LOCUS       NM_057109               2392 bp    mRNA    linear   ROD 21-MAR-2023
DEFINITION  Rattus norvegicus BarH-like homeobox 1 (Barhl1), mRNA.
ACCESSION   NM_057109
VERSION     NM_057109.2
KEYWORDS    RefSeq; RefSeq Select.
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 2392)
  AUTHORS   Barh D, Garcia-Solano ME, Tiwari S, Bhattacharya A, Jain N,
            Torres-Moreno D, Ferri B, Silva A, Azevedo V, Ghosh P, Blum K,
            Conesa-Zamora P and Perry G.
  TITLE     BARHL1 Is Downregulated in Alzheimer's Disease and May Regulate
            Cognitive Functions through ESR1 and Multiple Pathways
  JOURNAL   Genes (Basel) 8 (10), 245 (2017)
   PUBMED   28956815
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2392)
  AUTHORS   Chellappa R, Li S, Pauley S, Jahan I, Jin K and Xiang M.
  TITLE     Barhl1 regulatory sequences required for cell-specific gene
            expression and autoregulation in the inner ear and central nervous
            system
  JOURNAL   Mol Cell Biol 28 (6), 1905-1914 (2008)
   PUBMED   18212062
REFERENCE   3  (bases 1 to 2392)
  AUTHORS   Li S and Xiang M.
  TITLE     Barhl1 is required for maintenance of a large population of neurons
            in the zonal layer of the superior colliculus
  JOURNAL   Dev Dyn 235 (8), 2260-2265 (2006)
   PUBMED   16752387
REFERENCE   4  (bases 1 to 2392)
  AUTHORS   Li S, Qiu F, Xu A, Price SM and Xiang M.
  TITLE     Barhl1 regulates migration and survival of cerebellar granule cells
            by controlling expression of the neurotrophin-3 gene
  JOURNAL   J Neurosci 24 (12), 3104-3114 (2004)
   PUBMED   15044550
REFERENCE   5  (bases 1 to 2392)
  AUTHORS   Li S, Price SM, Cahill H, Ryugo DK, Shen MM and Xiang M.
  TITLE     Hearing loss caused by progressive degeneration of cochlear hair
            cells in mice deficient for the Barhl1 homeobox gene
  JOURNAL   Development 129 (14), 3523-3532 (2002)
   PUBMED   12091321
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JACYVU010000115.1.
            
            On Nov 27, 2020 this sequence version replaced NM_057109.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB043981.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760393, SAMEA5760433
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1226              JACYVU010000115.1  5704245-5705470     c
            1227-1449           JACYVU010000115.1  5700520-5700742     c
            1450-2392           JACYVU010000115.1  5698148-5699090     c
FEATURES             Location/Qualifiers
     source          1..2392
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3p12"
     gene            1..2392
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="BarH-like homeobox 1"
                     /db_xref="GeneID:117232"
                     /db_xref="RGD:620648"
     exon            1..1226
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    686..688
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="upstream in-frame stop codon"
     CDS             761..1744
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="barH-related homeobox protein 1; bar-class
                     homeodomain protein MBH2; BarH-like 2"
                     /codon_start=1
                     /product="barH-like 1 homeobox protein"
                     /protein_id="NP_476450.1"
                     /db_xref="GeneID:117232"
                     /db_xref="RGD:620648"
                     /translation="

MEGSNGFGIDSILSHRAGSPALPKGDPLLGDCRSPLELSPRSESSSDCSSPASPGRDCLETSTSRPGAASGPGLDSHLQPGQLSAPAQSRTVTSSFLIRDILADCKPLAACAPYSSSGQPAAPEPGGRLAAKAGEDFRDKLDKSVSSASSDSEYKVKEEGDREISSSRDSPPVRLKKPRKARTAFTDHQLAQLERSFERQKYLSVQDRMELAASLNLTDTQVKTWYQNRRTKWKRQTAVGLELLAEAGNYSALQRMFPSPYFYPQSLVSNLDPGAALYLYRGPSAPPPALQRPLVPRILIHGLQGASEPPPPLPPLPGVLPRAAQPR"

     misc_feature    761..1030
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="propagated from UniProtKB/Swiss-Prot (P63156.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1097..1303
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="propagated from UniProtKB/Swiss-Prot (P63156.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    order(1295..1309,1313..1315,1364..1366,1382..1384,
                     1421..1423,1427..1432,1439..1444,1448..1456,1460..1465)
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(1301..1303,1310..1312,1430..1432,1439..1444,
                     1451..1453)
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    1304..1462
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    1667..1741
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /note="propagated from UniProtKB/Swiss-Prot (P63156.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            1227..1449
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /inference="alignment:Splign:2.1.0"
     exon            1450..2392
                     /gene="Barhl1"
                     /gene_synonym="Barhl2; Mbh2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gaaacaacaacaaaaaagccagccctaaagtaaaagtgacacaagttctattttttttttaaaggaaggaggggggttggcggcgaaggcgcgcgccgaggacaggtgagagctgcagtgggagcggcagggagctgtccacggtgctgacgggccctggcggggccgagcgtgcacgcaggagctctggggccaggtggggctgcttgatcctggggccgcggccgctgtccgcggtgctgagacctccaggtgcgctccgttctgcctgctggtaacgcggcccgggccggctgctatccgccgtgctgacccctgccctgggctaccgtttgcctggaggaagcgtgccgtttggattttgctttttcaaaagacgatctttattcagattctatcagcctcgcgtttcttcagtgccaaaggggccctcgggccgttcttctaccctttggctcttcccaacttggcgcgccctcctcccattcctccctgacactcccaccaccaccaccccaccccctcggctcggcggctcggcgcggtgctgcagaagacgctttgagcccttttggatgtgatgcgcagaggaggttggcccagagctcccaggctcccccaaggctgaactccatccaaggtgcccacaggctccctgcccgccttccccatgccagcccgcagctaggggcaggggcagcggcggctggggttgggggtgggtggggagcttttggggaggacaggtcgcagcttggctatggaaggctccaatggctttgggattgactccattctctcccaccgagcgggcagccccgcccttcccaagggggaccccttgcttggggactgccgttcacccctggagctgagtccacgctcagagagcagcagcgactgctcttcaccagcctcgcccggaagagactgtctggagaccagtacctcgcggcctggtgcagcatctggcccaggtttggactcccacctgcagccggggcagctttcagccccagcccagtcgcgaactgtcacctcctcctttctgatcagggacatccttgctgactgcaaacctctggcggcctgtgcaccctactctagcagtgggcagcctgcagcccctgagcctgggggccgccttgcggccaaggccggggaggactttcgagacaagctggacaaaagtgtcagcagcgcttcatcggactctgagtacaaagtgaaggaggagggcgaccgcgaaatctccagctctcgggacagtcctcccgtgcgcctgaaaaagccacgcaaagcacgcaccgccttcaccgaccatcagctggcgcagctggagcgtagcttcgagcggcagaaatacctgagtgtgcaagaccgcatggagctggccgcctctctgaacctcaccgacacgcaggtcaagacctggtaccagaaccgcaggactaaatggaagcgacagaccgctgtggggctggagctgctagcggaggcaggcaattattcggcgctccagagaatgttcccgtcgccttatttctacccgcagagtctcgtttccaacctggaccccggcgccgcactctatctgtaccgcggacccagtgcgccaccacctgccctccagagacctctggtgccccgcatcctcatccacggactccagggcgccagcgagccgcccccaccgctgcccccgctgcccggcgtccttccgcgcgctgcgcagccccggtgaagcgcgcgcttgccccaagccatgctctgggacccacagctcagcctgggcgcgggtccctcccttcgtcccggggcagggctgcccggctccccgccgcagcccagtgtccccgtgggaaagaaattcactgaggctacccctcccctgcgtcctctcttggctgctccatccaggaaccactcacacccgccggatgtacatatgcgcccctgcccacctctcagccacccccaggtccctgccggcttccccaggtgtcccctgtcccctcagcagcaggtaggggacgccggtctcccagacctgggcccacccttcttgcgcctctgcgggacagggtgggagcgctgtacggagtttccctcccatttcttttattctccctgagccccgggctagcagcggagctgtacatacagtgtgcaaagtgtatatgaagttatttattcgtgacccatgagcccgtgaccgtgtccgtgaatcagtgagtctgtggcctgtgccctccccatcccgggtggggcaggaaggggccgagagggcttgcccacgcgtcctggcccccagccccgctcgctccacccaggtcccaggacagccagatctcttgggttctctttttttaaatgtggaaataaacttctt

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