LOCUS       XM_001055972            1694 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus forkhead box D4 (Foxd4), mRNA.
ACCESSION   XM_001055972
VERSION     XM_001055972.5
DBLINK      BioProject: PRJNA677964
KEYWORDS    RefSeq; corrected model.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_051336.1) annotated using gene prediction method: Gnomon,
            supported by mRNA evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            [WARNING] On Feb 22, 2024 this sequence was replaced by
            XM_001055972.6.
            
            On Jan 21, 2021 this sequence version replaced XM_001055972.4.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Updated annotation
            Annotation Name             :: GCF_015227675.2-RS_2023_06
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.1
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 06/06/2023
            ##Genome-Annotation-Data-END##
            
            ##RefSeq-Attributes-START##
            frameshifts          :: corrected 3 indels
            internal stop codons :: corrected 2 genomic stop codons
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1107              JACYVU010000047.1  9578876-9579982     c
            1108-1251           JACYVU010000047.1  9578731-9578874     c
            1252-1290           JACYVU010000047.1  9578690-9578728     c
            1291-1291           "N"                1-1
            1292-1694           JACYVU010000047.1  9578287-9578689     c
FEATURES             Location/Qualifiers
     source          1..1694
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="1"
                     /sex="male"
                     /tissue_type="kidney"
                     /geo_loc_name="USA: Wisconsin, Milwaukee, Medical College
                     of Wisconsin"
                     /collection_date="2019-03-08"
                     /collected_by="Rebecca Schilling"
     gene            1..1694
                     /gene="Foxd4"
                     /note="forkhead box D4; The sequence of the model RefSeq
                     transcript was modified relative to its source genomic
                     sequence to represent the inferred CDS: inserted 1 base in
                     1 codon; deleted 3 bases in 2 codons; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 1
                     mRNA, 9 Proteins, and 78% coverage of the annotated
                     genomic feature by RNAseq alignments"
                     /db_xref="GeneID:252886"
                     /db_xref="RGD:621716"
     CDS             31..1329
                     /gene="Foxd4"
                     /note="The sequence of the model RefSeq protein was
                     modified relative to its source genomic sequence to
                     represent the inferred CDS: inserted 1 base in 1 codon;
                     deleted 3 bases in 2 codons; substituted 2 bases at 2
                     genomic stop codons"
                     /codon_start=1
                     /transl_except=(pos:1189..1191,aa:OTHER)
                     /transl_except=(pos:1276..1278,aa:OTHER)
                     /product="LOW QUALITY PROTEIN: forkhead box protein D4"
                     /protein_id="XP_001055972.2"
                     /db_xref="GeneID:252886"
                     /db_xref="RGD:621716"
                     /translation="MNLARAGHLLSTPPPSPLSSDPEEVEIDVLAEEEDGDQTEDDGG
                     EESHKCLERSLQRPGARTLARRSAWDCGDLSNSSGFLRKFRAPRTRATTTTADGPQPA
                     KPPYSYIALITMAILQSPHKRLTLSGICAFISGRFPYYRRKFPAWQNSIRHNLSLNDC
                     FVKIPREPGHPGKGNYWSLDPASQDMFDNGSFLRRRKRFKRHHPPPGGHPHCPFPPPA
                     VPATVQVSQPGLLLRYSAPPQPNLAVHPASPPRSRPCAPLHPYPLRYLLLAAPAYADE
                     PRKAEGADPATSLAIPALQPAPGSQPWEGDQGSGSRSRRGCASFTIESIMQGVTGGGT
                     GSAQSPPFAPWSYCHLLQHPPCLLHPQAASPLFHVPAASRTVLQQQQPRPPPXQQEEH
                     HCAIRCSPGKGKRLGRHLSASEDXRLTTXLSGREGTLPAF"
ORIGIN      
        1 gtctcctctc cctcctccct cttatcctcc atgaacttag caagagctgg gcaccttctc
       61 tccactccgc cgcccagtcc tctaagctcc gacccagaag aggtggagat cgacgtgctg
      121 gcagaggagg aagatggaga tcagacggaa gacgacggtg gggaagagag tcataagtgc
      181 ctggagcgat cgctacagag gccgggagcc cgcacccttg caaggaggag cgcgtgggac
      241 tgcggcgacc tgagcaactc ctccgggttc ctccgcaagt tccgagcgcc gcggactcgg
      301 gccaccacca ccacagccga cggcccgcag cccgccaagc cgccgtactc ctacatcgcg
      361 ctcatcacca tggccatcct gcagagcccg cacaagcgcc tgacgctcag cggcatctgc
      421 gccttcatca gcggccgctt cccctattac cgccgcaagt tccccgcctg gcagaacagc
      481 attcgccaca acctgtcgct caacgactgc ttcgtcaaga tcccccgcga gccgggccac
      541 ccgggcaagg gcaactactg gagcttggac cccgcctctc aggacatgtt cgacaatggc
      601 agcttccttc ggcgtaggaa gcgcttcaag cgccaccacc cgcccccggg aggccacccg
      661 cactgtccct tccctccacc cgctgtgccc gccaccgtgc aggtctccca gcccggcctc
      721 ctgctccgct actctgcccc gccgcagcct aacctcgcag tccatcccgc ctccccgccc
      781 cggagccgcc cgtgcgcgcc gctgcatccg tatcccctcc gctacctgct gctcgctgcc
      841 cccgcctacg cggatgagcc tagaaaagcc gaaggtgcgg accccgccac ctccctcgcc
      901 atccccgctc tgcagcccgc accgggctcc cagccttggg agggagacca gggctctgga
      961 tctcggtccc gacgcgggtg cgcctctttc accatcgaga gcatcatgca gggggtgaca
     1021 gggggaggaa ctgggtctgc gcagagtccg cccttcgctc cgtggagcta ctgccacctg
     1081 ctgcagcacc caccgtgcct gctgcaccca caggccgctt cccctttgtt tcacgtgccc
     1141 gcagcttccc ggacagtgtt gcagcagcag cagccgcggc cgccgccgta gcagcaggaa
     1201 gagcatcact gtgccattag atgctctccc ggtaaaggca agcggctagg ccggcacctg
     1261 tctgcatctg aagactgaag gctgacaact ntcctttcgg gcagagaggg gaccttgccc
     1321 gcattttaag ccgtacccaa actcagcctc caggctgagt cgccttggca cacctggagc
     1381 caagtggcag aatggcactt gctttgtagt cgctagcggt ttgtgcgtgg aaaaccagca
     1441 tctgagcggg tctaaatcct tgcaaattgt tacaactgtg ttctgctcgc tttaagaccc
     1501 aaacgcggga aattcccggg actgcaagtc tcgccttgtc ttgtggactt cagttgtggc
     1561 ttccagggtt ttcctgattt acatacttgg acctatggac tatgaacgtg agtgaagtgt
     1621 ttgttgttaa taaaaaaaaa atctgtgaca caaaaacatc cccatcttca ttctctagga
     1681 actgcaagtg ttcc
//
