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2024-03-28 17:55:58, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_139036               1890 bp    mRNA    linear   ROD 20-MAR-2023
DEFINITION  Rattus norvegicus LIM homeobox 5 (Lhx5), mRNA.
ACCESSION   NM_139036
VERSION     NM_139036.2
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 1890)
  AUTHORS   Zhao Y, Kwan KM, Mailloux CM, Lee WK, Grinberg A, Wurst W,
            Behringer RR and Westphal H.
  TITLE     LIM-homeodomain proteins Lhx1 and Lhx5, and their cofactor Ldb1,
            control Purkinje cell differentiation in the developing cerebellum
  JOURNAL   Proc Natl Acad Sci U S A 104 (32), 13182-13186 (2007)
   PUBMED   17664423
REFERENCE   2  (bases 1 to 1890)
  AUTHORS   Pillai A, Mansouri A, Behringer R, Westphal H and Goulding M.
  TITLE     Lhx1 and Lhx5 maintain the inhibitory-neurotransmitter status of
            interneurons in the dorsal spinal cord
  JOURNAL   Development 134 (2), 357-366 (2007)
   PUBMED   17166926
REFERENCE   3  (bases 1 to 1890)
  AUTHORS   Zhao Y, Sheng HZ, Amini R, Grinberg A, Lee E, Huang S, Taira M and
            Westphal H.
  TITLE     Control of hippocampal morphogenesis and neuronal differentiation
            by the LIM homeobox gene Lhx5
  JOURNAL   Science 284 (5417), 1155-1158 (1999)
   PUBMED   10325223
REFERENCE   4  (bases 1 to 1890)
  AUTHORS   Tsuchida T, Ensini M, Morton SB, Baldassare M, Edlund T, Jessell TM
            and Pfaff SL.
  TITLE     Topographic organization of embryonic motor neurons defined by
            expression of LIM homeobox genes
  JOURNAL   Cell 79 (6), 957-970 (1994)
   PUBMED   7528105
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JACYVU010000228.1.
            
            On Dec 5, 2020 this sequence version replaced NM_139036.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: L35572.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760433, SAMN14984038
                                           [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
            1-510               JACYVU010000228.1  5339529-5340038     c
            511-734             JACYVU010000228.1  5337312-5337535     c
            735-1012            JACYVU010000228.1  5336428-5336705     c
            1013-1178           JACYVU010000228.1  5335598-5335763     c
            1179-1890           JACYVU010000228.1  5331599-5332310     c
FEATURES             Location/Qualifiers
     source          1..1890
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="12"
                     /map="12q16"
     gene            1..1890
                     /gene="Lhx5"
                     /note="LIM homeobox 5"
                     /db_xref="GeneID:124451"
                     /db_xref="RGD:71079"
     exon            1..510
                     /gene="Lhx5"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    248..250
                     /gene="Lhx5"
                     /note="upstream in-frame stop codon"
     CDS             338..1546
                     /gene="Lhx5"
                     /note="LIM homeobox protein 5; homeobox protein LIM-2"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx5"
                     /protein_id="NP_620605.1"
                     /db_xref="GeneID:124451"
                     /db_xref="RGD:71079"
                     /translation="
MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFRRFGTKCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEELYVIDENKFVCKDDYLSSSSLKEGSLNSVSSCTDRSLSPDLQDPLQDDPKETDNSTSSDKETANNENEEQNSGTKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRMKQLSALGARRHAFFRSPRRMRPLGGRLDESEMLGSTPYTYYGDYQSDYYAPGGNYDFFAHGPPSQAQSPADSSFLAASGPGSTPLGALEPPLAGPHGADNPRFTDMISHPDTPSPEPGLPGALHPMPGEVFSGGPSPPFPMSGTSGYSGPLSHPNPELNEAAVW"
     misc_feature    350..505
                     /gene="Lhx5"
                     /note="The first LIM domain of Lhx1 (also known as Lim1)
                     and Lhx5; Region: LIM1_Lhx1_Lhx5; cd09367"
                     /db_xref="CDD:188753"
     misc_feature    order(350..352,359..361,413..415,422..424,431..433,
                     440..442,491..493,500..502)
                     /gene="Lhx5"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188753"
     misc_feature    527..694
                     /gene="Lhx5"
                     /note="The second LIM domain of Lhx1 (also known as Lim1)
                     and Lhx5; Region: LIM2_Lhx1_Lhx5; cd09375"
                     /db_xref="CDD:188761"
     misc_feature    order(527..529,536..538,593..595,602..604,611..613,
                     620..622,680..682,689..691)
                     /gene="Lhx5"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188761"
     misc_feature    707..895
                     /gene="Lhx5"
                     /note="propagated from UniProtKB/Swiss-Prot (P61376.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    order(878..892,896..898,947..949,965..967,1004..1006,
                     1010..1015,1022..1027,1031..1039,1043..1048)
                     /gene="Lhx5"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    884..1045
                     /gene="Lhx5"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(884..886,893..895,1013..1015,1022..1027,1034..1036)
                     /gene="Lhx5"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    <1076..>1513
                     /gene="Lhx5"
                     /note="EBNA-3B; Provisional; Region: PHA03378"
                     /db_xref="CDD:223065"
     misc_feature    1229..1543
                     /gene="Lhx5"
                     /note="propagated from UniProtKB/Swiss-Prot (P61376.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            511..734
                     /gene="Lhx5"
                     /inference="alignment:Splign:2.1.0"
     exon            735..1012
                     /gene="Lhx5"
                     /inference="alignment:Splign:2.1.0"
     exon            1013..1178
                     /gene="Lhx5"
                     /inference="alignment:Splign:2.1.0"
     exon            1179..1890
                     /gene="Lhx5"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
cggcgcctccgccaaccgggaaagccgctcgccagtgccgaagccagcagccgccgaggacacctgctcgaagctggagcgagcgcccagacgcgacccgtgacatgaggctgtgaccgccgccgccctccacgccactctgggcagtgcagtgccaggccggagagcgtcggaggacttgaccccgagaagtcttggttgatctgtatcggactcgaccctaccgaagaccacagaccaggggggctgagagccacagcagcggggaccgagaggccctaagggcccaggggccccaaggaggacgaggcggcccgagccgccggggcgcgcggctatgatggtgcactgtgccggctgtgagcggcccatcctcgaccgctttctgctgaacgtgctggaccgcgcgtggcatatcaaatgtgttcaatgctgcgagtgcaaaaccaacctctcggagaagtgtttctcccgggagggcaagctgtactgtaaaaacgacttcttcaggcgctttggcacaaagtgcgccggctgtgcgcaaggtatctctcccagcgacctggtgcgcaaggcccggagcaaagtcttccacctcaactgcttcacctgcatggtgtgcaacaagcagctgtccaccggagaagaactctacgtgatcgacgagaacaagtttgtgtgcaaggacgactacttaagctcctctagtctcaaagagggaagcctcaactcagtgtcatcctgtacggaccgcagtttgtctccggacctccaagatccgttacaggacgaccccaaagagaccgacaactcgacctcatcggacaaggagaccgctaacaacgagaatgaggaacagaactccggcaccaaacggcgcggcccgcgcactaccatcaaggccaagcagctggagacgctcaaggcagccttcgcagccacgcccaagcccacgcgccacatccgcgaacagctggcacaagagaccggcctcaacatgagggtcattcaggtgtggtttcagaaccgaaggtccaaagaacgccgcatgaaacagctgagcgctctgggcgcccggagacacgccttcttccggagtccgcggcgcatgcgtcccctgggcggccgcttggacgagtctgagatgttggggtctaccccatatacttattatggagactaccaaagcgactactacgctccgggaggcaactacgatttcttcgcgcacggcccgccgtcgcaggcacagtctccggccgactcaagcttcttggcagcatcgggacctggctcgacgccgcttggcgcgctggaaccaccgctggctgggcctcacggcgcggacaaccctaggttcaccgacatgatctcgcacccggacacgcccagtccggagccaggcttgcccggagcgctgcaccccatgccgggagaggtgttcagcggcgggcccagcccgcccttccccatgagcggcaccagcggctacagcggacccctgtcgcaccccaatcctgagctcaacgaagcggccgtatggtaaggccgaggggccgagttgacccctgccaccaagccccggacgccgcctgggtaagccacaagagtcttctcttgagtttgcacccaccaggcaactcgcatcaccacccctcagagcttcggcacgcgcctgcacagtttctcgggaccaaagtcaatattctggagggtcgagattccaagcacaccctagaagccctccggacccccacccaaccatcacctctttgaattaagagggggaggggatgagacaaggaacggagatcgtggtactacccctccctgcgagccgaggcattgtggaatcctatttctcgctttctctttttaaaaaggaaggaa
//

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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]