2024-03-29 10:33:47, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001395572 9213 bp mRNA linear ROD 20-JUL-2021 DEFINITION Rattus norvegicus highly divergent homeobox (Hdx), transcript variant 2, mRNA. ACCESSION NM_001395572 VERSION NM_001395572.1 KEYWORDS RefSeq. 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 9213) AUTHORS Gaudet P, Livstone MS, Lewis SE and Thomas PD. TITLE Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium JOURNAL Brief Bioinform 12 (5), 449-462 (2011) PUBMED 21873635 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from JACYVU010000430.1. 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## RNAseq introns :: mixed/partial sample support SAMD00132265, SAMD00155304 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## inferred exon combination :: based on alignments, homology ##RefSeq-Attributes-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-113 JACYVU010000430.1 413802-413914 c 114-1223 JACYVU010000430.1 371079-372188 c 1224-1277 JACYVU010000430.1 360393-360446 c 1278-1424 JACYVU010000430.1 324482-324628 c 1425-1632 JACYVU010000430.1 311007-311214 c 1633-1712 JACYVU010000430.1 303786-303865 c 1713-1796 JACYVU010000430.1 294110-294193 c 1797-1919 JACYVU010000430.1 284034-284156 c 1920-9213 JACYVU010000430.1 272009-279302 c FEATURES Location/Qualifiers source 1..9213 /organism="Rattus norvegicus" /mol_type="mRNA" /strain="BN" /db_xref="taxon:10116" /chromosome="X" /map="Xq31" gene 1..9213 /gene="Hdx" /gene_synonym="RGD1563666" /note="highly divergent homeobox" /db_xref="GeneID:317617" /db_xref="RGD:1563666" exon 1..113 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" misc_feature 63..65 /gene="Hdx" /gene_synonym="RGD1563666" /note="upstream in-frame stop codon" exon 114..1223 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" CDS 141..2045 /gene="Hdx" /gene_synonym="RGD1563666" /note="isoform 2 is encoded by transcript variant 2" /codon_start=1 /product="highly divergent homeobox isoform 2" /protein_id="NP_001382501.1" /db_xref="GeneID:317617" /db_xref="RGD:1563666" /translation="
MSSKSCESGTAGTVSGTSLAAPDITVRNVVNIARPSSQQSSWTSANNDVIVTGIYSPAGSSSKQGTTKHTNTQITEAQKIPIQKAASKNDTEFQLHIPVQRQVAHCKNASVLLGEKTIILSRQTSVLNAGNSVYNHTKKSYASSPVQASEMTVPQKPSVCQRPCKIEPVGIQRSYKPEHAALASHNLCGQKPTSRDPCCRTQNLEIREVFSLAVSDYPQRILGGNTTQKPGSAEGTCLSIAMETGDAEDEYAREEELASMGAQITSYSRFYESGSSLRAENQSTTLPGPGRNLSNSQMVNIRDVSDNVLYQTRDYHLTPRTSLHTASSTMYSNTNPSRSNFSPHFVSTNQLRLSQNQNNYQISGNLSVPWITGCSRKRALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIEVPPPRGGPADFSEQPESGSLSVLTPGEEAGPEVGEDNDRNDEVSICLSEASSQEESNELIPNEARAHKDEEHQAVSADNVKIEIIDDEESDMISNSEVEQENSLLDYKNEEVRFIENELEIQKQKYFKLQTFVRNLILAMKADDKEQQQALLSDLPPELEEMDFSHASPDPDDTSFSVSSLSEKNASDSL"
misc_feature 1287..1457 /gene="Hdx" /gene_synonym="RGD1563666" /note="Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner; Region: homeodomain; cd00086" /db_xref="CDD:238039" misc_feature order(1293..1295,1425..1427,1434..1439,1446..1448) /gene="Hdx" /gene_synonym="RGD1563666" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" exon 1224..1277 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1278..1424 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1425..1632 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1633..1712 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1713..1796 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1797..1919 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" exon 1920..9213 /gene="Hdx" /gene_synonym="RGD1563666" /inference="alignment:Splign:2.1.0" ORIGIN
attgtctgaggcggcagtggagacccaggaaaaaatctcgcggattccgcctgatctggccctagtctcatcttggatcctctgatctcttccgtgaccgcaccacgcccgagacgtgggttggcaataagcgaagaaaaatgagtagtaaaagctgtgagtcaggaacagcaggaactgtgtctggtacctcattggcagctccggacattacagtcagaaatgtggttaatattgcccgcccttccagccagcaatcttcttggacttctgccaataatgatgtcattgtaactggcatatacagtccggcaggctcatcaagtaagcaaggcactacaaagcatacaaatacacaaattacagaagcacagaaaattcctattcagaaggcagccagtaaaaatgacactgaatttcaattgcacattcctgttcaaagacaagtagcacactgtaaaaatgcttctgtgctcctaggggaaaagacaattattttgtcaagacagacaagtgtactaaatgctggaaactcagtgtacaatcacacaaagaaaagctacgcaagttctccggtgcaagcttctgaaatgacagtacctcaaaagccatctgtgtgccagagaccttgcaaaattgaaccagttgggatccaaaggtcatataaacctgaacatgcagctctggcatcacataacttatgtgggcaaaagccaaccagtagagacccttgctgtagaacacaaaacttggaaattcgtgaagtgttttcattggccgtcagtgattaccctcagagaattctgggaggaaataccacacagaagccaggctcagcagaaggaacttgtttgtccattgcaatggagactggagatgcagaggatgaatatgccagagaggaagagctagcatcaatgggagcacagataacaagctactcaaggttttatgaaagtggcagttcccttcgagctgagaaccaaagtacaactttgcctggaccaggaagaaacctgtcaaattcacaaatggtgaatattagagatgtgtcagacaatgtactgtatcaaactagagactaccatttgacaccacggacctcattgcatacagcatcaagtactatgtacagcaatactaatccatcacggagtaatttttctccacattttgtatcaacaaaccaactgaggttatcacaaaaccaaaacaattaccagatttcaggaaacctttctgtgccttggattacagggtgttctaggaaaagagcactacaggaccgcactcaattcagtgaccgagacttggctactcttaagaagtactgggacaatggtatgaccagcctgggctcagtatgtagagagaagattgaagctgttgcaacagaattaaatgtcgactgtgaaatagttcggacttggattgggaatcgaagaagaaaataccgtttaatgggaattgaagttccacctccaagaggaggccctgctgatttctctgagcagcctgagtctggttctttgtctgtactcacaccaggagaggaagctgggcctgaagtaggagaggataatgacagaaatgatgaagtgtccatctgtttgtccgaagcaagctctcaagaggagtccaacgaactaatcccaaatgaggccagggcacataaggatgaagagcatcaggcagtatccgcagataatgtgaaaatagaaattatcgatgatgaagaaagtgacatgataagcaattctgaggtagaacaagagaattctctcctggattataagaacgaagaagtcagattcattgaaaatgagttagagattcagaagcaaaaatactttaagctccagacttttgtgagaaacctgatcctcgctatgaaagctgacgataaagagcagcagcaggcactgctgtcagatttacctccagaattagaagagatggatttcagtcatgcctcaccagatcctgatgatacctcattcagtgtgtcttcattatcagagaaaaatgcctcagacagtttgtgattgggggtgggaaagatgatatagtctcttggttgcctaactggtgtgtgtttcaagataactgtactctgtttcccatatagtcttcaactggaaaaacacattgttaaaacagacgtatgctgtgaaggaatgacaagatttaatggctacagtacaaaagaagcatgtaaaatacttgaaatggtttgtttttaaaacttataaaatcctagaaaattataaattttgaccaactcagctatgaaatttattatatctgacttctgaaaggtttttttttgcttattctttaagaagaatcttaattttattcagaaatatagaaatgagcacatctcaacattactaagttgctaacacttggttagtattatttttgtagccattacatctttcttcctacttcattttcttatgattcatatacatttttactcaggaaagtgggctaaaattttaaaacagacctaatcatatatttaacctggatgaatcctgggatttatttttcaactcctatgagaatttggcctaagataatgattgaaaatcgaagcaattataggatgtaattttaagttattggtactcccctgacactggggaaaggggaaaatcctctgaaaagtcgactcatcatcaagacatttaagtacacaaagactgtactttgtaaaaaacacttttaatctcaattcttgtataaagtgagtgatagtattgctgattcatattctaccatatagtaaatttatataattgagtcagacaaaatattgcacaaatattcaagtttaccaacattttcttaatatttttcatatcttaaaatttttgaaacaggaaatcaaagtatgccactgatatttggttgtttttatttaattctagacatacaaccttgccacaaagtttacctcatttccatatgaggcctgcacagagccaacaataatgtcaaaaaaagaactatagtactttgattatagatcaaagacctgaatctcctggatgctattctatgaatacacaccgaaaatgggcatggtacccagttgttactattagtaggtaccaaatggcagcagactgtagacatctttttgcatctccctttctggaataccagatggcattactaaggtctgtagatgggaaaatactagtttctgcctaaacttacaatgtcatatatttgtaactaggttgtatggaactatattacacaattaaattattatctattcccaaaagatgcttgaagcatctgtaaaactgtttcaattgtcaactttcagataagtttcttaactgcagctattctggtctcagaatttactgataccaatttatgattacagaaagaccctcataaatccctttagctcagaaatgtcccttctcatcgatatatacaagtaaagttcattggtgaccattcagttcatcaaatgtttgattttacactgttgccacacaacctctatggcttccttgtcagcagaaatatttcagtagtcagctaaacatgtcctttaactgagagtcatgtggttctttgcaaacaacttttggtattccttgctgacaaaccaaattccattcaggggaaagactactgagcaacagaagctcaaacattcagattaagctcttcggtcacataaatttctccataaaataagagtcctcactctatacaacaaataccaaatccattattttatgatatggagaattaagacaaattctccagtagctcaagctggcctttaactcccaatatagctgaggatgacttggagttctgctgttcctgcctttgtttcccaaatgccaggatggatttcttttattatgagcacatttatagtctcatgtctctctgtgactttctttcgtgtcattgagtttctctataaacttaaactgcttcagtttaagaatcttcgtagttggttttcattgcagagtaaatcaggtgagtctttcctatgtgttttaacacacaaaaatttatttttcacatcttagaaatgtgtcactacatttaaaaatatccttagagttctcactataggaaagatattgtgccagacgctggatttttaaataatctatggactataaaaaattatttcagctgggtactaggacacatagcgataactccagcactgtgtaggctgaggaaagctggcttcaaaacacaaagaaacatttcctgttaacctttttctgtctgttaataaaagtttttcaaatggcagctataattgattgaaggattcttatagatgtgattcttagaaagaatcttacatctctaattttggaaggatgtataaactgttctattattcctatttaaagtttcattcaaatagaagctatgtgtcctaacagtctaataggactacttttatcctggtgtatttcttctagccacaggattatatcttttatgaacataggaattaaaacatttaaaaattttaagtggcagagttcttttgttttgtttttgtttttaaaacatttgttccttttattcacaaaacataagacttacccctttgttgaatctcttttctttatgattttacacaaaggaccttgagatatatcaattataaaacatgtcaaaaagaaagcatctttaaaagtttacaagtatgtacttatacaatccatcaatgtaaaaaagacattggattgaatgtaaggtatgttcagttgtcattagaattatttttgttcttttggagacttttctctcctctggtcctgacttctctttgattctctatctgctaggtttttcgcagtgtctcttggcaccattctgacacctgttgtcatcgtcatctcctttatgaccagaatgctttctactcctctcccctggcttggagtgatcttttcttcttatattatcactgtcttgatttcatgttctttgtttccaattttcagaaaaagaatcttcactcttgctgcttcttccctggctcaccatgcttgtcttctagctctctgtgcgagccttgttctctttctgccattgccaactctgctgtaactattctcacggcttctgtcctccatgggctttgctaggggatcttgccagtctgcatctcgtgagttctgcgctctgtgtctttcagaccttgctctctcagtcctccctttggtcctccctgactacttctcacctcctgtcacgtgtctggtggcccctggctaacttatctactctttacctctggccttctcttgtctcttctttcttgtacctttagctgtaggaggagcagtcacttgcttcactggattactctaagctgctcttgctgctgtcagaatctgagtcagagggatcagacgccaagaaagactctgaagaatggagatgtcaagattggtttcttttgctcagcttctggtttctggactacaatcaccttgggcgtatttttcagatgttctcgaagttcatttatcaaacctcagagacctatggaagtgaagaaattgatggcaaactgggtattatgtgggttgtcttggagtaacagtccttcaaataatgactgaagagtttcatcctttaacctcgcattcagtttatgaagtcacatgtattcacacagttcctggaagaagatcttgacaaaaatcctactagatgatgtcacggtctcttcactcagctttacacattcgagaacactccatggaattgcatctgtatataaaaggtgagtaaacatcttagcaatatttctcaatttgtctctaagcaatgaatgctgttggattgtatcttgaatatactttcaaataattccatgtattctcttttttgcatacaaaaccacccagctaacaagccaaaaaatttctcatcggtcctttgttgggcacagcaatcaagtttcatgtggcagagttcttttgtttgggtctcagcaaaatccattttcagcaacttgtgtgcacattcttcaaaatctaaacttgactgaatggtaagatacattgtataacaaaatgagcctaggttgatttctgttgtgtcatgaatagttactttttgacctccttcctctcctttttcttcttctttctcttccttatattcactacttccagcttcttggtctgtgtctgaatcactgtctccttcatcaaggatttccttttttttaatagcctcacacttctcttcattctccataaaaattgtgacccatcttaaaaacattaagattgaagttatctccaaggagagcatatgtgtaaactgaccgtcctcttccactaaggccttccagaataacagggcggtccttgaatctatccttccgtacagcaaacatcacttcgatcatgtactgaactcttttgtccaccttaggctcatgtagaatctttcacaggcatcaaagtttgcattgattcctattggtgacaactggtttaatttgagaccacattccttgaggaagctgatagcttcttcaacactcttcaagactgttggtctctctagaagcaaagtgagcatctccagtcacagaacctcatgtgccacattttggctagtaagatgtgccaaaaattttgaagcagccaggtagttgttatcattcctttgatatcctttccaaaaattaagaattaatttcttgaggattaattctccaatttgtgggaattttgagttgatcattgccaccaaagctgcataagcatgagtagaagattggagaagcactcggtgattgcagaacagatctggacagccatcctctccctctgactatgttctcttgaaggagctcttggataaataatacttatattggagatgttgaccttattgaggagaacattgattgatttcttcagggcctcccaactcatcctctgttctgctaagctgtttttatctgtaacctgttcctgcatcatcctgagctttgtcagaggaatatatgctccccaagtgtgggtgagcagtagatccatctcatccttcttctatgtaggttcttcctgagtagaactctgggttattcctcagcctgggtttctcatttcaggatatggaaatttctgttactgtttctgatgatctgcagatctatctctgcattttgctcagtccctaccttgtgatcccatgctgctgtcattgtaagagtatcctcttctagaaccctcatggtctgaccagctgtagtcagagtagtctctatgtgtgtgttggggcgggggtccattcttgttctgcgtatctgtcttctgggggaggagctccagaggtacgagttgtggctattccttctgtctcccagaggactgtttcacgtgtgccacactacttttcattttctgctgtcagctgacccaataaaccagatgcctcaggttcattcaagagacatttactcaatggtcgaggcccttgacagttttctttttctgcctccacacatcacctacagctccaccatgctgccatcacacctgaagtgccaaaaggcggtgttctatagcaagacacaaaggaaatagctttgtcaatgcaaaatcaaccatctttggcagattgaaaatatagcaatgaccttgaagaagtcaagatcaagtattataaaatgattatcaaattggaacactagcttagcatgtacagaaggcccccaggttcaatcccaagcacttcaataggaaaaccatgaaactactataatggaaacattttttatatatatgtagtggatttggttttgagattgtttttaaaaaacaggaaaaataatagctgctggctgttttcatgaacatatttgttgacttgtgaaaatcaactaactagcatttccttgacagtattaaaaacattttatactaccagaagtatcactccgagaagcagaagtaaatgggaaattttttcctacttttacttgcatttaaatgcttaactttaggatatcaaggactttctaatgtttatctgagagtagttatgttctaaaatgcaagttaaaagtgcaacgctgaaactacaataacaacaaaaagaaggtaccttcctcattcagtgaagctaaaattagttgcaagaaatgaaaattgcagttgccctggagaataggaaaattaacacatgcaaagaaaatgttaaaagaaaattggcctgtttagggaacctggggatgttttgttgtaaggtcagttatcaacaggacttttccacagcaacagtaagcagtgtatgaaatgtttgttactattggagaagaaaatgctgtggcccactcacatcctgtgttcagtatattgttaatatcgggacctcaaaaaatgtccaagagcttatttctacaaagacagagacagcttcttttagggcccttttattagggagtcttaccagtttgtaagagaaatgttaagtggcctatataaacagacactgattgatcaaaatgactttgtctccctttttgtggagggttgttcagccacttagcctgattgtttataatcacctttgaacgaaatcctgaaaatgttaactgctgccttttatccaggaggtagtgatgaaataccaggaatggtgtgtccttttaacaaaatttatttttaatcacatcccccgaatttaaaaaaaaaagtttttgtgctttgaagtgttacctgtgccactgtttctaaatggtggctagatttgtttttaagttgttgttaaccttgacagacagcactgtgccatgccctttgccaagttctgctttataatgctctaatgagaagcctactaacttgtgaacctacagttgacataaacaagcctttattaagaacagatttgccaaggggtggaagaagaaagggatattttcatgctaatacaattatgattgttccattaaattgtatactgggtatattttgttcttcattgaaattttattttgcattaacttactgagtaattccatttagcaatcctgcatcccattttactggtactacctctgaaacatattatctccttaaaaccatatcagattgtaatgtgaatttttgtagagtttttatttaaacttttatagaggcaataaatgatttccaactaaca
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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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