2024-05-04 18:27:26, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001107837 3421 bp mRNA linear ROD 23-MAR-2023 DEFINITION Rattus norvegicus LIM homeobox 6 (Lhx6), mRNA. ACCESSION NM_001107837 XM_001079382 XM_231175 VERSION NM_001107837.2 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 3421) AUTHORS Oh SG, Hwang YG and Lee HS. TITLE LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project to the core portion of the lateral supramammillary nucleus in the rat JOURNAL Brain Res 1748, 147125 (2020) PUBMED 32931819 REMARK GeneRIF: LIM homeobox 6 (Lhx6)+ neurons in the ventral zona incerta project to the core portion of the lateral supramammillary nucleus in the rat. REFERENCE 2 (bases 1 to 3421) AUTHORS Jeong MS, Hwang EY, Kim HT, Yoo MA and Jang SB. TITLE Purification of caudal-related homeodomain transcription factor and its binding characterization JOURNAL J Microbiol Biotechnol 19 (12), 1557-1564 (2009) PUBMED 20075618 REMARK GeneRIF: Studied the DNA binding activity of human CDX2. Three CDX2-binding proteins were found in rat gastric tissue, and those proteins were identified to the homeobox protein Hox-D8, LIM homeobox protein 6, and SMC1L1 protein. REFERENCE 3 (bases 1 to 3421) AUTHORS Du T, Xu Q, Ocbina PJ and Anderson SA. TITLE NKX2.1 specifies cortical interneuron fate by activating Lhx6 JOURNAL Development 135 (8), 1559-1567 (2008) PUBMED 18339674 REFERENCE 4 (bases 1 to 3421) AUTHORS Liodis P, Denaxa M, Grigoriou M, Akufo-Addo C, Yanagawa Y and Pachnis V. TITLE Lhx6 activity is required for the normal migration and specification of cortical interneuron subtypes JOURNAL J Neurosci 27 (12), 3078-3089 (2007) PUBMED 17376969 REFERENCE 5 (bases 1 to 3421) AUTHORS Mori T, Yuxing Z, Takaki H, Takeuchi M, Iseki K, Hagino S, Kitanaka J, Takemura M, Misawa H, Ikawa M, Okabe M and Wanaka A. TITLE The LIM homeobox gene, L3/Lhx8, is necessary for proper development of basal forebrain cholinergic neurons JOURNAL Eur J Neurosci 19 (12), 3129-3141 (2004) PUBMED 15217369 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from JACYVU010000115.1. On Dec 7, 2020 this sequence version replaced NM_001107837.1. ##Evidence-Data-START## RNAseq introns :: single sample supports all introns SAMN11044071 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## inferred exon combination :: based on alignments, homology RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-147 JACYVU010000115.1 12912692-12912838 c 148-219 JACYVU010000115.1 12911451-12911522 c 220-402 JACYVU010000115.1 12910888-12911070 c 403-524 JACYVU010000115.1 12910400-12910521 c 525-745 JACYVU010000115.1 12901837-12902057 c 746-846 JACYVU010000115.1 12899204-12899304 c 847-942 JACYVU010000115.1 12898918-12899013 c 943-1117 JACYVU010000115.1 12898560-12898734 c 1118-1221 JACYVU010000115.1 12894777-12894880 c 1222-3421 JACYVU010000115.1 12889285-12891484 c FEATURES Location/Qualifiers source 1..3421 /organism="Rattus norvegicus" /mol_type="mRNA" /strain="BN" /db_xref="taxon:10116" /chromosome="3" /map="3p11" gene 1..3421 /gene="Lhx6" /note="LIM homeobox 6" /db_xref="GeneID:311901" /db_xref="RGD:1306174" exon 1..147 /gene="Lhx6" /inference="alignment:Splign:2.1.0" CDS 64..1242 /gene="Lhx6" /note="LIM homeobox protein 6" /codon_start=1 /product="LIM/homeobox protein Lhx6" /protein_id="NP_001101307.2" /db_xref="GeneID:311901" /db_xref="RGD:1306174" /translation="
MYWKHESAAPALPEGCRLPAEGGPTTDQVMAQPGSGCKATTRCLEGTAPPAMAQSDAEALAGALDKDEGRASPCTPSTPSVCSPPSAASSVPSAGKNICSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQQNSCYIKNKEIYCKMDYFSRFGTKCARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHYDTMIENLKRAAENGNGLTLEGAVPSEQDSQPKPAKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKHTPQHPVPPSGAPPSRLPSSLSDDIHYSPFSSPERARMVTLHGYIESQVQCGQVHCRLPYTAPPVHLKADMDGPLSSRGEKVILFQY"
misc_feature 358..519 /gene="Lhx6" /note="The first LIM domain of Lhx6; Region: LIM1_Lhx6; cd09380" /db_xref="CDD:188766" misc_feature order(358..360,367..369,421..423,430..432,439..441, 448..450,505..507,514..516) /gene="Lhx6" /note="Zn binding site [ion binding]; other site" /db_xref="CDD:188766" misc_feature 541..705 /gene="Lhx6" /note="The second LIM domain of Lhx6; Region: LIM2_Lhx6; cd09382" /db_xref="CDD:188768" misc_feature order(541..543,550..552,607..609,616..618,625..627, 634..636,691..693,700..702) /gene="Lhx6" /note="Zn binding site [ion binding]; other site" /db_xref="CDD:188768" misc_feature order(808..822,826..828,877..879,895..897,934..936, 940..945,952..957,961..969,973..978) /gene="Lhx6" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature order(814..816,823..825,943..945,952..957,964..966) /gene="Lhx6" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 817..975 /gene="Lhx6" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" exon 148..219 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 220..402 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 403..524 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 525..745 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 746..846 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 847..942 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 943..1117 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 1118..1221 /gene="Lhx6" /inference="alignment:Splign:2.1.0" exon 1222..3421 /gene="Lhx6" /inference="alignment:Splign:2.1.0" ORIGIN
cgaggccccactccgtgctgctctttgcgctgcgcgcccttcgagccctcagttcccgggcccatgtactggaagcatgagagcgccgccccggcgctgcccgagggctgccggttaccggcggagggcggccccaccaccgaccaggtgatggcccagccagggtccggctgcaaagcgaccacccgctgtcttgaagggaccgctccgcctgccatggctcagtcagacgccgaggccttggcaggcgctctggacaaggacgaaggtagagcctccccatgtacgcccagcacaccctctgtctgctcgccgccctctgccgcctcttccgtgccgtctgctggcaagaatatctgctccagttgcggtctcgagatcctggaccggtatctgctcaaggtcaacaacctcatctggcacgtgcggtgcctcgagtgctccgtgtgtcgcacatcgctgaggcagcagaatagctgctacatcaagaacaaggagatctactgcaagatggactacttcagccgatttggaaccaagtgtgcccggtgcggcagacaaatctatgccagtgactgggtgcggcgcgcgcgcggcaatgcctaccacctggcctgcttcgcttgcttttcctgcaagcgccagctatccacgggcgaggaattcggcctggttgaggagaaggtgctttgccgcatccattacgacaccatgatcgagaacctcaagagggccgccgagaacgggaacggtctcacgttggagggggcagtgccctcggaacaggacagtcagcccaagccagctaagcgcgcgcggacgtccttcacggcagagcaattgcaggttatgcaggctcagttcgcgcaggacaacaaccccgacgcgcagacgctgcagaagctagcggacatgacgggcctcagtcgcagggtcatccaggtgtggtttcaaaactgccgagcgcgtcataaaaagcatacaccgcagcacccagtgccgccctctggggcacccccgtcccgcctcccctcctccctgtccgacgacatccactattctccgttcagcagcccagagcgggcacgcatggtcaccttgcacggctacatcgagagtcaggtacagtgcgggcaggtgcactgccgactgccttacaccgcgccccctgtccacctcaaagccgacatggatgggccgctctccagccggggtgagaaggtcatcctttttcagtactaactctgccggcgcttgcacatctgtccatgggcaccacacagctgcccctcagccgctgagcatccagcgtccagctgtggccagggatccaccgcctctgggcacaccctcctcacccgctgccgccctgccctctgccagtggccccatcaacccagccccggtatttccctctcctgctgagaaccagaacccgccaggagcagcagagccctctctgggaaggcaggctccctgaaatgtggtatcagcatgaaaacaagcagcctgtctttcctcatcatctgggagtcttgcttatctgggagtcagctgatcgcagcagcaacagctaattcaacaacagcctcccacttcacaggttttcttcttcccccatattggccttcatttactacttccttggaaccgtctctgagttctgaacagccaaaacaacccccaacattatatactccgctgcttttgtctggaaaactctacagtgtttgtgggatgtccccaaaggaaagccgtgttctgattttatcatttccatctgtctggttatgtcaagttaactcagaaaaagaagagacactgaccaaccctgagaggcccaacagggcagagatggaggcctgcccagatgaagaggcagagggatgggcagggatgggtgccaaagaccccccattggcttggagaaggaggactgggtatgctggacttggagaggtgatgagagtttcatggagagaaaagaggaaacttgagggggggtgtcccccacctaattacccagcaggagttgtggaaagaatggcgtctgatcggcacgatgacaccactgaatgtttaggtgggctagcattagggacccttgttggccacttttcagtcctgagatgagggcctgagccagtcttctctgggggtggggtgagactactcatgaggaccaaggaacagagcccagagaaatagcagccatgatattagctcggattcatccacgaggggagagaggtgcccgtggcctcagtgagtgcgtgccaagcccaggattccagctggcacctcggcagtctccccaccaactgcacagagccagctctacccactcctgagagcagaggccagctccaaataaaggtctcaggttacacaggccctcgattcatgttttcagggggtgcccatctgccccgagcttatcctgtaattctacaaccacttggtggcctgatgcactactcaccagaggctgcctagcagcgtgtgttagccaaagtcttcctccctgttttgaggagactccaggtcaggaaaggcaaattccgagtctgtatgctgtccctccttcacctgtggcagacatcactaatcgctaatcgatcacacctctctctctctctctctctctctctctctctctctctctctctgtctctcgctctcgctctcgctctcgctctcgctctctctcgctttctctcgctctcggagtctggataaggtttcagaattcccaagcttgaagttgggatgtgaccaactgtgctattgctgaaggacctggaggagggttaggcctgggtgaccccccagaagggaacttgcatcttttcccttccaaaaattgtcaactgacggaggacagagagaaagttcctcccagaaagctgagagtgtggttcattccggtcagaactccagcaccctgtgccaggcactgactcaagcaagaggaacctggcctgatccctgacttggggaacccagatattccctttgatttattttgctcctaaggatcaaaacccccagttgcaaccatgtggcaagtggccagctgagcccaggttacttggtacccactctgccttgagccttcccccagggtctatttcttgtgtggatcacgtggcagtagcatgttgcagttcagacgtctccactactctgttcaaaacagcctgggaatgtacaggccattgaggctatttatttaaatacacacacacacacacacacacacacacacacacatgcgcacacacaaaggggggaacacacacaaatggaaacaattgtaagcacttttttttgtaaaaccaatgtctgttttgttacatacctttcatgttgtgctttgtaaatgtcttatttgtgtaataaataaagttaatgcgagtag
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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.
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