LOCUS       NM_001102413            2493 bp    mRNA    linear   ROD 26-OCT-2024
DEFINITION  Rattus norvegicus iroquois homeobox 6 (Irx6), transcript variant 1,
            mRNA.
ACCESSION   NM_001102413 XM_001064772 XM_226359
VERSION     NM_001102413.2
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 2493)
  AUTHORS   Star,E.N., Zhu,M., Shi,Z., Liu,H., Pashmforoush,M., Sauve,Y.,
            Bruneau,B.G. and Chow,R.L.
  TITLE     Regulation of retinal interneuron subtype identity by the Iroquois
            homeobox gene Irx6
  JOURNAL   Development 139 (24), 4644-4655 (2012)
   PUBMED   23172916
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000019.1.
            
            On Oct 26, 2024 this sequence version replaced NM_001102413.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360190.1163183.1,
                                           SRR26360190.3260949.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN14984041 [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-785               JAXUCZ010000019.1  30508598-30509382   c
            786-1034            JAXUCZ010000019.1  30507499-30507747   c
            1035-1144           JAXUCZ010000019.1  30506809-30506918   c
            1145-1452           JAXUCZ010000019.1  30506343-30506650   c
            1453-2067           JAXUCZ010000019.1  30505008-30505622   c
            2068-2493           JAXUCZ010000019.1  30503416-30503841   c
FEATURES             Location/Qualifiers
     source          1..2493
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="19"
                     /map="19p11"
     gene            1..2493
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="iroquois homeobox 6"
                     /db_xref="GeneID:307715"
                     /db_xref="RGD:1564830"
     exon            1..785
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    675..677
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="upstream in-frame stop codon"
     CDS             741..2072
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="isoform 1 is encoded by transcript variant 1;
                     Iroquois related homeobox 6; iroquois-class homeodomain
                     protein IRX-6"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-6 isoform
                     1"
                     /protein_id="NP_001095883.1"
                     /db_xref="GeneID:307715"
                     /db_xref="RGD:1564830"
                     /translation="

MAFPPFGHPYGGASQFLVSASSSATCCETAPRSVSDVASASTSASTLCCAPYDSRLLGSARPELGAALGIYGAPYAAAQSYPGYLTYGPEPPTLCGALNPQYEFKDAAGSFTPSLTQPGAYYPYETTLGQYQYDRYGGVELSSAGRRKNATRESTSALKAWLHEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWVPKNKGGEERKADGGGEDALGCLNGDTKDATASQEAQGLQLSDLEDLEEEEEEEEEEEAEKEEAAVSAARRLVGFPKSAQPLPAPCAAAQEGCLESTECGLAVPRFSFTEAPQSGEADFITAEPSGPTMIVHYPSGHKPRIWSLAHTAASSAVKGAPSTPPRGQSPECHMIPRQPSSVRRLLVPRFSGGEENSPAVKAFGNSTFALQGLPLNCAPCPRRREPEVRFQYPSGAEG"

     misc_feature    <1164..1406
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(1176..1184,1188..1190,1248..1250,1266..1268,
                     1305..1307,1311..1316,1323..1328,1332..1340,1344..1349)
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1176..1178,1185..1187,1314..1316,1323..1328,
                     1335..1337)
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1224..1340
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     exon            786..1034
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
     exon            1035..1144
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
     exon            1145..1452
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
     exon            1453..2067
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
     exon            2068..2493
                     /gene="Irx6"
                     /gene_synonym="RGD1564830"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

tgtattctctcctccctcgccgccccacttgcctcttgcctcctccgggccgcaggggaggaggcgagcacgctgcaccctgggcccgcacagctcgcagggaggcgtatttcccacttctcctggggaatttggagagggtctgtgcgtgcgcgcgcgcgtgagccgcaggcgaaagcgggtaggatctagcggcgagcagagggtcagggtctttgacgtttctcgccggttgcacaaacctcgcggagcaagaaagagtgtatccgagagtgcgtgcgtgtacacgggctggctgcccttggcacattcggtggcccggggccccggggcccgcggtcccctctggcggcccgggattaccgtgacgtcacattgagcctctggccaccttggactgggacacctccgcaacctcacagcccgacgccgctgcgctgtacctcaccttgccaccgcgcgcctttggtaccctgtaccttcttcttaattctgccgatccatgggcccctctgtcttctggaacgcacaggccgtaggggtgccttcccaaccgcaggactcggcagcccctctgcctttgactctgcctccagactctccccgcgggctaaggaactggcggtcagctcctgcagccctgtaaggaaaccagacaccgcgcgctggtgtcatagaatcaccgacctgagcaagggactcgaaagaaaggggaatcaaatccccgaagaccccctgctatggccttcccgccctttggacacccgtatggcggcgcatcccagtttctggtgtctgcaagttccagtgccacttgctgtgaaacggcccctcggtcagtgtcagatgtggcctcagcctccacctctgcctctactctttgctgtgcaccctatgacagtcggctgctgggcagtgctcggccagagctgggcgctgccttgggcatctatggagcaccttatgcagctgcccagagttacccagggtacctgacctatggcccagagccacctacactgtgtggtgcactgaatcctcagtatgagtttaaggatgctgcaggaagctttactcccagtctgacccagccaggggcctactacccctatgagacaactctggggcagtatcaatatgacaggtatggtggagtggagttgagcagcgctggccgcaggaagaatgccacaagagagagcaccagcgcactgaaggcctggctccacgaacaccgcaagaacccgtaccccactaagggcgagaagatcatgctggccatcatcaccaagatgaccctcacccaggtgtccacctggttcgccaacgcgcgccggcgcctcaagaaggaaaacaaaatgacgtgggtgcccaagaacaagggtggggaggagaggaaagcagatggtggaggagaagacgctctggggtgcctgaatggtgacaccaaagacgctactgccagccaagaggcccaggggctgcagctgagtgacttggaagatctggaggaagaggaggaagaggaggaagaggaagaagcagaaaaagaggaggcagcggtctcagcagcacggaggctggttggttttccgaagagcgcacagcccttgcctgctccctgtgctgccgctcaggagggctgcttggagagcacagagtgcggcttggctgtgccccgcttctcctttactgaagccccacaatcaggggaagctgactttattacagcagagccaagtggccccacgatgatcgtgcactacccaagcggccacaaaccccgcatttggtccttagctcacactgcagcatccagcgctgtcaaaggtgctccctcaactccgcccaggggacaaagtccagagtgccacatgattcccagacagcccagttctgtcaggcgactcctggtccccagattctcgggaggcgaagaaaattctcctgcagtcaaagctttcggaaactccacgttcgctctgcaggggctgccactgaactgtgcaccatgcccgaggcggagagagcctgaagtgcgcttccagtacccatctggagcagaaggttagctcaatgaccgcggtttgcagaagacttttggaaatggctgcttctggattcaccttcatattaagaaaactccaggccttggcagggtctgggagctctctcactttgcctaagacacacacacagaaccatccttgcacgccgggctggggctagccagacagacatgtacctaatcagacttggaggggagatggccttggggaaagccctgtgtgtgctcacagggtactcttaccaagtctctcttcctcctgtggatggaggtcccgaagagcatctcctcctgttcacccacccctgcccagtccactcactgtgtaactttcttgttgaaatggtctccaaggactgtctgtgtcttcttcctctccgtttttcctgacccaggttataccttcaaaaaatgactaagctgga

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