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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
//

by @meso_cacase at DBCLS
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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. [Full Text]