2024-04-20 09:51:43, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001108348 1908 bp mRNA linear ROD 20-MAR-2023 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 MB, Bering T, Rohde K, Moller M, Granau AM, Coon SL, Klein DC and Rath MF. 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 PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, 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 BS, Hemberger M, Geyer R, Stewart MD, Behringer RR 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 LT, Ward R and Camper SA. 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 TM 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 HZ, Lettieri K, Li H, Karavanov A, Potter S, Westphal H and Pfaff SL. 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 JACYVU010000243.1. 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 :: mixed/partial sample support SAMD00132261, SAMD00132262 [ECO:0000350] ##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 1-318 JACYVU010000243.1 2773569-2773886 c 319-490 JACYVU010000243.1 2755995-2756166 c 491-693 JACYVU010000243.1 2740743-2740945 c 694-848 JACYVU010000243.1 2737217-2737371 c 849-1020 JACYVU010000243.1 2736747-2736918 c 1021-1908 JACYVU010000243.1 2733776-2734663 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" misc_feature 129..131 /gene="Lhx4" /note="upstream in-frame stop codon" 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="
MMQSAAVPAEGAVKGLPEMLGVPMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQNDDSEAGAKRPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRHRWGQFYKSVKRSRGGSKQEKESSAEDCGVSDSELSFREDQILSELGHTNRIYGNVGDVTGGQLMNGSFSMDGTGQSYQDLRDGSPYGIPQSPSSISSLPSHAPLLSGLDYTVDSNLGVIAHPGQGVSQTLRAMAGGPTSDLSTGSSVGYPDFPTSPASWLDEMDHPPF"
misc_feature 330..485 /gene="Lhx4" /note="The first LIM domain of Lhx4; Region: LIM1_Lhx4; cd09468" /db_xref="CDD:188852" misc_feature order(330..332,339..341,393..395,402..404,411..413, 420..422,471..473,480..482) /gene="Lhx4" /note="Zn binding site [ion binding]; other site" /db_xref="CDD:188852" misc_feature 507..674 /gene="Lhx4" /note="The second LIM domain of Lhx3-Lhx4 family; Region: LIM2_Lhx3_Lhx4; cd09376" /db_xref="CDD:188762" misc_feature order(507..509,516..518,573..575,582..584,591..593, 600..602,660..662,669..671) /gene="Lhx4" /note="Zn binding site [ion binding]; other site" /db_xref="CDD:188762" misc_feature order(543..545,618..620) /gene="Lhx4" /note="Isl binding site; other site" /db_xref="CDD:188762" misc_feature order(714..728,732..734,783..785,801..803,840..842, 846..851,858..863,867..875,879..884) /gene="Lhx4" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature 720..881 /gene="Lhx4" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" misc_feature order(720..722,729..731,849..851,858..863,870..872) /gene="Lhx4" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" 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
cccgggatgtgcaccagcccgggagagcgagatcaaagggatttgaaacagcctgaggactggaggggggagggggccggccagcttgtggagtcctcccggagaggcggagggctcggcttcctctgtgacttcagcggcctggttggttttattattattattttcaaatctccgaatccagccagagggagagagcgagagatctcggtagactgcgacttgctgcctctggctccaagatgatgcagagcgcggctgtccccgcggagggggctgtcaaggggctcccggagatgctcggtgtgccgatgcaacagattccccagtgcgccggttgcaaccagcacatcctggataagttcatcctgaaggtcctggacagacactggcacagctcctgcctcaagtgtgcagactgccagatgcagctagctgacaggtgcttctccagggccgggagtgtctactgcaaagaagattttttcaagcgctttggcacaaaatgcacagcgtgccagcagggcatccccccgacccaggtggttcgcaaggctcaggacttcgtctatcacctgcactgctttgcctgcatcatctgcaaccggcagctggccacgggggacgagttctaccttatggaggatggccggctagtgtgcaaggaagactacgagacagccaagcagaacgatgactcggaggctggggcgaagcggccgcggaccaccatcacggcaaagcagctggagacactaaagaatgcatacaagaactccccaaagcctgcccggcatgtgagggagcagctctcctccgagacaggcctggacatgagagtggtacaggtttggtttcagaacagaagggccaaggagaaaaggctgaagaaggacgcggggcggcatcgttgggggcagttctacaagagcgtcaagaggagccggggaggcagcaagcaggagaaggagagctcagcagaggactgtggggttagtgacagtgagctgagcttccgagaagatcaaatactctcagagcttggccacaccaataggatttatggcaacgtgggggacgttacaggcggacagttaatgaatgggagcttctccatggatgggacaggacaatcctatcaggacttgagggatgggagcccctatggaatcccccagtctccatcctccatatcgtccttgccatcccatgctcctttgctcagtgggctggattacacagtggacagtaatctgggcgtcattgcccatccagggcagggagtaagccagacactgagagccatggctggggggcccacctctgacctctcgacaggaagcagtgtaggctaccctgattttccaactagcccagcctcctggcttgatgaaatggaccatcctcctttttagaccttccttgccaccttacttgtcctggcgggagagaatgtcttcaaggatcaaaaatacgccaatgtgaatttccattattttcaatggaaggcctcggccgattcctaggaggtggagaccacactaggatgctgctttcttgggaagagacaggagagcggcctcatctctaccacagcacaggggtggacagcctaggactccaaggatgctggcttgttggctccctcccttcccaccctgcttacaggctttggctgctcagcgcttggacagcaccaggtgaccgtgacaggccaccttggcctttgggaactctgctccagctggtacatttctcacttggcctccctaatcacccctctcaccagaatcaggattcctgagggagaggcaccatggtcccctgagaataataaaatggtttctggacctccttgattacaccttaattttcaaaataaagtcagttattaaaggctagtaaaaa
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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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