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Previous release (v1)
2026-06-30 05:08:56, GGRNA.v2 : RefSeq release 233 (Jan, 2026)
LOCUS NM_001388512 2107 bp mRNA linear ROD 30-APR-2025
DEFINITION Rattus norvegicus hypoxia inducible factor 3 subunit alpha (Hif3a),
transcript variant 2, mRNA.
ACCESSION NM_001388512
VERSION NM_001388512.1
KEYWORDS RefSeq; RefSeq Select.
SOURCE Rattus norvegicus (Norway rat)
ORGANISM Rattus norvegicus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
REFERENCE 1 (bases 1 to 2107)
AUTHORS Xu,Y., Hu,T., Ding,H., Yuan,Y. and Chen,R.
TITLE miR-485-5p alleviates obstructive sleep apnea syndrome with
hypertension by inhibiting PI3K/AKT signaling pathway via
downregulating HIF3A expression
JOURNAL Sleep Breath 27 (1), 109-119 (2023)
PUBMED 35132534
REMARK GeneRIF: miR-485-5p alleviates obstructive sleep apnea syndrome
with hypertension by inhibiting PI3K/AKT signaling pathway via
downregulating HIF3A expression.
REFERENCE 2 (bases 1 to 2107)
AUTHORS Yang,M., Yan,X., Yuan,F.Z., Ye,J., Du,M.Z., Mao,Z.M., Xu,B.B.,
Chen,Y.R., Song,Y.F., Fan,B.S. and Yu,J.K.
TITLE MicroRNA-210-3p Promotes Chondrogenic Differentiation and Inhibits
Adipogenic Differentiation Correlated with HIF-3alpha Signalling in
Bone Marrow Mesenchymal Stem Cells
JOURNAL Biomed Res Int 2021, 6699910 (2021)
PUBMED 33937412
REMARK GeneRIF: MicroRNA-210-3p Promotes Chondrogenic Differentiation and
Inhibits Adipogenic Differentiation Correlated with HIF-3alpha
Signalling in Bone Marrow Mesenchymal Stem Cells.
Publication Status: Online-Only
REFERENCE 3 (bases 1 to 2107)
AUTHORS Coelho,N.R., Tomkiewicz,C., Correia,M.J., Goncalves-Dias,C.,
Barouki,R., Pereira,S.A., Coumoul,X. and Monteiro,E.C.
TITLE First evidence of aryl hydrocarbon receptor as a druggable target
in hypertension induced by chronic intermittent hypoxia
JOURNAL Pharmacol Res 159, 104869 (2020)
PUBMED 32416216
REFERENCE 4 (bases 1 to 2107)
AUTHORS Drevytska,T., Gonchar,E., Okhai,I., Lynnyk,O., Mankovska,I.,
Klionsky,D. and Dosenko,V.
TITLE The protective effect of Hif3a RNA interference and HIF-prolyl
hydroxylase inhibition on cardiomyocytes under anoxia-reoxygenation
JOURNAL Life Sci 202, 131-139 (2018)
PUBMED 29660430
REMARK GeneRIF: Hif3a RNA interference and HIF-prolyl hydroxylase
inhibition protect cardiomyocytes against anoxia-reoxygenation
injury via the HIF signaling pathway
REFERENCE 5 (bases 1 to 2107)
AUTHORS Cuomo,F., Coppola,A., Botti,C., Maione,C., Forte,A., Scisciola,L.,
Liguori,G., Caiafa,I., Ursini,M.V., Galderisi,U., Cipollaro,M.,
Altucci,L. and Cobellis,G.
TITLE Pro-inflammatory cytokines activate hypoxia-inducible factor 3alpha
via epigenetic changes in mesenchymal stromal/stem cells
JOURNAL Sci Rep 8 (1), 5842 (2018)
PUBMED 29643458
REMARK GeneRIF: Study in human mesenchymal stromal/stem cells revealed
robust hypermethylation of histone H3 across HIF3A locus driven by
pro-inflammatory cytokines. Experiments in a murine model of
arteriotomy highlighted the activation of Hif3alpha expression in
infiltrated inflammatory cells, suggesting a new role for Hif3alpha
in inflammation in vivo.
Erratum:[Sci Rep. 2020 Apr 17;10(1):6776. doi:
10.1038/s41598-020-62861-8. PMID: 32303693]
Publication Status: Online-Only
REFERENCE 6 (bases 1 to 2107)
AUTHORS Li,Q.F. and Dai,A.G.
TITLE Differential expression of three hypoxia-inducible factor-alpha
subunits in pulmonary arteries of rat with hypoxia-induced
hypertension
JOURNAL Acta Biochim Biophys Sin (Shanghai) 37 (10), 665-672 (2005)
PUBMED 16215633
REMARK GeneRIF: HIF-1alpha, HIF-2alpha and HIF-3alpha may not only confer
different target genes, but also play key pathogenetic roles in
hypoxic-induced pulmonary hypertension.
REFERENCE 7 (bases 1 to 2107)
AUTHORS Heidbreder,M., Frohlich,F., Johren,O., Dendorfer,A., Qadri,F. and
Dominiak,P.
TITLE Hypoxia rapidly activates HIF-3alpha mRNA expression
JOURNAL FASEB J 17 (11), 1541-1543 (2003)
PUBMED 12824304
REMARK GeneRIF: Hypoxia rapidly activates HIF-3alpha mRNA expression
REFERENCE 8 (bases 1 to 2107)
AUTHORS Hara,S., Hamada,J., Kobayashi,C., Kondo,Y. and Imura,N.
TITLE Expression and characterization of hypoxia-inducible factor
(HIF)-3alpha in human kidney: suppression of HIF-mediated gene
expression by HIF-3alpha
JOURNAL Biochem Biophys Res Commun 287 (4), 808-813 (2001)
PUBMED 11573933
REFERENCE 9 (bases 1 to 2107)
AUTHORS Kietzmann,T., Cornesse,Y., Brechtel,K., Modaressi,S. and
Jungermann,K.
TITLE Perivenous expression of the mRNA of the three hypoxia-inducible
factor alpha-subunits, HIF1alpha, HIF2alpha and HIF3alpha, in rat
liver
JOURNAL Biochem J 354 (Pt 3), 531-537 (2001)
PUBMED 11237857
REFERENCE 10 (bases 1 to 2107)
AUTHORS Gu,Y.Z., Moran,S.M., Hogenesch,J.B., Wartman,L. and Bradfield,C.A.
TITLE Molecular characterization and chromosomal localization of a third
alpha-class hypoxia inducible factor subunit, HIF3alpha
JOURNAL Gene Expr 7 (3), 205-213 (1998)
PUBMED 9840812
COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
JAXUCZ010000001.1.
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.
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##
RNAseq introns :: mixed sample support SAMEA5760383, SAMEA5760389
[ECO:0006172]
##Evidence-Data-END##
##RefSeq-Attributes-START##
inferred exon combination :: based on alignments, homology
RefSeq Select criteria :: based on conservation, expression,
longest protein
##RefSeq-Attributes-END##
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-65 JAXUCZ010000001.1 86877774-86877838 c
66-256 JAXUCZ010000001.1 86871770-86871960 c
257-402 JAXUCZ010000001.1 86870256-86870401 c
403-487 JAXUCZ010000001.1 86867879-86867963 c
488-600 JAXUCZ010000001.1 86866999-86867111 c
601-809 JAXUCZ010000001.1 86866431-86866639 c
810-916 JAXUCZ010000001.1 86864244-86864350 c
917-1064 JAXUCZ010000001.1 86863842-86863989 c
1065-1177 JAXUCZ010000001.1 86860356-86860468 c
1178-1368 JAXUCZ010000001.1 86859373-86859563 c
1369-1470 JAXUCZ010000001.1 86857163-86857264 c
1471-1742 JAXUCZ010000001.1 86855165-86855436 c
1743-1854 JAXUCZ010000001.1 86853682-86853793 c
1855-1936 JAXUCZ010000001.1 86852083-86852164 c
1937-2107 JAXUCZ010000001.1 86850554-86850724 c
FEATURES Location/Qualifiers
source 1..2107
/organism="Rattus norvegicus"
/mol_type="mRNA"
/strain="BN"
/db_xref="taxon:10116"
/chromosome="1"
/map="1q21"
gene 1..2107
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="hypoxia inducible factor 3 subunit alpha"
/db_xref="GeneID:64345"
/db_xref="RGD:70332"
exon 1..65
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
CDS 40..2034
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="isoform 2 is encoded by transcript variant 2;
HIF3-alpha; HIF-3-alpha; HIF3-alpha-1; hypoxia inducible
factor 3, alpha subunit; hypoxia inducible factor 3a;
Inhibitory PAS (Per/Arnt/Sim) domain protein;
hypoxia-inducible factor 3-alpha"
/codon_start=1
/product="hypoxia-inducible factor 3-alpha isoform 2"
/protein_id="NP_001375441.1"
/db_xref="GeneID:64345"
/db_xref="RGD:70332"
/translation="
MALGLQRVRSSTELRKEKSRDAARSRRSQETEVLYQLAHTLPFARGVSAHLDKASIMRLTISYLRMHRLCAAGEWNQVGKEGEPLDACYLKALEGFVMVLTAEGDMAYLSENVSKHLGLSQLELIGHSIFDFIHPCDQEELQDALTPRPSLSKKKSEAATGRHFSLRMKSTLTSRGRTLNLKAATWKVLHCSGHMRAYKPPAQTSPAGSPRSEPPLQCLVLICEAIPHPASLEPPLGRGAFLSRHSLDMKFTYCDERIAEVAGYSPDDLIGCSAYEYIHALDSDAVSRSIHTLLSKGQAVTGQYRFLARTGGYLWTQTQATVVSGGRGPQSESIICVHFLISRVEENGVVLSLEQTEQHTRRPPQLGTSSKKGIPGNSLDPPAPRILAFLHPPALSEASLAADPRRFCSPDLRRLMAPILDGPPTAATPSTPQAARRPQSPLPADLPDQLAVGLENAHRLSTARKNKTMETDLDIAQDPDTLDLEMLAPYISMDDDFQLNSSEQLPKVHRRPPRTARRPRARSFHGLSPPIPEATLLPRWGSDPRLNCSSSSKGDPPTAPLTPRTRKRALAQSSEDKGLELLETKPPKRSPRLEPGSVLLPPLSLSFLLQGRQLPGNQPDPRAPLVDSHEPLGLAPSLLSLYQHEETIQPRNHFLPAAGLAQTH"
misc_feature 73..261
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS)
domain found in hypoxia-inducible factor 3-alpha (HIF3a)
and similar proteins; Region: bHLH-PAS_HIF3a_PASD7;
cd19729"
/db_xref="CDD:381572"
misc_feature order(82..87,91..99,106..111,115..120,193..198)
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="putative DNA binding site [nucleotide binding];
other site"
/db_xref="CDD:381572"
misc_feature order(124..129,133..138,145..150,157..162,193..201,
208..213,220..222,229..234,241..243)
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="putative dimer interface [polypeptide binding];
other site"
/db_xref="CDD:381572"
misc_feature 307..474
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="PAS domain; Region: PAS; smart00091"
/db_xref="CDD:214512"
misc_feature 790..1053
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="PAS fold; Region: PAS_3; pfam08447"
/db_xref="CDD:430001"
misc_feature order(799..801,811..813,829..831,868..879,955..957,
970..972)
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="putative active site [active]"
/db_xref="CDD:238075"
misc_feature order(859..861,871..873,895..897,904..909,991..993,
997..999)
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="heme pocket [chemical binding]; other site"
/db_xref="CDD:238075"
misc_feature <1117..1938
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="large tegument protein UL36; Provisional; Region:
PHA03247"
/db_xref="CDD:223021"
misc_feature 1462..1557
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/note="Hypoxia-inducible factor-1; Region: HIF-1;
pfam11413"
/db_xref="CDD:463274"
exon 66..256
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 257..402
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 403..487
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 488..600
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 601..809
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 810..916
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 917..1064
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1065..1177
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1178..1368
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1369..1470
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1471..1742
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1743..1854
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1855..1936
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
exon 1937..2107
/gene="Hif3a"
/gene_synonym="Ipas; Mop7"
/inference="alignment:Splign:2.1.0"
ORIGIN
gctgggcatcgagggctctggaaccgcgaagggcgagccatggcgttggggctgcagcgcgtgaggtcgagcaccgagctgcggaaggagaagtcgcgggatgcggcccgcagcaggcgcagccaggagacggaggtgctgtaccaactggcgcacaccctgccctttgcgcgcggcgtcagcgcgcacctggacaaggcctccatcatgcgcctcacaatcagctacttgcgcatgcaccgcctctgcgctgcaggggagtggaaccaggtgggaaaagagggagaaccactggacgcctgctacctgaaggccctggagggtttcgtcatggtgctcaccgctgagggagacatggcttacctgtcggaaaatgtcagcaagcacctgggcctcagtcagctggagctcattggacacagtatctttgattttatccatccctgtgaccaagaggaactccaggatgccctgaccccgagaccaagcctgtcaaagaagaagtcagaagcagcaacaggacgccacttttccctgcgaatgaagagcacactcaccagcagggggcgcacgctgaacctcaaagcggccacctggaaggtgctgcactgctcaggacatatgagggcctacaagccccctgcacagacttcccccgccgggagccctcgctccgagcctcccctgcaatgcctggtgcttatctgtgaagccatcccccacccagccagtctggagcccccactgggccgaggggcctttctcagtcgccacagcctggacatgaagttcacatactgcgacgagaggattgcagaagttgctggctacagccccgatgacctgattggctgttctgcctatgaatacatccacgctttggactctgatgcagtcagcaggagcatccacactttgctgagcaagggccaggcagtaacagggcagtatcgcttcctggcccggactggaggctatctgtggactcagactcaggctacagtggtgtcaggggggcggggcccccagtcggaaagtatcatctgcgtccacttcctgatcagccgtgtagaagagaacggagtggtgctgtccctggaacaaacggagcaacatactcgcagaccccctcagctgggtacctcctcgaagaagggtatcccaggcaacagtctagaccctcccgctccacggatcctggccttcctgcaccctccagccctgagtgaggcctccctggctgctgaccctcgccgtttttgtagcccagacctgcgccgcctcatggcacccatcctggatggacctcccacagccgctacccccagcaccccgcaagctgcacggagaccccaaagtcctcttccggctgatctcccagatcagttggctgtgggcttggagaatgcacacagactctccactgcccggaaaaacaagaccatggagacagatctagatatagctcaggaccctgacactctggacttggagatgttggctccgtacatctccatggatgatgacttccagctcaactccagcgagcaattgcccaaagtccaccgcagacctcccaggacggcccgcaggcctcgtgctcggagcttccatggcctgtcgcctcccatccctgaggccaccctgctgccccgctgggggagtgatccacgactgaactgttccagctcctccaagggggatccccccacagcccccctgacgcctagaactcggaagagggccttggcccagagctcagaggacaaagggttggagctgctggaaacgaagccccccaagcggtccccaagactagaacctggaagtgtcctgctgcctccgctcagcctgagtttccttctgcaaggtcgacaacttccagggaaccagccggatcccagagccccactcgtggattcgcatgagcccttgggcctagctccctcgctgctctctctctaccagcatgaggaaactatccagcccaggaaccacttcctcccagcagcaggcttggcccagacacactgagtcagccttcctctcagccctcttcttctaccccagaaaggactcagccgcactccacaccagcagcctacac
//
by
@meso_cacase at
DBCLS
This page is licensed under a
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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