LOCUS       NM_001079962            2869 bp    mRNA    linear   VRT 19-APR-2025
DEFINITION  Danio rerio nuclear factor I/A (nfia), mRNA.
ACCESSION   NM_001079962 XM_679514 XM_679693
VERSION     NM_001079962.1
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 2869)
  AUTHORS   Emmerich,K., Walker,S.L., Wang,G., White,D.T., Ceisel,A., Wang,F.,
            Teng,Y., Chunawala,Z., Graziano,G., Nimmagadda,S., Saxena,M.T.,
            Qian,J. and Mumm,J.S.
  TITLE     Transcriptomic comparison of two selective retinal cell ablation
            paradigms in zebrafish reveals shared and cell-specific
            regenerative responses
  JOURNAL   PLoS Genet 19 (10), e1010905 (2023)
   PUBMED   37819938
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2869)
  AUTHORS   Shainer,I., Kuehn,E., Laurell,E., Al Kassar,M., Mokayes,N.,
            Sherman,S., Larsch,J., Kunst,M. and Baier,H.
  TITLE     A single-cell resolution gene expression atlas of the larval
            zebrafish brain
  JOURNAL   Sci Adv 9 (8), eade9909 (2023)
   PUBMED   36812331
REFERENCE   3  (bases 1 to 2869)
  AUTHORS   Ogura,Y., Uehara,T., Ujibe,K., Yoshihashi,H., Yamada,M., Suzuki,H.,
            Takenouchi,T., Kosaki,K. and Hirata,H.
  TITLE     The p.Thr395Met missense variant of NFIA found in a patient with
            intellectual disability is a defective variant
  JOURNAL   Am J Med Genet A 188 (4), 1184-1192 (2022)
   PUBMED   35018717
REFERENCE   4  (bases 1 to 2869)
  AUTHORS   Ogawa,Y., Shiraki,T., Fukada,Y. and Kojima,D.
  TITLE     Foxq2 determines blue cone identity in zebrafish
  JOURNAL   Sci Adv 7 (41), eabi9784 (2021)
   PUBMED   34613771
REFERENCE   5  (bases 1 to 2869)
  AUTHORS   Uehara,T., Sanuki,R., Ogura,Y., Yokoyama,A., Yoshida,T.,
            Futagawa,H., Yoshihashi,H., Yamada,M., Suzuki,H., Takenouchi,T.,
            Matsubara,K., Hirata,H., Kosaki,K. and Takano-Shimizu,T.
  TITLE     Recurrent NFIA K125E substitution represents a loss-of-function
            allele: Sensitive in vitro and in vivo assays for nontruncating
            alleles
  JOURNAL   Am J Med Genet A 185 (7), 2084-2093 (2021)
   PUBMED   33973697
  REMARK    GeneRIF: Recurrent NFIA K125E substitution represents a
            loss-of-function allele: Sensitive in vitro and in vivo assays for
            nontruncating alleles.
REFERENCE   6  (bases 1 to 2869)
  AUTHORS   Takeuchi,M., Yamaguchi,S., Sakakibara,Y., Hayashi,T., Matsuda,K.,
            Hara,Y., Tanegashima,C., Shimizu,T., Kuraku,S. and Hibi,M.
  TITLE     Gene expression profiling of granule cells and Purkinje cells in
            the zebrafish cerebellum
  JOURNAL   J Comp Neurol 525 (7), 1558-1585 (2017)
   PUBMED   27615194
  REMARK    Erratum:[J Comp Neurol. 2021 Aug 1;529(11):3127. doi:
            10.1002/cne.25135. PMID: 34050936]
REFERENCE   7  (bases 1 to 2869)
  AUTHORS   Elkon,R., Milon,B., Morrison,L., Shah,M., Vijayakumar,S.,
            Racherla,M., Leitch,C.C., Silipino,L., Hadi,S., Weiss-Gayet,M.,
            Barras,E., Schmid,C.D., Ait-Lounis,A., Barnes,A., Song,Y.,
            Eisenman,D.J., Eliyahu,E., Frolenkov,G.I., Strome,S.E., Durand,B.,
            Zaghloul,N.A., Jones,S.M., Reith,W. and Hertzano,R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   8  (bases 1 to 2869)
  AUTHORS   Roberto,V.P., Tiago,D.M., Gautvik,K. and Cancela,M.L.
  TITLE     Evidence for the conservation of miR-223 in zebrafish (Danio
            rerio): Implications for function
  JOURNAL   Gene 566 (1), 54-62 (2015)
   PUBMED   25869932
  REMARK    Erratum:[Gene. 2016 Jan 15;576(1 Pt 3):589]
REFERENCE   9  (bases 1 to 2869)
  AUTHORS   Diotel,N., Rodriguez Viales,R., Armant,O., Marz,M., Ferg,M.,
            Rastegar,S. and Strahle,U.
  TITLE     Comprehensive expression map of transcription regulators in the
            adult zebrafish telencephalon reveals distinct neurogenic niches
  JOURNAL   J Comp Neurol 523 (8), 1202-1221 (2015)
   PUBMED   25556858
REFERENCE   10 (bases 1 to 2869)
  AUTHORS   Pistocchi,A., Gaudenzi,G., Foglia,E., Monteverde,S.,
            Moreno-Fortuny,A., Pianca,A., Cossu,G., Cotelli,F. and Messina,G.
  TITLE     Conserved and divergent functions of Nfix in skeletal muscle
            development during vertebrate evolution
  JOURNAL   Development 140 (7), 1528-1536 (2013)
   PUBMED   23482488
  REMARK    Erratum:[Development. 2013 Jun;140(11):2443]
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC128847.1.
            
            On or before Mar 11, 2007 this sequence version replaced
            XM_679514.2, XM_679693.2.
            
            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 :: BC128847.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA3505370,
                                           SAMEA3505371 [ECO:0006172]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2869
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="22"
                     /map="22"
     gene            1..2869
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /note="nuclear factor I/A"
                     /db_xref="GeneID:556665"
                     /db_xref="ZFIN:ZDB-GENE-050208-501"
     exon            1..256
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    38..40
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /note="upstream in-frame stop codon"
     CDS             230..1675
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /codon_start=1
                     /product="nuclear factor 1 A-type"
                     /protein_id="NP_001073431.1"
                     /db_xref="GeneID:556665"
                     /db_xref="ZFIN:ZDB-GENE-050208-501"
                     /translation="

MYSPLCLTQDEFHPFIEALLPHVRAFAYTWFNLQARKRKYFKKHEKRMSKEEERAVKDELLSEKPEVKQKWASRLLAKLRKDIRPEFREDFVLTVTGKKPPCCVLSNPDQKGKMRRIDCLRQADKVWRLYLVMVILFKGIPLESTDGERLVKSPQCSNPGLCVQPHHIGVSVKELDLYLAYFVHAEAGQSDSPNQPSEGDIKDQPENGHLGFQDSFVTSGVFTVSELVRVSQTPIAAGTGPNFSLADLDSSSYYSMSPGAMRRPLPSTSSSSSAKRIKCMEDEVDSPGEESYYPGQGRSPGSGSQASSWHEVEPAGYKLRGSLASSFISRQASPHATPSSLHFPTSPIIQQPGSYFSHHAIRYHPQETLKEFVQLVCPDSGQQAGQVGFLNPNGSSQGKVHNPFLPTPMLPPPPPPPMARPVPLPVPDSKPPSTSTDGGGNSPTSPTYSTPSTSPAQRFVSVGPRDPSFVNIPQQPQWYLG"

     misc_feature    254..367
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /note="Nuclear factor I protein pre-N-terminus; Region:
                     NfI_DNAbd_pre-N; pfam10524"
                     /db_xref="CDD:463134"
     misc_feature    431..745
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /note="MH1 domain; Region: MH1; pfam03165"
                     /db_xref="CDD:460833"
     misc_feature    866..1651
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /note="CTF/NF-I family transcription modulation region;
                     Region: CTF_NFI; pfam00859"
                     /db_xref="CDD:459967"
     exon            257..785
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            786..851
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            852..926
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            927..1044
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1045..1172
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1173..1223
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1224..1402
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1403..1568
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1569..1660
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
     exon            1661..2868
                     /gene="nfia"
                     /gene_synonym="si:ch211-88d2.2; wu:fq27e07; zgc:158351"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gctgaagcgtcgcgcgcacttcgcagagttggaaatgtgaaagcaagaagcaaggctttattttccctctctcccttcttctctgtctctctttttttctcttttcatacacacacatatacatacacaccccatacattcacacatacacacaccctcacccacacgcacactcacgcgcgcacacacaacatatacatcgccaattcaagagttaaaaccgacagatatgtattctccgctatgcctaacacaggatgaattccatcctttcattgaagcactgctgccccatgtgagagcgtttgcctacacttggttcaacttgcaggcccgcaagagaaaatacttcaagaagcacgagaagcgcatgtcgaaggaagaggagcgagccgtgaaggacgagctgctcagcgagaagccggaggtcaagcagaagtgggcatcgcggctgctggccaaactccgcaaggacatccggcccgagttccgcgaggattttgtgctcaccgtcaccgggaagaagcccccttgctgtgttctctcgaaccccgaccagaagggcaagatgaggagaatcgactgcctgcgtcaggcggacaaagtgtggcgcttgtacctggtcatggtgattttattcaaaggtattcctcttgaaagtactgacggcgaaaggctggttaagtcaccgcagtgctcgaacccagggctgtgcgtgcagccgcatcacataggagtttccgtaaaggagctcgacctgtacttggcctacttcgtccatgcagaagcagggcagtctgacagtccgaaccagcccagtgaaggcgacatcaaggaccagccagaaaatgggcaccttggcttccaggacagtttcgtcacatcaggtgtcttcaccgtctctgagctagtgcgagtctcacagacgcccatcgcggcagggacggggcccaacttttcgttggcagacttggacagctcttcctactacagtatgagccctggggccatgaggcgccccctacccagcacttcttctagcagttctgcaaagcgaatcaaatgcatggaggatgaggtggacagcccgggagaggagtcctactacccaggtcagggacgctcgcctggaagcggcagccaagccagcagctggcatgaagtggagccagctggatataaactgcgtggctcgctagctagttcgttcatctcaagacaagcgagtccacacgccacgccgtcaagtcttcatttcccgacgtcgccaatcatccagcagcccggctcctacttctcccaccacgccattcgctaccacccacaggagacgctaaaggagtttgtccaacttgtctgtcctgacagtggtcagcaggctggacaggtgggcttccttaatcccaatgggagcagtcaagggaaggtgcacaacccgttcctgcccaccccgatgctgccgccccctccaccgcccccgatggcgcgacccgttcctctgcccgtgccagactctaaacctccatccacctccactgacggaggaggaaactcacccacttcacccacctactccacaccgagcacgtctcccgctcagcgttttgtcagcgtgggccccagagaccccagctttgtaaatatccctcagcagcctcagtggtacctgggctaaagactcccgaacacggacacacggccgctccgaggtcactcgaccaccccctctgtctcccctgagtacgacccgcaaacatgtacaccagtctgaacagagagaagccacttgctgccccgtaccggacagacccacagcatggctccagccgaacaaccccgccaagccctggaacaagaggaaccgcttacacccacttactatatatctatatagtccagatgtattcttccatatgtatggtttacatgcctatattcatatatagtagctgtccagctcttctgagggtggagctcagataaaaaaaaaaaacgaagagcttttttttgttttcctaattttttttttttgttttgaaaacgtgcacgttttatttttattttctgttcgtttgtttgtttttgttttttatggttcaccctcacagatagacgaggaaaaacgtaacatgacgcaatcaaagagcttcccgcttctgtgcctgtggtgttaaaaagagaggcgtttcgagatcaaaaacgcagtcgacggccaagggtcgcgaacccacaaccatctggaggtcggagctctgcctttcaatcactcgtgtttcgacgctgttggaggtttcgcctgggtcagatttaccaccagctaaaaaacaaactaatctaaacaaatgtgtattgcgtcttctggaccatttgcttcccttccaccgccatcatcaccaccaccgccatcaaggactcaaccccatttttatctgttgtttttgtcatttttggggcaggcgatgaagaagtcatgaacggtgatgtttgatatcaggtcattttacaggagatctccccacttggaggcatgttcatattttgtgtttttcttacaaaaaaaatgaggaaaaaaaagagagaaagtcatagtgattgtttctactaaaccccagccggaaggtctgtggcacgccaagggccgagtgaaggttcaatcttccagaaacttcaagggaaggttaaccgtgaatactgaattgaggaaagtgcaattttgttgggtagatgttggattgttaaatatctttgtaagatagatcgttgaagcgatttgttgaaaagtatatatatataaatatatatatttttcttcctagtccgttcacacctccaggactctaaaatatcggggtacaaaaaaaaaaaaaaa

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