GGRNA ver.2 Home | Help | Advanced search    Previous release (v1)

2021-10-29 03:38:20, GGRNA.v2 : RefSeq release 207 (Jul, 2021)

LOCUS       NM_145880               3390 bp    mRNA    linear   ROD 02-JUL-2021
DEFINITION  Rattus norvegicus LIM homeobox 1 (Lhx1), mRNA.
ACCESSION   NM_145880
VERSION     NM_145880.4
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 3390)
  AUTHORS   Costello I, Nowotschin S, Sun X, Mould AW, Hadjantonakis AK, Bikoff
            EK and Robertson EJ.
  TITLE     Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern
            anterior mesendoderm, node, and midline development
  JOURNAL   Genes Dev 29 (20), 2108-2122 (2015)
   PUBMED   26494787
REFERENCE   2  (bases 1 to 3390)
  AUTHORS   Boualia SK, Gaitan Y, Murawski I, Nadon R, Gupta IR and Bouchard M.
  TITLE     Vesicoureteral reflux and other urinary tract malformations in mice
            compound heterozygous for Pax2 and Emx2
  JOURNAL   PLoS One 6 (6), e21529 (2011)
   PUBMED   21731775
REFERENCE   3  (bases 1 to 3390)
  AUTHORS   Palmesino E, Rousso DL, Kao TJ, Klar A, Laufer E, Uemura O, Okamoto
            H, Novitch BG and Kania A.
  TITLE     Foxp1 and lhx1 coordinate motor neuron migration with axon
            trajectory choice by gating Reelin signalling
  JOURNAL   PLoS Biol 8 (8), e1000446 (2010)
   PUBMED   20711475
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3390)
  AUTHORS   Poche RA, Kwan KM, Raven MA, Furuta Y, Reese BE and Behringer RR.
  TITLE     Lim1 is essential for the correct laminar positioning of retinal
            horizontal cells
  JOURNAL   J Neurosci 27 (51), 14099-14107 (2007)
   PUBMED   18094249
REFERENCE   5  (bases 1 to 3390)
  AUTHORS   Kittappa R, Chang WW, Awatramani RB and McKay RD.
  TITLE     The foxa2 gene controls the birth and spontaneous degeneration of
            dopamine neurons in old age
  JOURNAL   PLoS Biol 5 (12), e325 (2007)
   PUBMED   18076286
REFERENCE   6  (bases 1 to 3390)
  AUTHORS   Shimono A and Behringer RR.
  TITLE     Isolation of novel cDNAs by subtractions between the anterior
            mesendoderm of single mouse gastrula stage embryos
  JOURNAL   Dev Biol 209 (2), 369-380 (1999)
   PUBMED   10328927
REFERENCE   7  (bases 1 to 3390)
  AUTHORS   Karavanov AA, Karavanova I, Perantoni A and Dawid IB.
  TITLE     Expression pattern of the rat Lim-1 homeobox gene suggests a dual
            role during kidney development
  JOURNAL   Int J Dev Biol 42 (1), 61-66 (1998)
   PUBMED   9496787
REFERENCE   8  (bases 1 to 3390)
  AUTHORS   Karavanov AA, Saint-Jeannet JP, Karavanova I, Taira M and Dawid IB.
  TITLE     The LIM homeodomain protein Lim-1 is widely expressed in neural,
            neural crest and mesoderm derivatives in vertebrate development
  JOURNAL   Int J Dev Biol 40 (2), 453-461 (1996)
   PUBMED   8793615
REFERENCE   9  (bases 1 to 3390)
  AUTHORS   Richman DD and Bozzette SA.
  TITLE     The impact of the syncytium-inducing phenotype of human
            immunodeficiency virus on disease progression
  JOURNAL   J Infect Dis 169 (5), 968-974 (1994)
   PUBMED   7909549
REFERENCE   10 (bases 1 to 3390)
  AUTHORS   Furuyama T, Inagaki S, Iwahashi Y and Takagi H.
  TITLE     Distribution of Rlim, an LIM homeodomain gene, in the rat brain
  JOURNAL   Neurosci Lett 170 (2), 266-268 (1994)
   PUBMED   7914684
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JACYVU010000220.1.
            On Nov 25, 2020 this sequence version replaced NM_145880.3.
            
            Summary: may play a role in the regulation of genes in specific
            neuronal subtypes [RGD, Feb 2006].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-770               JACYVU010000220.1  26227706-26228475   c
            771-997             JACYVU010000220.1  26225805-26226031   c
            998-1275            JACYVU010000220.1  26225436-26225713   c
            1276-1441           JACYVU010000220.1  26223982-26224147   c
            1442-3390           JACYVU010000220.1  26221687-26223635   c
FEATURES             Location/Qualifiers
     source          1..3390
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="10"
                     /map="10q26"
     gene            1..3390
                     /gene="Lhx1"
                     /note="LIM homeobox 1"
                     /db_xref="GeneID:257634"
                     /db_xref="RGD:71074"
     exon            1..770
                     /gene="Lhx1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    556..558
                     /gene="Lhx1"
                     /note="upstream in-frame stop codon"
     CDS             601..1821
                     /gene="Lhx1"
                     /note="LIM homeobox protein 1; rlim; homeobox protein
                     Lim-1"
                     /codon_start=1
                     /product="LIM/homeobox protein Lhx1"
                     /protein_id="NP_665887.3"
                     /db_xref="GeneID:257634"
                     /db_xref="RGD:71074"
                     /translation="
MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFGTKCAGCAQGISPSDLVRRARSKVFHLNCFTCMMCNKQLSTGEELYIIDENKFVCKEDYLSNSSVAKENSLHSATTGSDPSLSPDSQDPSQDDAKDSESANVSDKEGGSNENDDQNLGAKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRMKQLSALGARRHAFFRSPRRMRPLVDRLEPGELIPNGPFSFYGDYQSEYYGPGGNYDFFPQGPPSSQAQTPVDLPFVPSSGPSGTPLGGLDHPLPGHHPSSEAQRFTDILAHPPGDSPSPEPSLPGPLHSMSAEVFGPSPPFSSLSVNGGASYGNHLSHPPEMNEAAVW"
     misc_feature    610..765
                     /gene="Lhx1"
                     /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(610..612,619..621,673..675,682..684,691..693,
                     700..702,751..753,760..762)
                     /gene="Lhx1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188753"
     misc_feature    787..954
                     /gene="Lhx1"
                     /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(787..789,796..798,853..855,862..864,871..873,
                     880..882,940..942,949..951)
                     /gene="Lhx1"
                     /note="Zn binding site [ion binding]; other site"
                     /db_xref="CDD:188761"
     misc_feature    982..1167
                     /gene="Lhx1"
                     /note="propagated from UniProtKB/Swiss-Prot (P63007.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    1084..1086
                     /gene="Lhx1"
                     /note="Phosphoserine.
                     /evidence=ECO:0007744|PubMed:22673903; propagated from
                     UniProtKB/Swiss-Prot (P63007.1); phosphorylation site"
     misc_feature    order(1141..1155,1159..1161,1210..1212,1228..1230,
                     1267..1269,1273..1278,1285..1290,1294..1302,1306..1311)
                     /gene="Lhx1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    1147..1311
                     /gene="Lhx1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:395001"
     misc_feature    order(1147..1149,1156..1158,1276..1278,1285..1290,
                     1297..1299)
                     /gene="Lhx1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    <1387..>1746
                     /gene="Lhx1"
                     /note="chromosomal replication initiator protein DnaA;
                     Region: dnaA; PRK14086"
                     /db_xref="CDD:237605"
     misc_feature    1480..1716
                     /gene="Lhx1"
                     /note="propagated from UniProtKB/Swiss-Prot (P63007.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            771..997
                     /gene="Lhx1"
                     /inference="alignment:Splign:2.1.0"
     exon            998..1275
                     /gene="Lhx1"
                     /inference="alignment:Splign:2.1.0"
     exon            1276..1441
                     /gene="Lhx1"
                     /inference="alignment:Splign:2.1.0"
     exon            1442..3390
                     /gene="Lhx1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
ccctcccaggcccagcgcgggtgcccagagcgtcccgactcgcttcaagaagccggcaatgtaggatccaaagcttttctactcccgtgttttctttccgtgttttttttaagggggaaaccgggtggtgggcagtctgacacgcacacaacctgccttcatactctgacaaaagcagatgcactttgacttctgacagctctacctcaagctggagagaacccagctttcccgaatcctgagctctttgcgtcttccttttcgtctgtttccattttatttatttacgtcccgccgcctctctgggtgaccttcactccttcgcgggctttgggcagaagagccgctttcttgcccgattgagactgattttcctcgcctggtgagcggaggtggcgctgctccaccccgctgccccgggactccggggctgccctctaccagcctggtctctccctcttttgatttgacagtacgggtttttgctttcccgagtacagcgggtttcttctttttggaggagctggttgtcttcagaagtcattccctggactctaattgccctgtcgctccgggcctcaccggaccaaaccaaagaccatggtgcactgtgcgggctgcaaaaggcccattctggaccgtttcctcttgaacgtgctggacagggcctggcatgtcaagtgcgtccagtgctgtgaatgtaaatgcaacctgaccgagaagtgcttctcccgggaaggcaagctctactgtaaaaacgacttcttccgatgtttcggtaccaaatgcgcgggttgtgcgcagggcatctctccaagcgatctggttcggagagcgcgaagcaaagtgtttcacctcaactgcttcacctgcatgatgtgtaacaagcagctctccacgggcgaggagctctacatcatcgatgagaacaagttcgtttgtaaagaggattacctgagtaacagcagtgtcgccaaagagaacagcctccactcggccaccacaggcagtgaccctagtttatctccggattcccaagatccatcgcaggatgatgccaaggactctgaaagtgccaacgtatcggataaggaaggtggtagcaatgagaacgatgaccagaacctaggtgccaagcgcaggggaccgcggaccacgatcaaagccaagcaactggagacgttgaaggcagcctttgcagctacgcctaagcccacacgccatatccgcgagcaattggcccaggagactggcctcaacatgcgtgttatccaggtctggttccagaatcgacgctccaaggagcggaggatgaagcagctaagcgcgctgggtgcgcggcgccacgcctttttccgcagtcctcgccggatgcggcctctggtggaccgcttggagccgggcgaactcatccctaacggccccttctccttttatggagattaccagagtgagtactacggtcctggaggcaactacgacttcttcccgcaaggaccaccgtcctcgcaggcccagacaccagtggacctaccctttgtgccatcatctgggccttcggggacgccccttggaggtctggaccacccgctgcctggccaccatccttccagcgaggcgcagcgattcactgacatcctggcacatcccccaggggactcgcctagtcctgagcccagcttgcccgggcctctccactccatgtctgcggaggtctttgggcccagtccacctttctcatctctgtcggtcaatggtggagccagctacgggaatcacttgtctcaccctcctgaaatgaatgaggcagccgtgtggtagcggggtctcgcatgggccacgggagctcgtggttgtacagagacgagcttttatttcagaaaataggagatttaaaaaaaaaaacattaaaaaaaaaaaaaagcaagcctcctgctccacttccttcagcctcggggaccattctttttggggagactggatggcaaaggggtccaaaacaggatccaaatccgcctcgcagtagagctggtatatccacacagcggctgacaaagcgcagaactggggctccggaaggggaattccgaggcatccccaccttcgcgacctggatctggatccatggacagactccaccagcggctcctctggctaacggaagacgtcttagacagcctcgctcagtcctgggcaatgccaggagcctggggagggagacctacctagaagcgctctgccagatgaggaaggaaaagatgtcaggggcgctccagtccagagggctctagttctagttctgggagatcccttcttagtgttgtctcagagttcagcgatgacaacaaactcttaatagcttcagaaacaccgacctgctgtgcatcaggtgggactatatatatatatattttttgtctatctgggtttttgatttttgttttcgccaaaattgcaaaattctaaatgtaaagccctcagtatcaactattctaccttcacacctctctctctctctctctctttctctctctctctctctctctctctctccctctcccctacacacacacacacacacacacacacacacacacacacacacacacacatgctcactcacactcaacttctttccacagtagggtctccagccagacctcttagtaaaatgacttgaacatcacctctacaaaaaagtattctacctttacatgaaagttaaaaaaaaaaaagactattgaactaaaaacagtcaactgtttacgtataatgttaaattcaggagttcagtgttttaataatatatcctgttttgaaacctcttgttcaaaaacaaaatgttttgagcaatcaaccaaaattgttccttttcttttcctgtagatgttctgacaggtttgcagggcttgcggctcactgtgctagtatgtaaaaaggtgttgtttacacgaggcaaagggaaaacatgatattcagacagttgccaaatagaataaactatagcacaattactgtaatggttgcctggcaccagcaacctgagaaagtgttttaaaaaaaaagtgttacaaggtttaaaaaaaaaacatctttgctaacttttagtcctgttaaacattcatgaaattgttaatatgacttatatagacccacacaggttttatttttgtgtctttaaaataaaagtccaaaatatttaaattttatggtcaaatatgcagtcaacagctgctactttttcctttatatattaaatttctcatatgtcttttattgttctaataaacctaagcttgtgtgacctccagtgcatattagaccattcactgtatgaaagaaaacatgttgaataaatttgtgagtttttaataaaaatagaaaacctga
//

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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]