2024-05-05 04:38:14, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001030855 3417 bp mRNA linear VRT 23-SEP-2023 DEFINITION Gallus gallus hepatocyte nuclear factor 4 alpha (HNF4A), transcript variant 1, mRNA. ACCESSION NM_001030855 XM_417376 VERSION NM_001030855.2 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 3417) 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 3417) 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 3417) 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 3417) 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 3417) 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 NM_001030855.1. 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 :: SRR13267652.18040.1, SRR13267659.312519.1 [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 237-411 JAENSK010000328.1 5476207-5476381 c 412-506 JAENSK010000328.1 5474973-5475067 c 507-613 JAENSK010000328.1 5472837-5472943 c 614-769 JAENSK010000328.1 5471087-5471242 c 770-857 JAENSK010000328.1 5468043-5468130 c 858-1013 JAENSK010000328.1 5467375-5467530 c 1014-1250 JAENSK010000328.1 5466855-5467091 c 1251-1373 JAENSK010000328.1 5466357-5466479 c 1374-3417 JAENSK010000328.1 5463667-5465710 c FEATURES Location/Qualifiers source 1..3417 /organism="Gallus gallus" /mol_type="mRNA" /db_xref="taxon:9031" /chromosome="20" /map="20" gene 1..3417 /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..1516 /gene="HNF4A" /gene_synonym="HNF4alpha" /note="isoform 1 is encoded by transcript variant 1; nuclear receptor; hepatic nuclear factor 4alpha" /codon_start=1 /product="hepatocyte nuclear factor 4-alpha isoform 1" /protein_id="NP_001026026.2" /db_xref="CGNC:50941" /db_xref="GeneID:419198" /translation="
MRLSKALIDMEMADYSAALDPAYTTLEFENMQVLAMGSDTSPSEAANLNTSNSIGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFNRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINVLLQAEVLAQQISSPVLVMNGDIRGKKIANIADVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVAKRSMVFKDVLLLGNDHIVPRNCPELVEVSRVAIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSDPSKIKRMRYQVQVSLEDYINDRQYDSRGRFGELLLLLPVLQSITWQMIEQIQFVKLFGMAKIDNLLQEMLLGGSSSETPHAHHPLHPHLIQENLGTNVIVANTMPPQMHNGQMSTPETPQPSPPAGSGPEQYKLLPGAIATVAKQPTSIPQPAITKQEVI"
misc_feature 299..526 /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(299..301,308..310,350..352,359..361,407..409, 425..427,455..457,464..466) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="zinc binding site [ion binding]; other site" /db_xref="CDD:143518" misc_feature order(317..319,329..337,353..358,362..364,368..370, 374..379,386..388,446..451,458..460,467..469,506..514, 518..520) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:143518" misc_feature order(410..412,449..454,458..460) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="homodimer interface [polypeptide binding]; other site" /db_xref="CDD:143518" misc_feature 572..1240 /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(671..673,689..691,701..703,803..805,815..817, 824..826,854..859,911..913,1181..1186,1193..1195) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="ligand binding site [chemical binding]; other site" /db_xref="CDD:132729" misc_feature order(716..718,728..730,758..763,767..772,779..784, 1223..1228,1235..1240) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="coactivator recognition site [polypeptide binding]; other site" /db_xref="CDD:132729" misc_feature order(932..934,995..997,1013..1015,1055..1060,1067..1072, 1079..1084,1112..1117,1121..1129,1133..1138,1142..1150, 1154..1159,1166..1168) /gene="HNF4A" /gene_synonym="HNF4alpha" /note="dimer interface [polypeptide binding]; other site" /db_xref="CDD:132729" exon 237..411 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 412..506 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 507..613 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 614..769 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 770..857 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 858..1013 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 1014..1250 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 1251..1373 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" exon 1374..3417 /gene="HNF4A" /gene_synonym="HNF4alpha" /inference="alignment:Splign:2.1.0" ORIGIN
agagaaatatttgaaataaaagacaacagataggggacgcagcgaaggcagagagaggcagcggggccaatagcctcggacaagggaatcggcacgacctggcccgtgtttgcccatgataatgcgcctttccaaagccctgatagacatggagatggccgattatagcgcggcgctggacccggcgtacaccaccctggagtttgagaacatgcaggtgctggccatgggcagcgacacatctccatcagaggcagccaacctcaacacctccaacagcatcggggtgagcgcactgtgtgccatctgcggggaccgcgccacagggaagcactacggggcttccagctgcgatggctgcaaaggcttcttcaggaggagcgtgaggaagaaccacatgtactcctgcaggtttaacaggcagtgtgtggtagacaaagacaaaagaaaccagtgccgatactgcaggcttaagaagtgcttccgagcagggatgaagaaggaagctgtacaaaatgaacgggaccgaatcagcacccgaagatcaagttacgaagacagcagcttgccctccatcaacgtcttactgcaggcagaagtcctggcacaacagatatcatccccagtcctcgtgatgaacggagacatccgagggaagaagattgccaacatcgccgacgtgtgcgagtccatgaagcagcagctgctggtgctggtggagtgggccaagtacatccctgcgttctgcgagctgcccctggacgaccaggtggcactgctgcgggcacatgcaggtgaacatctgttactgggagttgccaagaggtccatggtgttcaaggatgtcttgctgctagggaacgaccacatcgtccctcggaactgccccgagctggtagaggtgagccgcgtggccatccgcatcctggatgagctggtcctccccttccaggagctgcagatagacgacaatgaatatgcctgcttgaaagccatcatcttcttcgacccagatgccaaaggactgagcgatccctccaagatcaagcggatgcggtaccaggtgcaggtcagcctggaggactacatcaatgacaggcagtacgactcgcggggccgcttcggggagctgctgctgctgctgcctgtgctgcagagcatcacctggcagatgatagagcagatccagtttgtcaagctcttcggcatggctaagattgacaacctgttgcaggagatgctgctgggaggttcatcaagtgaaacgccacatgctcaccaccccttgcatcctcatctgatccaggagaacctgggaacaaacgtcattgtggccaacacaatgcctcctcagatgcacaacgggcagatgtctactccagaaactcctcagccatctcctcctgcaggttcagggccggagcagtacaaactgctgcccggagccattgcaaccgtggcaaaacagcccacctccatcccacagcctgccatcacaaagcaggaggtcatctagcagcctgcagagcagctggccgcattgagaagaccgtgtgggagaaaagcccgagcagactccgtcactgtgaaaaaagccatcccgaggtcctcgggcaccaacacacggacttgcttatcggactagcccaccactaccaaaagctgtcttcctgcagctacagacagcattgcaccatggagagcctcgagtcacagaactaagactgaagccttactgaaacccatgttccttgtaagaagggccagactgctgcctttccccatcaggaggctgcagtgcctggctggggacaccacagctcgctgttccgccattgctacctctcagcacccgttcagtgtacaccagaccctgtgaacaagtgatcctccaaaccaggaggccgtgctgggtgaaaggaaaggcttcattcccacagctgtgccggctccccaggcagcccctggtgcagccaagcttcactgaggcgggagctgccccaggagcgccgctgcatcaaagcacgctggggttcacccggcagcactgtcagaactgctcctcagcctcagcccatcccagatcttcccttggtcgctctccagcaaaccaagccctcggccaggtctaacagatctttccagctgatgcgggggcaaagtctgtcccaccaagattctccactgttcggaccctctggatgggttttgccgtttcctcaccgtggctgccccccaccccaggcctcagaggccgccactgccaaacccttcacactgctgccttctcaccacccacacagggcagctggggcctgtgggattcaggaaatgtcacctagcaggatggggccagccctgcacaggctggctgtgggcagaactgcctgtagcatcagccggcccagtgctgcttctgagcagccagaggaccatgtggtgctggttgagaagaagccggggcagggcgtgtgaaggggagagagcctcacacacgggctgctgaatgccaggggatctgagacccagtaattcagttcagagccagcttaatgctgaggtacgtgtccagttcagtgccactccctttgcatagagtgagtggctgataacagatttacagggcttcgtaacaggataagaattccttacggctcctccagatctcagagggtttggtgaacagtcgcctcaaagcagagcacttcaggtcctgctgtgagcactgccagaggtcagggccaaatccctgcagcctgcgctggcagcgctgccccagcagtgccctgggctcccatctgcccgctgcttctgcccgctgaggcctgccagggctgcagccacagcgatacaacctttggtttacagctgaaatcaggccagcagcctccctgctgcctccctggagctcgcacagcaacttcaggcttcccttctccctcattgctggcagcaccaaaggagaggcaccaagaaaacctggaacgagcgctttccatcagaagggactgaacagcagatgcacagcacctgtgctctgggaaatccagcatgaaagaaaacaatcctggtttcgtactgaggcagcagcagggctaaccatccacagaccgtgttcctgagggtcccagccctgtggtgggcacccacagctgccgaggggactggagaggtccctgggatggatctgagctgagccagaggagctgcagatccctccctcgatcgccaatgcaaaaaggaaccgcctggccttgcgctggtggcatcccaagtattgtatcatctctcagagctggtggcattagacccagtaatttattgcaatgatgaagccaatcattttctgtaaattattttgtaaatcacattgattatttataattgggaaattaaatgcaaaaaaaaaaaaaaaaa
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Creative Commons Attribution 4.0 International License (CC BY 4.0).
If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
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