LOCUS       XM_017598146            2199 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus HHLA2 member of B7 family (Hhla2),
            mRNA.
ACCESSION   XM_017598146
VERSION     XM_017598146.2
DBLINK      BioProject: PRJNA677964
KEYWORDS    RefSeq; corrected model; includes ab initio.
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_051346.1) annotated using gene prediction method: Gnomon.
            Also see:
                Documentation of NCBI's Annotation Process
            
            [WARNING] On Feb 22, 2024 this sequence was replaced by
            XM_017598146.3.
            
            On Jan 21, 2021 this sequence version replaced XM_017598146.1.
            
            ##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##
            ab initio            :: 14% of CDS bases
            frameshifts          :: corrected 1 indel
            internal stop codons :: corrected 4 genomic stop codon
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-62                JACYVU010000222.1  30567455-30567516
            63-219              JACYVU010000222.1  30569270-30569426
            220-306             JACYVU010000222.1  30570004-30570090
            307-422             JACYVU010000222.1  30578253-30578368
            423-423             "N"                1-1
            424-562             JACYVU010000222.1  30578369-30578507
            563-672             JACYVU010000222.1  30578906-30579015
            673-2199            JACYVU010000222.1  30579656-30581182
FEATURES             Location/Qualifiers
     source          1..2199
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="11"
                     /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..2199
                     /gene="Hhla2"
                     /note="HHLA2 member of B7 family; 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; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 3
                     Proteins, and 75% coverage of the annotated genomic
                     feature by RNAseq alignments"
                     /db_xref="GeneID:108352332"
                     /db_xref="RGD:11472061"
     CDS             255..1163
                     /gene="Hhla2"
                     /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;
                     substituted 4 bases at 4 genomic stop codons"
                     /codon_start=1
                     /transl_except=(pos:738..740,aa:OTHER)
                     /transl_except=(pos:804..806,aa:OTHER)
                     /transl_except=(pos:855..857,aa:OTHER)
                     /transl_except=(pos:915..917,aa:OTHER)
                     /product="LOW QUALITY PROTEIN: HERV-H LTR-associating
                     protein 2"
                     /protein_id="XP_017453635.2"
                     /db_xref="GeneID:108352332"
                     /db_xref="RGD:11472061"
                     /translation="MKAHFVSVITLSPHGSQAFHTLVMNYIKRNIESCFLVCSILGVY
                     PRSHIAWEMDNTXIPESSSEETGAPGPFHIKSTENITGSNSSFECAIENSLLKKTWRR
                     EMVQCAYGIQRMICGSWFCPSAMWILAIELRLPDLAAGAHWRNQSDSISLWCTVRSNF
                     SXPNQNFHVTWFEVENGRYSVLDXNMSSPQDTIATYPQFSXNKELIDHSSFPVTLKDR
                     HVXDRGEHLCNVSSTECSFLTLHRVHVGKLQIGLANQLLMLQQRFGKTFQNVTDEATF
                     PHGGRRHNHLLISYSQKSSFSLFLCF"
ORIGIN      
        1 gaccatatga agatcaagaa gaaagaagac caaaatgtgg atgcttcagt ccttcatgga
       61 agcaaggcca catcaagtaa acctcagcaa gaaaaaagga ccaccaacaa ggaactgagg
      121 gttcgaatac acgaccatat gcaacatttc acattcaaac agagacactc ggagctcccc
      181 ggcccccatt ttaacagcag ccttgtgggt tacactaagc acagttaaca cagttaacat
      241 gagctctgcg agacatgaag gcacatttcg tctctgttat cacattgtcc cctcatggat
      301 ctcaagcttt ccacacgctg gtaatgaact atataaagag gaacatagag agctgcttcc
      361 tggtgtgcag tatcctgggt gtttatcctc gttcacatat cgcatgggaa atggacaata
      421 ctngtatccc ggaaagcagt tcagaagaaa ctggggctcc tggtccattt catattaaaa
      481 gtacagagaa tattacagga tccaattcat cttttgagtg tgctattgaa aattctcttc
      541 tcaagaaaac atggaggcga gagatggtac aatgtgccta tggaattcag agaatgatat
      601 gtgggagttg gttctgccct tctgccatgt ggatactggc tattgaacta aggttgccag
      661 acttggcggc aggtgctcat tggaggaatc aaagtgactc catttcactc tggtgtacgg
      721 tcaggagcaa tttttcttga ccaaaccaaa attttcatgt tacttggttc gaggtagaaa
      781 atgggagata ctctgtcttg gactagaata tgagttcacc acaggacaca attgctactt
      841 accctcaatt ctcatagaat aaagagctga tagatcacag ttccttccct gtcactttga
      901 aagatcgtca tgtgtgagat cgtggcgaac atttgtgtaa tgtttcttca actgagtgta
      961 gttttctcac tctccacagg gtgcatgtag gtaagttgca aataggactg gctaatcaac
     1021 ttctgatgtt acaacaaagg ttcggtaaga cttttcaaaa tgtcactgat gaagctactt
     1081 ttcctcatgg tggtaggaga cacaaccatc ttttgatcag ctactcccag aagagttctt
     1141 tttcattgtt tctgtgtttt taaaggaagg gaaatacgca tgttttggtg gttctaagat
     1201 aaataccttc aattcttgct cactgccctt tgtaatatat accctatagt tttggtttgg
     1261 gagctgaagc tgtaggcaca ggggaagtta gcattgggta ctactggatg ctggcaaacg
     1321 ttaatttggt ggaaaaaatg accacataat atatgaagcc cattcttgat gtactcaggt
     1381 ctgctcattt ttcactcctc tcagttgcca aaatctttgt ttataaggaa tatttctagt
     1441 ctactggcca tagtcaaaga atgtgggcca tgtagttggc tttctgggta acgtggttga
     1501 cttccccact cttactctat ggccttgtca cagaggaaac cccaatttca tcccttaata
     1561 aggatatttg atgttatgaa aattattatg tgtctcaaga atttttagtt atccatgtgt
     1621 tatgtgatct tcaaagaagg cttctatgct cagtgataaa atcccttttg atgatataga
     1681 atggaaaaat aaggatgcat ttataattcc tattttttct ccccaataag agtgttagtt
     1741 ttatgtaaaa tgcagtgaag cccaaattct atttttaaaa ccattgcctc atattggatt
     1801 cattttggag tatagaaaaa caatcaggaa gtagctgtcg gaagacaaca tgtgcccatc
     1861 tccttaagca gaaatttaga tttcatttca ccaaaagtaa agcatcaggg taattccagc
     1921 tccagaaaag attttacttt cagaacctct cattctcaca caagccctgt ccagtgcagc
     1981 ctggagagat tccgtccaca ttccctaaga agaggctgat agcaggagca tcccatcaga
     2041 gaaggaacca ggatgacagt catgtactag gtatgaagtt ttaactgaga cttgctttct
     2101 tagctagttc tctttctatt gccgtgacaa aacaccatga ccaaagcaac tcgtgaagga
     2161 aagcatttaa tttgggctca cagttgcaga gtgttagaa
//
