LOCUS       NM_001108348            1908 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus LIM homeobox 4 (Lhx4), mRNA.
ACCESSION   NM_001108348 XM_001072440 XM_039090907 XM_341135
VERSION     NM_001108348.2
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 1908)
  AUTHORS   Hertz,H., Carstensen,M.B., Bering,T., Rohde,K., Moller,M.,
            Granau,A.M., Coon,S.L., Klein,D.C. and Rath,M.F.
  TITLE     The Lhx4 homeobox transcript in the rat pineal gland: Adrenergic
            regulation and impact on transcripts encoding
            melatonin-synthesizing enzymes
  JOURNAL   J Pineal Res 68 (1), e12616 (2020)
   PUBMED   31609018
  REMARK    GeneRIF: The current study was undertaken to clarify the mechanisms
            driving rhythmic LIM homeobox 4 (Lhx4) expression in the pineal
            gland and the possible regulatory impact of Lhx4 on gene
            transcripts involved in melatonin synthesis and other biological
            processes.
REFERENCE   2  (bases 1 to 1908)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   3  (bases 1 to 1908)
  AUTHORS   Tian,G., Singh,U., Yu,Y., Ellsworth,B.S., Hemberger,M., Geyer,R.,
            Stewart,M.D., Behringer,R.R. and Fundele,R.
  TITLE     Expression and function of the LIM homeobox containing genes Lhx3
            and Lhx4 in the mouse placenta
  JOURNAL   Dev Dyn 237 (5), 1517-1525 (2008)
   PUBMED   18425848
REFERENCE   4  (bases 1 to 1908)
  AUTHORS   Machinis,K. and Amselem,S.
  TITLE     Functional relationship between LHX4 and POU1F1 in light of the
            LHX4 mutation identified in patients with pituitary defects
  JOURNAL   J Clin Endocrinol Metab 90 (9), 5456-5462 (2005)
   PUBMED   15998782
REFERENCE   5  (bases 1 to 1908)
  AUTHORS   Raetzman,L.T., Ward,R. and Camper,S.A.
  TITLE     Lhx4 and Prop1 are required for cell survival and expansion of the
            pituitary primordia
  JOURNAL   Development 129 (18), 4229-4239 (2002)
   PUBMED   12183375
REFERENCE   6  (bases 1 to 1908)
  AUTHORS   Arber,S., Han,B., Mendelsohn,M., Smith,M., Jessell,T.M. and
            Sockanathan,S.
  TITLE     Requirement for the homeobox gene Hb9 in the consolidation of motor
            neuron identity
  JOURNAL   Neuron 23 (4), 659-674 (1999)
   PUBMED   10482234
REFERENCE   7  (bases 1 to 1908)
  AUTHORS   Sharma,K., Sheng,H.Z., Lettieri,K., Li,H., Karavanov,A., Potter,S.,
            Westphal,H. and Pfaff,S.L.
  TITLE     LIM homeodomain factors Lhx3 and Lhx4 assign subtype identities for
            motor neurons
  JOURNAL   Cell 95 (6), 817-828 (1998)
   PUBMED   9865699
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000013.1.
            
            On or before Mar 12, 2021 this sequence version replaced
            XM_039090907.1, NM_001108348.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMN12840120,
                              SAMN17050745 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-318               JAXUCZ010000013.1  70467188-70467505   c
            319-490             JAXUCZ010000013.1  70449606-70449777   c
            491-693             JAXUCZ010000013.1  70434358-70434560   c
            694-848             JAXUCZ010000013.1  70430835-70430989   c
            849-1020            JAXUCZ010000013.1  70430365-70430536   c
            1021-1908           JAXUCZ010000013.1  70427394-70428281   c
FEATURES             Location/Qualifiers
     source          1..1908
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="13"
                     /map="13q21"
     gene            1..1908
                     /gene="Lhx4"
                     /note="LIM homeobox 4"
                     /db_xref="GeneID:360858"
                     /db_xref="RGD:1308044"
     exon            1..318
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
     CDS             243..1415
                     /gene="Lhx4"
                     /note="LIM homeobox protein 4"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx4"
                     /protein_id="NP_001101818.2"
                     /db_xref="GeneID:360858"
                     /db_xref="RGD:1308044"
                     /translation="MMQSAAVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILK
                     VLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVV
                     RKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRP
                     RTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD
                     AGRHRWGQFYKSVKRSRGGSKQEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGN
                     VGDVTGGQLMNGSFSMDGTGQSYQDLRDGSPYGIPQSPSSISSLPSHAPLLSGLDYTV
                     DSNLGVIAHPGQGVSQTLRAMAGGPTSDLSTGSSVGYPDFPTSPASWLDEMDHPPF"
     exon            319..490
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            491..693
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            694..848
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            849..1020
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
     exon            1021..1908
                     /gene="Lhx4"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cccgggatgt gcaccagccc gggagagcga gatcaaaggg atttgaaaca gcctgaggac
       61 tggagggggg agggggccgg ccagcttgtg gagtcctccc ggagaggcgg agggctcggc
      121 ttcctctgtg acttcagcgg cctggttggt tttattatta ttattttcaa atctccgaat
      181 ccagccagag ggagagagcg agagatctcg gtagactgcg acttgctgcc tctggctcca
      241 agatgatgca gagcgcggct gtccccgcgg agggggctgt caaggggctc ccggagatgc
      301 tcggtgtgcc gatgcaacag attccccagt gcgccggttg caaccagcac atcctggata
      361 agttcatcct gaaggtcctg gacagacact ggcacagctc ctgcctcaag tgtgcagact
      421 gccagatgca gctagctgac aggtgcttct ccagggccgg gagtgtctac tgcaaagaag
      481 attttttcaa gcgctttggc acaaaatgca cagcgtgcca gcagggcatc cccccgaccc
      541 aggtggttcg caaggctcag gacttcgtct atcacctgca ctgctttgcc tgcatcatct
      601 gcaaccggca gctggccacg ggggacgagt tctaccttat ggaggatggc cggctagtgt
      661 gcaaggaaga ctacgagaca gccaagcaga acgatgactc ggaggctggg gcgaagcggc
      721 cgcggaccac catcacggca aagcagctgg agacactaaa gaatgcatac aagaactccc
      781 caaagcctgc ccggcatgtg agggagcagc tctcctccga gacaggcctg gacatgagag
      841 tggtacaggt ttggtttcag aacagaaggg ccaaggagaa aaggctgaag aaggacgcgg
      901 ggcggcatcg ttgggggcag ttctacaaga gcgtcaagag gagccgggga ggcagcaagc
      961 aggagaagga gagctcagca gaggactgtg gggttagtga cagtgagctg agcttccgag
     1021 aagatcaaat actctcagag cttggccaca ccaataggat ttatggcaac gtgggggacg
     1081 ttacaggcgg acagttaatg aatgggagct tctccatgga tgggacagga caatcctatc
     1141 aggacttgag ggatgggagc ccctatggaa tcccccagtc tccatcctcc atatcgtcct
     1201 tgccatccca tgctcctttg ctcagtgggc tggattacac agtggacagt aatctgggcg
     1261 tcattgccca tccagggcag ggagtaagcc agacactgag agccatggct ggggggccca
     1321 cctctgacct ctcgacagga agcagtgtag gctaccctga ttttccaact agcccagcct
     1381 cctggcttga tgaaatggac catcctcctt tttagacctt ccttgccacc ttacttgtcc
     1441 tggcgggaga gaatgtcttc aaggatcaaa aatacgccaa tgtgaatttc cattattttc
     1501 aatggaaggc ctcggccgat tcctaggagg tggagaccac actaggatgc tgctttcttg
     1561 ggaagagaca ggagagcggc ctcatctcta ccacagcaca ggggtggaca gcctaggact
     1621 ccaaggatgc tggcttgttg gctccctccc ttcccaccct gcttacaggc tttggctgct
     1681 cagcgcttgg acagcaccag gtgaccgtga caggccacct tggcctttgg gaactctgct
     1741 ccagctggta catttctcac ttggcctccc taatcacccc tctcaccaga atcaggattc
     1801 ctgagggaga ggcaccatgg tcccctgaga ataataaaat ggtttctgga cctccttgat
     1861 tacaccttaa ttttcaaaat aaagtcagtt attaaaggct agtaaaaa
//
