LOCUS       NM_001396805            3420 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus hepatocyte nuclear factor 4 alpha (HNF4A), transcript
            variant 2, mRNA.
ACCESSION   NM_001396805 XM_015296366
VERSION     NM_001396805.1
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 3420)
  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 3420)
  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 3420)
  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 3420)
  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 3420)
  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_015296366.3.
            
            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 :: SRR13267655.239473.1,
                                           SRR13267648.8134.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA103992290,
                                           SAMEA103992323 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: upstream AUG and CDS extension
                                                is not conserved
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-236               JAENSK010000328.1  5479665-5479900     c
            237-414             JAENSK010000328.1  5476207-5476384     c
            415-509             JAENSK010000328.1  5474973-5475067     c
            510-616             JAENSK010000328.1  5472837-5472943     c
            617-772             JAENSK010000328.1  5471087-5471242     c
            773-860             JAENSK010000328.1  5468043-5468130     c
            861-1016            JAENSK010000328.1  5467375-5467530     c
            1017-1253           JAENSK010000328.1  5466855-5467091     c
            1254-1376           JAENSK010000328.1  5466357-5466479     c
            1377-3420           JAENSK010000328.1  5463667-5465710     c
FEATURES             Location/Qualifiers
     source          1..3420
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="20"
                     /map="20"
     gene            1..3420
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="hepatocyte nuclear factor 4 alpha"
                     /db_xref="CGNC:50941"
                     /db_xref="GeneID:419198"
     exon            1..236
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    71..73
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="upstream in-frame stop codon"
     misc_feature    116..118
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="upstream_AUG_codon; putative N-terminal extension:
                     MI"
     CDS             122..1519
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="isoform 2 is encoded by transcript variant 2;
                     nuclear receptor; hepatic nuclear factor 4alpha"
                     /codon_start=1
                     /product="hepatocyte nuclear factor 4-alpha isoform 2"
                     /protein_id="NP_001383734.1"
                     /db_xref="CGNC:50941"
                     /db_xref="GeneID:419198"
                     /translation="

MRLSKALIDMEMADYSAALDPAYTTLEFENMQVLAMGSADTSPSEAANLNTSNSIGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFNRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINVLLQAEVLAQQISSPVLVMNGDIRGKKIANIADVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVAKRSMVFKDVLLLGNDHIVPRNCPELVEVSRVAIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSDPSKIKRMRYQVQVSLEDYINDRQYDSRGRFGELLLLLPVLQSITWQMIEQIQFVKLFGMAKIDNLLQEMLLGGSSSETPHAHHPLHPHLIQENLGTNVIVANTMPPQMHNGQMSTPETPQPSPPAGSGPEQYKLLPGAIATVAKQPTSIPQPAITKQEVI"

     misc_feature    302..529
                     /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(302..304,311..313,353..355,362..364,410..412,
                     428..430,458..460,467..469)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="zinc binding site [ion binding]; other site"
                     /db_xref="CDD:143518"
     misc_feature    order(320..322,332..340,356..361,365..367,371..373,
                     377..382,389..391,449..454,461..463,470..472,509..517,
                     521..523)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:143518"
     misc_feature    order(413..415,452..457,461..463)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="homodimer interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:143518"
     misc_feature    575..1243
                     /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(674..676,692..694,704..706,806..808,818..820,
                     827..829,857..862,914..916,1184..1189,1196..1198)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="ligand binding site [chemical binding]; other site"
                     /db_xref="CDD:132729"
     misc_feature    order(719..721,731..733,761..766,770..775,782..787,
                     1226..1231,1238..1243)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="coactivator recognition site [polypeptide binding];
                     other site"
                     /db_xref="CDD:132729"
     misc_feature    order(935..937,998..1000,1016..1018,1058..1063,1070..1075,
                     1082..1087,1115..1120,1124..1132,1136..1141,1145..1153,
                     1157..1162,1169..1171)
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /note="dimer interface [polypeptide binding]; other site"
                     /db_xref="CDD:132729"
     exon            237..414
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            415..509
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            510..616
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            617..772
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            773..860
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            861..1016
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            1017..1253
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            1254..1376
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
     exon            1377..3420
                     /gene="HNF4A"
                     /gene_synonym="HNF4alpha"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agagaaatatttgaaataaaagacaacagataggggacgcagcgaaggcagagagaggcagcggggccaatagcctcggacaagggaatcggcacgacctggcccgtgtttgcccatgataatgcgcctttccaaagccctgatagacatggagatggccgattatagcgcggcgctggacccggcgtacaccaccctggagtttgagaacatgcaggtgctggccatgggcagcgcagacacatctccatcagaggcagccaacctcaacacctccaacagcatcggggtgagcgcactgtgtgccatctgcggggaccgcgccacagggaagcactacggggcttccagctgcgatggctgcaaaggcttcttcaggaggagcgtgaggaagaaccacatgtactcctgcaggtttaacaggcagtgtgtggtagacaaagacaaaagaaaccagtgccgatactgcaggcttaagaagtgcttccgagcagggatgaagaaggaagctgtacaaaatgaacgggaccgaatcagcacccgaagatcaagttacgaagacagcagcttgccctccatcaacgtcttactgcaggcagaagtcctggcacaacagatatcatccccagtcctcgtgatgaacggagacatccgagggaagaagattgccaacatcgccgacgtgtgcgagtccatgaagcagcagctgctggtgctggtggagtgggccaagtacatccctgcgttctgcgagctgcccctggacgaccaggtggcactgctgcgggcacatgcaggtgaacatctgttactgggagttgccaagaggtccatggtgttcaaggatgtcttgctgctagggaacgaccacatcgtccctcggaactgccccgagctggtagaggtgagccgcgtggccatccgcatcctggatgagctggtcctccccttccaggagctgcagatagacgacaatgaatatgcctgcttgaaagccatcatcttcttcgacccagatgccaaaggactgagcgatccctccaagatcaagcggatgcggtaccaggtgcaggtcagcctggaggactacatcaatgacaggcagtacgactcgcggggccgcttcggggagctgctgctgctgctgcctgtgctgcagagcatcacctggcagatgatagagcagatccagtttgtcaagctcttcggcatggctaagattgacaacctgttgcaggagatgctgctgggaggttcatcaagtgaaacgccacatgctcaccaccccttgcatcctcatctgatccaggagaacctgggaacaaacgtcattgtggccaacacaatgcctcctcagatgcacaacgggcagatgtctactccagaaactcctcagccatctcctcctgcaggttcagggccggagcagtacaaactgctgcccggagccattgcaaccgtggcaaaacagcccacctccatcccacagcctgccatcacaaagcaggaggtcatctagcagcctgcagagcagctggccgcattgagaagaccgtgtgggagaaaagcccgagcagactccgtcactgtgaaaaaagccatcccgaggtcctcgggcaccaacacacggacttgcttatcggactagcccaccactaccaaaagctgtcttcctgcagctacagacagcattgcaccatggagagcctcgagtcacagaactaagactgaagccttactgaaacccatgttccttgtaagaagggccagactgctgcctttccccatcaggaggctgcagtgcctggctggggacaccacagctcgctgttccgccattgctacctctcagcacccgttcagtgtacaccagaccctgtgaacaagtgatcctccaaaccaggaggccgtgctgggtgaaaggaaaggcttcattcccacagctgtgccggctccccaggcagcccctggtgcagccaagcttcactgaggcgggagctgccccaggagcgccgctgcatcaaagcacgctggggttcacccggcagcactgtcagaactgctcctcagcctcagcccatcccagatcttcccttggtcgctctccagcaaaccaagccctcggccaggtctaacagatctttccagctgatgcgggggcaaagtctgtcccaccaagattctccactgttcggaccctctggatgggttttgccgtttcctcaccgtggctgccccccaccccaggcctcagaggccgccactgccaaacccttcacactgctgccttctcaccacccacacagggcagctggggcctgtgggattcaggaaatgtcacctagcaggatggggccagccctgcacaggctggctgtgggcagaactgcctgtagcatcagccggcccagtgctgcttctgagcagccagaggaccatgtggtgctggttgagaagaagccggggcagggcgtgtgaaggggagagagcctcacacacgggctgctgaatgccaggggatctgagacccagtaattcagttcagagccagcttaatgctgaggtacgtgtccagttcagtgccactccctttgcatagagtgagtggctgataacagatttacagggcttcgtaacaggataagaattccttacggctcctccagatctcagagggtttggtgaacagtcgcctcaaagcagagcacttcaggtcctgctgtgagcactgccagaggtcagggccaaatccctgcagcctgcgctggcagcgctgccccagcagtgccctgggctcccatctgcccgctgcttctgcccgctgaggcctgccagggctgcagccacagcgatacaacctttggtttacagctgaaatcaggccagcagcctccctgctgcctccctggagctcgcacagcaacttcaggcttcccttctccctcattgctggcagcaccaaaggagaggcaccaagaaaacctggaacgagcgctttccatcagaagggactgaacagcagatgcacagcacctgtgctctgggaaatccagcatgaaagaaaacaatcctggtttcgtactgaggcagcagcagggctaaccatccacagaccgtgttcctgagggtcccagccctgtggtgggcacccacagctgccgaggggactggagaggtccctgggatggatctgagctgagccagaggagctgcagatccctccctcgatcgccaatgcaaaaaggaaccgcctggccttgcgctggtggcatcccaagtattgtatcatctctcagagctggtggcattagacccagtaatttattgcaatgatgaagccaatcattttctgtaaattattttgtaaatcacattgattatttataattgggaaattaaatgcaaaaaaaaaaaaaaaaa

//