITLE     The transcription factor Rfx7 limits metabolism of NK cells and
            promotes their maintenance and immunity
  JOURNAL   Nat Immunol 19 (8), 809-820 (2018)
   PUBMED   29967452
REFERENCE   2  (bases 1 to 4369)
  AUTHORS   Horiuchi,K., Perez-Cerezales,S., Papasaikas,P., Ramos-Ibeas,P.,
            Lopez-Cardona,A.P., Laguna-Barraza,R., Fonseca Balvis,N.,
            Pericuesta,E., Fernandez-Gonzalez,R., Planells,B., Viera,A.,
            Suja,J.A., Ross,P.J., Alen,F., Orio,L., Rodriguez de Fonseca,F.,
            Pintado,B., Valcarcel,J. and Gutierrez-Adan,A.
  TITLE     Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12
            Intron Splicing-Defective Zrsr1 Mutant Mice
  JOURNAL   Cell Rep 23 (1), 143-155 (2018)
   PUBMED   29617656
REFERENCE   3  (bases 1 to 4369)
  AUTHORS   Ludigs,K., Seguin-Estevez,Q., Lemeille,S., Ferrero,I., Rota,G.,
            Chelbi,S., Mattmann,C., MacDonald,H.R., Reith,W. and Guarda,G.
  TITLE     NLRC5 exclusively transactivates MHC class I and related genes
            through a distinctive SXY module
  JOURNAL   PLoS Genet 11 (3), e1005088 (2015)
   PUBMED   25811463
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 4369)
  AUTHORS   Hanna,S. and Etzioni,A.
  TITLE     MHC class I and II deficiencies
  JOURNAL   J Allergy Clin Immunol 134 (2), 269-275 (2014)
   PUBMED   25001848
  REMARK    Review article
REFERENCE   5  (bases 1 to 4369)
  AUTHORS   Karim,S.A., Johnson,K.J., Griffiths,I.R. and Vouyiouklis,D.A.
  TITLE     A physical map of the genomic region on mouse chromosome 3
            containing the hindshaker (hsh) mutation
  JOURNAL   Genomics 83 (2), 225-230 (2004)
   PUBMED   14706451
REFERENCE   6  (bases 1 to 4369)
  AUTHORS   Villard,J., Peretti,M., Masternak,K., Barras,E., Caretti,G.,
            Mantovani,R. and Reith,W.
  TITLE     A functionally essential domain of RFX5 mediates activation of
            major histocompatibility complex class II promoters by promoting
            cooperative binding between RFX and NF-Y
  JOURNAL   Mol Cell Biol 20 (10), 3364-3376 (2000)
   PUBMED   10779326
REFERENCE   7  (bases 1 to 4369)
  AUTHORS   Clausen,B.E., Burkhardt,C., Reith,W., Renkawitz,R. and Forster,I.
  TITLE     Conditional gene targeting in macrophages and granulocytes using
            LysMcre mice
  JOURNAL   Transgenic Res 8 (4), 265-277 (1999)
   PUBMED   10621974
REFERENCE   8  (bases 1 to 4369)
  AUTHORS   Clausen,B.E., Waldburger,J.M., Schwenk,F., Barras,E., Mach,B.,
            Rajewsky,K., Forster,I. and Reith,W.
  TITLE     Residual MHC class II expression on mature dendritic cells and
            activated B cells in RFX5-deficient mice
  JOURNAL   Immunity 8 (2), 143-155 (1998)
   PUBMED   9491996
REFERENCE   9  (bases 1 to 4369)
  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
REFERENCE   10 (bases 1 to 4369)
  AUTHORS   Steimle,V., Durand,B., Barras,E., Zufferey,M., Hadam,M.R., Mach,B.
            and Reith,W.
  TITLE     A novel DNA-binding regulatory factor is mutated in primary MHC
            class II deficiency (bare lymphocyte syndrome)
  JOURNAL   Genes Dev 9 (9), 1021-1032 (1995)
   PUBMED   7744245
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC087062.25.
            
            On Aug 13, 2022 this sequence version replaced NM_001355705.1.
            
            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 :: SRR13862051.3038339.1,
                                           ERR3363659.142537.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849375, SAMN00849380
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-392               AC087062.25        115585-115976
            393-524             AC087062.25        116440-116571
            525-558             AC087062.25        116777-116810
            559-641             AC087062.25        117171-117253
            642-761             AC087062.25        117697-117816
            762-881             AC087062.25        117912-118031
            882-963             AC087062.25        118146-118227
            964-1165            AC087062.25        118522-118723
            1166-1269           AC087062.25        119207-119310
            1270-4369           AC087062.25        119675-122774
FEATURES             Location/Qualifiers
     source          1..4369
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 40.74 cM"
     gene            1..4369
                     /gene="Rfx5"
                     /note="regulatory factor X, 5 (influences HLA class II
                     expression)"
                     /db_xref="GeneID:53970"
                     /db_xref="MGI:MGI:1858421"
     exon            1..392
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            393..524
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     CDS             412..2388
                     /gene="Rfx5"
                     /note="isoform 1 is encoded by transcript variant 2;
                     regulatory factor X 5; DNA-binding protein Rfx5"
                     /codon_start=1
                     /product="DNA-binding protein Rfx5 isoform 1"
                     /protein_id="NP_001342634.1"
                     /db_xref="CCDS:CCDS17598.1"
                     /db_xref="GeneID:53970"
                     /db_xref="MGI:MGI:1858421"
                     /translation="MAEDKPDAKSPKTGARPQGGADAGEPTTLLQRLRGTISKAVQNK
                     VEGILQEVQKFSDNDKLYLYLQLPSGPSVGEKSSEPSLLSNEEYMYAYRWIRNHLEEH
                     MDTCLPKQSVYDAYRKYCESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCY
                     SGIRRKTLVSMPPLPGLDLKGSESPEMGPEVSPAPRDELVEAACALTCDWAERILKRS
                     FSSIVQVARYLLQQHLISARSAHAHVLKAGGLAEEDERAPRERSLCKSKNVVESLEGG
                     GPKKPERPAQPPKEQEARAGTDLPGRAERKKSVIDSSVPAASKPQVNALVARLPVLLP
                     RAPRSLITPISGTLKVATLPLPTRVGGPQTAVPIINMILPPVPTLSGAGPGPGPGLGP
                     RFGPGPGLGPGPGPGLGAGLGPGLGPGLGAGPGPGLGAGLGAGLGLGPGRVPPRAPIL
                     PRGAENREVGISSDPRPHDKGIKRTAEVPLSEASGQDPPVKEMKHETQDTTVSEAKRK
                     RGRPRKKPGGSGERNATPEKSAAIVNSPRSPRLLWETWGSKRENNFIGRPEGPGPGGE
                     AERETVLVQGQQDGAVSKGERSLSSQEAKEAEDKIPPVTSKVSVIKGRIQKEALQLVK
                     GEADAATQGNKGLKGRVLQSSLTPEHKDPKATPP"
     exon            525..558
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            559..641
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            642..761
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            762..881
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            882..963
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            964..1165
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            1166..1269
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     exon            1270..4369
                     /gene="Rfx5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4360..4365
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rfx5"
                     /note="hexamer: TATAAA"
     polyA_site      4369
                     /gene="Rfx5"
                     /note="major polyA site"
ORIGIN      
        1 gtggggctgg gcaggagctg aggtagccac agggtagttt ctctttctct ctcacctatc
       61 taatgtccgt gctggaaggc gacggttccg aggtaggagg ggcaacagca ctccggagct
      121 agcaggacca gctccttgcc cctgcgcacg tgcccgaatc tgggaccctg ttccccgcag
      181 ggtttcctgc gcccagcccc ctgagttcgg agacctagcc cagcacctgg ggttggggtg
      241 gaggggcccg aggggagtgg ggacgcttcg gagtgggatg tcgtgggatg acgtagggtc
      301 cgcgccgcgg cgaggggggc agcgggggaa gccgtggcga gactcagtaa tgagaacttg
      361 ggcccagttt ttttcaaacc tggaaaggcc gactgtagcc ctcatgctgg gatggcagaa
      421 gataaacctg atgctaagag ccccaagact ggggcaaggc cccaaggtgg tgctgacgct
      481 ggagaaccta ccaccctcct ccaaaggctc cgaggtacca tttccaaggc cgtgcagaac
      541 aaagtagagg gaattctgca agaagtacag aaattctcgg acaacgacaa gctgtacctc
      601 taccttcagc tcccatcggg gcccagcgtt ggcgagaaga gctcagagcc aagtctgctc
      661 agcaatgagg agtatatgta tgcctatagg tggatccgca accacctgga agagcacatg
      721 gatacctgcc tgccaaagca gagcgtctat gatgcctatc gaaagtactg cgagagcctc
      781 gcctgttgcc gcccgctcag cacagccaac ttcggtaaaa tcatcagaga gatcttccct
      841 gacatcaagg cccgaagact cggtggccgg ggccagtcca aatattgcta cagtggcatt
      901 cgaaggaaga ccttggtatc catgccacca ttgcctggac tcgacttgaa gggatctgaa
      961 agtccagaaa tgggcccaga agtaagccca gcacctcggg atgaactggt agaagcagcc
     1021 tgtgccctga cttgtgactg ggcagagcgg atcctgaagc ggtccttcag ttccatcgtc
     1081 caggtcgccc gctacctcct gcagcagcat ctcatctctg cccggtcggc acatgctcat
     1141 gtgcttaagg ccggggggct tgctgaagag gatgaaagag cccctcgaga acggtcatta
     1201 tgtaagtcca agaatgtcgt agaaagcctg gaagggggag gccctaagaa accagagaga
     1261 ccggcccagc ctcctaaaga gcaagaagcc cgagctggga cagaccttcc agggcgtgca
     1321 gaacggaaga agagtgtaat tgacagctcg gttccagcag ccagtaagcc acaagttaat
     1381 gctcttgtgg cccgactgcc tgtgctgctt ccaagagcac cacgatcact tatcacaccc
     1441 atttcaggca ctctgaaagt agctacgctg cctctaccca ctagggttgg agggccccag
     1501 acagctgtgc ccatcatcaa catgatctta ccacctgttc ctactttgtc aggggctggg
     1561 cctgggcctg ggcctggcct tgggcctagg tttgggccag ggcctgggct tgggcctggg
     1621 ccggggcctg gtctgggggc tggtctgggg cctgggttag ggcctgggct tggagctgga
     1681 ccagggcccg ggcttggagc tgggcttggg gctggcctag ggcttgggcc tgggcgagtt
     1741 ccacctagag cacccattct gcctcgaggt gcagagaaca gggaggtagg cataagtagt
     1801 gatccaagac ctcatgacaa gggtatcaaa aggacagctg aagtgcctct gagtgaggcc
     1861 agtgggcagg acccaccagt taaagaaatg aagcacgaaa cacaggatac tacagtaagt
     1921 gaagcaaaaa ggaagcgagg acgccctcga aagaagccag gagggagtgg ggaaagaaac
     1981 gctactcctg agaagtctgc agctattgtg aactctcccc gatccccaag gctactctgg
     2041 gagacatggg gctcaaaaag agaaaacaac ttcattggga gaccagaagg accagggcca
     2101 gggggtgagg ctgagcggga aacagtgctt gtgcaaggtc agcaagatgg tgctgtttcc
     2161 aaaggagaaa ggagcttgag ttcccaggaa gccaaagaag cagaagataa aattcctcct
     2221 gtcacttcaa aagtgagtgt tatcaagggc agaattcaaa aagaggctct tcagttggta
     2281 aagggagagg ctgatgctgc aacacagggc aacaaagggt taaagggtcg tgtacttcaa
     2341 agttccctaa cccctgagca taaagacccc aaagcaacac ccccatgata gacagatagg
     2401 tctgtggggg aagagtggct atgttcatgt gagctctgcc tgctgcctgg cagaggccct
     2461 tcactgagcc tccttctcat ccagctagtc ttcccccaca gggaacccag tggcctggct
     2521 tgctttgtgc ctcgtggctg cttcaggcct ttctagctca gtaccatggc tttaatacaa
     2581 acagcaaatc tgtaatgact tcccacctat atccctgtgt tctcctagga gatagggtaa
     2641 gtaggttagg gatattctgg cttctaatca tagggaactt aactcaaaac tcattaaaga
     2701 taaaagcagt ttatcagctg aagttgcaga atcaagaggc agtcctggct gcaggtgagg
     2761 cttgatctga ttgcacactc tgttcttctg cttcacataa tgtaaaacca tccttagttt
     2821 ggaccacttc acagccacca acactcccag gcttctgttt gaccgttata tctaagcaga
     2881 aagaaagggt atctatcatt gtgccaggaa tcctagcaaa agcccaaaga tttaccatga
     2941 ttaaccagcc aaggtcagtt ccacccttgg ccagctagta tggccaggaa gatgtttatg
     3001 caaatgtgtc tctacacatc gtggaccacc cttgggaaag ggtggagtcc gccgtctcac
     3061 agtcccaggt tccccagatg gaggcttggg tggaggatgg aattgttgct ggggagcagc
     3121 taacgaccgc tgggtgcggt ttagcttgct aggctgggat gagctggact gctgcctgtc
     3181 ccctgaacct tgcatctccc tcagtgcagc tctaactttt atctcattgt agcctcggaa
     3241 ggacagagaa ggaagccatt ctcgttagtc tcttcattct tacaggacag ctttcgcacc
     3301 tctgtctccc agaacaagct ccttttaggg tctgaatctt aaactttctc cgcagccgtg
     3361 tttcctacct cccaacctag tgtcaccttc tcagaggata tgaatgcccc tcccaagcca
     3421 tttcattaca ttaccttcat tctgcagcca ccagatgtca tgcacttgtc acatgtgtca
     3481 ggacctagcc aggactgtgg gcttaggctg gattaacaga tgctgcgagt cagggagcac
     3541 ctgcaggaag gatgcagacg ctccagctgt gtccttggga acagcaggaa accagcccat
     3601 attaatcaag gacctactcc gtcctcccca caggacagct tcttgtcagg gaatcttggt
     3661 tttattccca agaaatagat tttctttcag ggagatacca cccatttgtc catttatttc
     3721 catgagaaca gattttttaa aaattataag taatctttga tatctataaa gaaatatgta
     3781 ctataaatta tgaaatgcaa tgaataccta tgacccatca ttcaatttat acattgaaag
     3841 tagttttttc ccccttgccc ggcctcttcc tagaggtaat cactgtcttt aatttttggt
     3901 tattaatcat ttgtttatat atattggcca tgtgtatata tattctttag gaatgtataa
     3961 ttttgtattg cttgtatttt tagctttaaa aaatgttgtc ctgtgttcct tgaggtttgc
     4021 ttttttgcac ttacccattg tttctccgac tcctctgttg taattgctat gacttgttcc
     4081 tctgcatctg tataataccc catcaagcaa cttagccact cacctactga gtaacacttg
     4141 ggctgtcggc aggcttctgt tattatacac aatgctgcta tgaacattct tgtatatgag
     4201 tgcctttgtt tttagtaaga tttctaaaga ggtttctaag atggtccttt tggtctgtgt
     4261 accctctgag ctggggactg ttgcctcttg tcttacttta tggaagagtt tacatcacat
     4321 agaaatgaac tgttcttgaa tgtttgataa aaactcacct ataaagcca
//
