LOCUS       XM_039096438            2604 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus synaptonemal complex protein 2-like
            (Sycp2l), mRNA.
ACCESSION   XM_039096438
VERSION     XM_039096438.1
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_051352.1) 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_039096438.2.
            
            ##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            :: 9% of CDS bases
            frameshifts          :: corrected 1 indel
            internal stop codons :: corrected 1 genomic stop codon
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-171               JACYVU010000288.1  9090837-9091007     c
            172-276             JACYVU010000288.1  9086997-9087101     c
            277-301             JACYVU010000288.1  9086523-9086547     c
            302-387             JACYVU010000288.1  9082008-9082093     c
            388-476             JACYVU010000288.1  9081813-9081901     c
            477-511             JACYVU010000288.1  9076769-9076803     c
            512-654             JACYVU010000288.1  9075366-9075508     c
            655-707             JACYVU010000288.1  9072835-9072887     c
            708-753             JACYVU010000288.1  9072045-9072090     c
            754-846             JACYVU010000288.1  9070649-9070741     c
            847-907             JACYVU010000288.1  9070492-9070552     c
            908-1053            JACYVU010000288.1  9068982-9069127     c
            1054-1147           JACYVU010000288.1  9067123-9067216     c
            1148-1245           JACYVU010000288.1  9066601-9066698     c
            1246-1303           JACYVU010000288.1  9064853-9064910     c
            1304-1382           JACYVU010000288.1  9064687-9064765     c
            1383-1431           JACYVU010000288.1  9061387-9061435     c
            1432-1576           JACYVU010000288.1  9058722-9058866     c
            1577-1626           JACYVU010000288.1  9058223-9058272     c
            1627-1760           JACYVU010000288.1  9055879-9056012     c
            1761-1843           JACYVU010000288.1  9054070-9054152     c
            1844-1917           JACYVU010000288.1  9047749-9047822     c
            1918-1987           JACYVU010000288.1  9047520-9047589     c
            1988-2062           JACYVU010000288.1  9043621-9043695     c
            2063-2166           JACYVU010000288.1  9042249-9042352     c
            2167-2264           JACYVU010000288.1  9041069-9041166     c
            2265-2394           JACYVU010000288.1  9038659-9038788     c
            2395-2431           JACYVU010000288.1  9038620-9038656     c
            2432-2492           JACYVU010000288.1  9036028-9036088     c
            2493-2604           JACYVU010000288.1  9034951-9035062     c
FEATURES             Location/Qualifiers
     source          1..2604
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="17"
                     /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..2604
                     /gene="Sycp2l"
                     /note="synaptonemal complex protein 2-like; The sequence
                     of the model RefSeq transcript was modified relative to
                     its source genomic sequence to represent the inferred CDS:
                     deleted 2 bases in 1 codon; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 1
                     Protein, and 53% coverage of the annotated genomic feature
                     by RNAseq alignments"
                     /db_xref="GeneID:364688"
                     /db_xref="RGD:1564922"
     CDS             1..2604
                     /gene="Sycp2l"
                     /note="The sequence of the model RefSeq protein was
                     modified relative to its source genomic sequence to
                     represent the inferred CDS: deleted 2 bases in 1 codon;
                     substituted 1 base at 1 genomic stop codon"
                     /codon_start=1
                     /transl_except=(pos:1759..1761,aa:OTHER)
                     /product="LOW QUALITY PROTEIN: synaptonemal complex
                     protein 2-like"
                     /protein_id="XP_038952366.1"
                     /db_xref="GeneID:364688"
                     /db_xref="RGD:1564922"
                     /translation="MWVTPGRALKSVCSDAQELDKNEFQNCSLLLKCIQRFFKEDSDQ
                     EESLLIQQGLIPKMVSWFETMTGFLMTEVLASEALLTNAVEDFLDTALIVSRHSRTGT
                     IQMLDSFILRLGFLVTEGSVKPYIQQEALKTVNCILNAAPREERRKLSSTEGARCLMK
                     ELARTILTVGDYSQQVALSEALCRMAVGSWRNELATQWFEDTVLAEAFKEVKNWEFET
                     DCRQFLNFLNNRLGDQRRVYSFPCLAAFADAQEMRKPADEKLEEFWIDFNLGSQSVTF
                     YIDNAESALWEPVQLLKEAVTKFFIIENESIKMFIVYLKQPIVISKREAKKIEIYFDR
                     QLDISQASIQALEEDEQAHSFQASVLIKVSSGLEKEDGEIPSSLEGETEDKEESTVLP
                     EFVDAEVDQCLITRRFNVQSVPTQTKSEDCSPENSKPDEPEQVTSEYEYSVDVQDLSI
                     QNQASTLNNTKEESAFARDREQGRRMSFNDRKHYILESNEGSSSNTSERSWTQNHKRK
                     SLRTYSQRRKTRVSSLRILPLSPIRSGRVPEKDEAELTPLWKGIPRRNNSTPLNISET
                     KLRESSVLLTPEASTQKIGTXFEMPERRGSEPSSSTKKTGETDGLHWREFQSPHSSSS
                     LSSLERPEVEKNEPQIVNCEPFMGNRSSKHKLESSEHRETPDGSAVALKQSRLEDAPG
                     SPIVADISTPSQEDVPENTNSSALKMAFENFTRDLKRKFELRLKQREIPLSSEKAKEV
                     PACLIRLWNQIHTCRQDKLEGFHSSVLQELGSLEKDLQTLECLEKDALASLLFVLSLG
                     KERTSSRPKSMDCLTKLVLIRKARAWLYDGTLRGSSLRRKMEMESGVLEAKNCPSELH
                     SAANSPSELLS"
ORIGIN      
        1 atgtgggtaa caccgggcag agctttgaag tcagtgtgtt ccgatgccca ggagctggat
       61 aaaaacgagt tccagaattg ttccctgctg ctgaaatgta tccagagatt cttcaaagag
      121 gactcagacc aggaggagtc tttgcttatc cagcagggac tgatcccaaa gatggtttcc
      181 tggtttgaaa cgatgacggg ctttctgatg accgaagtgc tggcctcgga ggcactgctg
      241 accaacgccg tggaagactt cctcgacaca gcactgatcg tttccaggca tagcaggaca
      301 gggacaatcc agatgctgga ttccttcata cttcgtttag gattcctggt gacagaaggc
      361 tcggtgaagc cctacattca gcaggaggct ctgaagaccg tgaactgcat tttgaacgct
      421 gcaccccggg aagagagaag aaagctctct tcgacagaag gcgcacgctg tcttatgaaa
      481 gaattggcaa gaacgatctt gaccgtgggc gattatagcc agcaggtcgc gctctctgag
      541 gcgctatgtc gaatggctgt tggatcatgg aggaatgaac tcgctactca gtggtttgag
      601 gataccgtcc tggctgaagc tttcaaagaa gttaagaatt gggagtttga gacggactgt
      661 cggcagtttc tcaatttcct caataacaga ctcggcgacc agagaagggt ctactcattc
      721 ccatgcctgg ctgcttttgc cgacgctcag gagatgagaa aaccagcaga tgaaaaatta
      781 gaggaatttt ggatcgattt caacctagga agccagagtg tgacttttta catagataac
      841 gcagagagtg ctctgtggga gccagtacaa cttttgaagg aagccgtgac caaattcttc
      901 attatcgaaa atgaaagcat aaagatgttc attgtttacc tgaagcagcc aattgttatc
      961 agcaagagag aagcaaagaa aatagaaatc tacttcgata ggcaacttga catatcacaa
     1021 gcttccattc aagctttgga agaagacgaa caggcccatt catttcaggc ttctgttttg
     1081 ataaaagtct cctctggcct tgaaaaagaa gatggtgaga ttcctagtag cctcgaagga
     1141 gaaacagagg ataaagaaga atccacagtc ctgccagagt tcgtggatgc tgaagttgac
     1201 caatgcctaa taactcgccg ctttaacgtc cagtcggtgc ccactcaaac aaaatctgag
     1261 gactgttcac ctgaaaactc aaagccagat gagcccgaac aagttacttc agaatatgag
     1321 tattctgtgg atgtgcaaga tctgtcaatt caaaatcagg cttccacatt aaataataca
     1381 aaggaagagt ctgcctttgc gagggacaga gaacagggca gaaggatgtc gtttaatgat
     1441 aggaaacatt acatcttgga gagtaacgaa ggttcaagtt caaataccag tgaacgatcc
     1501 tggacccaga accacaaaag gaaatcccta agaacttact cccagaggag gaagacgaga
     1561 gtcagctctc tacggatcct accactctcc cccatcagaa gtggccgtgt tcctgagaaa
     1621 gatgaagccg agctaacacc actatggaaa ggcatcccca ggagaaacaa ttccactcct
     1681 ctaaacattt ctgagacaaa actacgagaa agttctgtgc tgttaacgcc tgaggcatct
     1741 acacagaaaa taggtacttg attcgagatg cctgaacgta ggggctcaga acccagctcc
     1801 tccacaaaga agacaggaga gacagatggt ctacactgga gagaattcca aagtcctcat
     1861 tcgtccagca gtctgtcttc cttggagcgc ccggaagtag agaaaaatga accccagatt
     1921 gtgaactgcg aaccattcat ggggaaccgt agctcaaagc acaagctaga aagctcggaa
     1981 cacagagaga cacccgatgg gagtgctgtt gccctaaagc agtcaagatt agaagatgct
     2041 ccaggatccc ccattgtggc agacatttct actccatctc aagaagatgt gccagaaaac
     2101 acaaatagtt ctgctttaaa aatggccttt gaaaacttca ctagagatct gaaaagaaaa
     2161 tttgagctta ggctcaagca gagggagatt ccactctctt cagaaaaggc aaaggaagtg
     2221 ccagcttgcc taatcagact ttggaaccag atacacacat gcagacagga caagctggag
     2281 gggtttcaca gctctgtcct tcaggagctg ggcagcttgg agaaggatct tcaaacactg
     2341 gaatgcctcg agaaggatgc tctggcaagt ttactgtttg tgctgtccct gggaaaagag
     2401 aggacctctt ctaggccaaa aagcatggat tgtttgacca aactcgtttt aataagaaaa
     2461 gccagagctt ggctttatga cggcaccctc aggggcagca gcctgaggag gaagatggag
     2521 atggagtctg gggtgctgga ggccaagaac tgtccttcgg aactacactc ggcagcaaac
     2581 agcccttcgg agctgctgag ctag
//
