LOCUS       NM_001396806            3375 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus hepatocyte nuclear factor 4 alpha (HNF4A), transcript
            variant 3, mRNA.
ACCESSION   NM_001396806 XM_025142196
VERSION     NM_001396806.1
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 3375)
  AUTHORS   Jiang S, Tanaka T, Yagami R, Hasegawa G, Umezu H, Fujiyoshi Y,
            Kodama T, Naito M and Ajioka Y.
  TITLE     Immunohistochemical detection of hepatocyte nuclear factor-4alpha
            in vertebrates
  JOURNAL   Microsc Res Tech 84 (12), 2906-2914 (2021)
   PUBMED   34196449
  REMARK    GeneRIF: Immunohistochemical detection of hepatocyte nuclear
            factor-4alpha in vertebrates.
REFERENCE   2  (bases 1 to 3375)
  AUTHORS   Tang H, Finn RD and Thomas PD.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
REFERENCE   3  (bases 1 to 3375)
  AUTHORS   Yang Q, Tang S, Dong L, Chen Q, Liu X, Jiang J and Deng Y.
  TITLE     Transcriptional regulation of chicken cytochrome P450 2D49 basal
            expression by CCAAT/enhancer-binding protein alpha and hepatocyte
            nuclear factor 4alpha
  JOURNAL   FEBS J 281 (5), 1379-1392 (2014)
   PUBMED   24418194
  REMARK    GeneRIF: The results of overexpressing C/EBPalpha and HNF4alpha in
            cultured cells confirmed that both C/EBPalpha and HNF4alpha
            contribute significantly to sustaining a high level of CYP2D49
            transcription.
REFERENCE   4  (bases 1 to 3375)
  AUTHORS   Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C,
            Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3375)
  AUTHORS   Handschin C, Gnerre C, Fraser DJ, Martinez-Jimenez C, Jover R and
            Meyer UA.
  TITLE     Species-specific mechanisms for cholesterol 7alpha-hydroxylase
            (CYP7A1) regulation by drugs and bile acids
  JOURNAL   Arch Biochem Biophys 434 (1), 75-85 (2005)
   PUBMED   15629111
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000328.1.
            
            On Oct 25, 2021 this sequence version replaced XM_025142196.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13267654.159657.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA103992290,
                                           SAMEA103992323 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-194               JAENSK010000328.1  5493113-5493306     c
            195-369             JAENSK010000328.1  5476207-5476381     c
            370-464             JAENSK010000328.1  5474973-5475067     c
            465-571             JAENSK010000328.1  5472837-5472943     c
            572-727             JAENSK010000328.1  5471087-5471242     c
            728-815             JAENSK010000328.1  5468043-5468130     c
            816-971             JAENSK010000328.1  5467375-5467530     c
            972-1208            JAENSK010000328.1  5466855-5467091     c
            1209-1331           JAENSK010000328.1  5466357-5466479     c
            1332-3375           JAENSK010000328.1  5463667-5465710     c
FEATURES             Location/Qualifiers
     source          1..3375
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="20"
                     /map="20"
     gene            1..3375
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="hepatocyte nuclear factor 4 alpha"
                     /db_xref="CGNC:50941"
                     /db_xref="GeneID:419198"
     exon            1..194
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    35..37
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="upstream in-frame stop codon"
     CDS             146..1474
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="isoform 3 is encoded by transcript variant 3;
                     nuclear receptor; hepatic nuclear factor 4alpha"
                     /codon_start=1
                     /product="hepatocyte nuclear factor 4-alpha isoform 3"
                     /protein_id="NP_001383735.1"
                     /db_xref="CGNC:50941"
                     /db_xref="GeneID:419198"
                     /translation="

MVNVSTQLSAKMEAPYDTSPSEAANLNTSNSIGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFNRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINVLLQAEVLAQQISSPVLVMNGDIRGKKIANIADVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVAKRSMVFKDVLLLGNDHIVPRNCPELVEVSRVAIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSDPSKIKRMRYQVQVSLEDYINDRQYDSRGRFGELLLLLPVLQSITWQMIEQIQFVKLFGMAKIDNLLQEMLLGGSSSETPHAHHPLHPHLIQENLGTNVIVANTMPPQMHNGQMSTPETPQPSPPAGSGPEQYKLLPGAIATVAKQPTSIPQPAITKQEVI"

     misc_feature    257..484
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="DNA-binding domain of heptocyte nuclear factor 4
                     (HNF4) is composed of two C4-type zinc fingers; Region:
                     NR_DBD_HNF4A; cd06960"
                     /db_xref="CDD:143518"
     misc_feature    order(257..259,266..268,308..310,317..319,365..367,
                     383..385,413..415,422..424)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="zinc binding site [ion binding]; other site"
                     /db_xref="CDD:143518"
     misc_feature    order(275..277,287..295,311..316,320..322,326..328,
                     332..337,344..346,404..409,416..418,425..427,464..472,
                     476..478)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:143518"
     misc_feature    order(368..370,407..412,416..418)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="homodimer interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:143518"
     misc_feature    530..1198
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="The ligand binding domain of heptocyte nuclear
                     factor 4, which is explosively expanded in nematodes;
                     Region: NR_LBD_HNF4_like; cd06931"
                     /db_xref="CDD:132729"
     misc_feature    order(629..631,647..649,659..661,761..763,773..775,
                     782..784,812..817,869..871,1139..1144,1151..1153)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="ligand binding site [chemical binding]; other site"
                     /db_xref="CDD:132729"
     misc_feature    order(674..676,686..688,716..721,725..730,737..742,
                     1181..1186,1193..1198)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="coactivator recognition site [polypeptide binding];
                     other site"
                     /db_xref="CDD:132729"
     misc_feature    order(890..892,953..955,971..973,1013..1018,1025..1030,
                     1037..1042,1070..1075,1079..1087,1091..1096,1100..1108,
                     1112..1117,1124..1126)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="dimer interface [polypeptide binding]; other site"
                     /db_xref="CDD:132729"
     exon            195..369
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            370..464
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            465..571
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            572..727
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            728..815
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            816..971
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            972..1208
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            1209..1331
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            1332..3375
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gccctgcctctccgcactctctcctgccttcacctagttccttagaaatacattctcatttatttattttactttattttatttcattattccgacacttgctctgcttttcgcccccagtccccatagaggtacccgacgagacatggtcaatgtaagcacccagctaagcgctaagatggaggctccatatgacacatctccatcagaggcagccaacctcaacacctccaacagcatcggggtgagcgcactgtgtgccatctgcggggaccgcgccacagggaagcactacggggcttccagctgcgatggctgcaaaggcttcttcaggaggagcgtgaggaagaaccacatgtactcctgcaggtttaacaggcagtgtgtggtagacaaagacaaaagaaaccagtgccgatactgcaggcttaagaagtgcttccgagcagggatgaagaaggaagctgtacaaaatgaacgggaccgaatcagcacccgaagatcaagttacgaagacagcagcttgccctccatcaacgtcttactgcaggcagaagtcctggcacaacagatatcatccccagtcctcgtgatgaacggagacatccgagggaagaagattgccaacatcgccgacgtgtgcgagtccatgaagcagcagctgctggtgctggtggagtgggccaagtacatccctgcgttctgcgagctgcccctggacgaccaggtggcactgctgcgggcacatgcaggtgaacatctgttactgggagttgccaagaggtccatggtgttcaaggatgtcttgctgctagggaacgaccacatcgtccctcggaactgccccgagctggtagaggtgagccgcgtggccatccgcatcctggatgagctggtcctccccttccaggagctgcagatagacgacaatgaatatgcctgcttgaaagccatcatcttcttcgacccagatgccaaaggactgagcgatccctccaagatcaagcggatgcggtaccaggtgcaggtcagcctggaggactacatcaatgacaggcagtacgactcgcggggccgcttcggggagctgctgctgctgctgcctgtgctgcagagcatcacctggcagatgatagagcagatccagtttgtcaagctcttcggcatggctaagattgacaacctgttgcaggagatgctgctgggaggttcatcaagtgaaacgccacatgctcaccaccccttgcatcctcatctgatccaggagaacctgggaacaaacgtcattgtggccaacacaatgcctcctcagatgcacaacgggcagatgtctactccagaaactcctcagccatctcctcctgcaggttcagggccggagcagtacaaactgctgcccggagccattgcaaccgtggcaaaacagcccacctccatcccacagcctgccatcacaaagcaggaggtcatctagcagcctgcagagcagctggccgcattgagaagaccgtgtgggagaaaagcccgagcagactccgtcactgtgaaaaaagccatcccgaggtcctcgggcaccaacacacggacttgcttatcggactagcccaccactaccaaaagctgtcttcctgcagctacagacagcattgcaccatggagagcctcgagtcacagaactaagactgaagccttactgaaacccatgttccttgtaagaagggccagactgctgcctttccccatcaggaggctgcagtgcctggctggggacaccacagctcgctgttccgccattgctacctctcagcacccgttcagtgtacaccagaccctgtgaacaagtgatcctccaaaccaggaggccgtgctgggtgaaaggaaaggcttcattcccacagctgtgccggctccccaggcagcccctggtgcagccaagcttcactgaggcgggagctgccccaggagcgccgctgcatcaaagcacgctggggttcacccggcagcactgtcagaactgctcctcagcctcagcccatcccagatcttcccttggtcgctctccagcaaaccaagccctcggccaggtctaacagatctttccagctgatgcgggggcaaagtctgtcccaccaagattctccactgttcggaccctctggatgggttttgccgtttcctcaccgtggctgccccccaccccaggcctcagaggccgccactgccaaacccttcacactgctgccttctcaccacccacacagggcagctggggcctgtgggattcaggaaatgtcacctagcaggatggggccagccctgcacaggctggctgtgggcagaactgcctgtagcatcagccggcccagtgctgcttctgagcagccagaggaccatgtggtgctggttgagaagaagccggggcagggcgtgtgaaggggagagagcctcacacacgggctgctgaatgccaggggatctgagacccagtaattcagttcagagccagcttaatgctgaggtacgtgtccagttcagtgccactccctttgcatagagtgagtggctgataacagatttacagggcttcgtaacaggataagaattccttacggctcctccagatctcagagggtttggtgaacagtcgcctcaaagcagagcacttcaggtcctgctgtgagcactgccagaggtcagggccaaatccctgcagcctgcgctggcagcgctgccccagcagtgccctgggctcccatctgcccgctgcttctgcccgctgaggcctgccagggctgcagccacagcgatacaacctttggtttacagctgaaatcaggccagcagcctccctgctgcctccctggagctcgcacagcaacttcaggcttcccttctccctcattgctggcagcaccaaaggagaggcaccaagaaaacctggaacgagcgctttccatcagaagggactgaacagcagatgcacagcacctgtgctctgggaaatccagcatgaaagaaaacaatcctggtttcgtactgaggcagcagcagggctaaccatccacagaccgtgttcctgagggtcccagccctgtggtgggcacccacagctgccgaggggactggagaggtccctgggatggatctgagctgagccagaggagctgcagatccctccctcgatcgccaatgcaaaaaggaaccgcctggccttgcgctggtggcatcccaagtattgtatcatctctcagagctggtggcattagacccagtaatttattgcaatgatgaagccaatcattttctgtaaattattttgtaaatcacattgattatttataattgggaaattaaatgcaaaaaaaaaaaaaaaaa

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