2024-05-17 02:14:49, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_131109 1653 bp mRNA linear VRT 16-AUG-2023 DEFINITION Danio rerio caudal type homeobox 4 (cdx4), mRNA. ACCESSION NM_131109 XM_001336183 XM_001336267 VERSION NM_131109.3 KEYWORDS RefSeq. SOURCE Danio rerio (zebrafish) ORGANISM Danio rerio Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio. REFERENCE 1 (bases 1 to 1653) AUTHORS Prummel KD, Crowell HL, Nieuwenhuize S, Brombacher EC, Daetwyler S, Soneson C, Kresoja-Rakic J, Kocere A, Ronner M, Ernst A, Labbaf Z, Clouthier DE, Firulli AB, Sanchez-Iranzo H, Naganathan SR, O'Rourke R, Raz E, Mercader N, Burger A, Felley-Bosco E, Huisken J, Robinson MD and Mosimann C. TITLE Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma JOURNAL Nat Commun 13 (1), 1677 (2022) PUBMED 35354817 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 1653) AUTHORS Rocha M, Kushkowski E, Schnirman R, Booth C, Singh N, Beadell A and Prince VE. TITLE Zebrafish Cdx4 regulates neural crest cell specification and migratory behaviors in the posterior body JOURNAL Dev Biol 480, 25-38 (2021) PUBMED 34389276 REMARK GeneRIF: Zebrafish Cdx4 regulates neural crest cell specification and migratory behaviors in the posterior body. REFERENCE 3 (bases 1 to 1653) AUTHORS Wang B, Rong X, Zhou Y, Liu Y, Sun J, Zhao B, Deng B, Lu L, Lu L, Li Y and Zhou J. TITLE Eukaryotic initiation factor 4A3 inhibits Wnt/beta-catenin signaling and regulates axis formation in zebrafish embryos JOURNAL Development 148 (9) (2021) PUBMED 33914867 REFERENCE 4 (bases 1 to 1653) AUTHORS Ye Z and Kimelman D. TITLE Hox13 genes are required for mesoderm formation and axis elongation during early zebrafish development JOURNAL Development 147 (22) (2020) PUBMED 33154036 REMARK Publication Status: Online-Only REFERENCE 5 (bases 1 to 1653) AUTHORS Rogers KW, ElGamacy M, Jordan BM and Muller P. TITLE Optogenetic investigation of BMP target gene expression diversity JOURNAL Elife 9, e58641 (2020) PUBMED 33174840 REMARK Publication Status: Online-Only REFERENCE 6 (bases 1 to 1653) AUTHORS Hammerschmidt M, Pelegri F, Mullins MC, Kane DA, Brand M, van Eeden FJ, Furutani-Seiki M, Granato M, Haffter P, Heisenberg CP, Jiang YJ, Kelsh RN, Odenthal J, Warga RM and Nusslein-Volhard C. TITLE Mutations affecting morphogenesis during gastrulation and tail formation in the zebrafish, Danio rerio JOURNAL Development 123, 143-151 (1996) PUBMED 9007236 REFERENCE 7 (bases 1 to 1653) AUTHORS Griffin K, Patient R and Holder N. TITLE Analysis of FGF function in normal and no tail zebrafish embryos reveals separate mechanisms for formation of the trunk and the tail JOURNAL Development 121 (9), 2983-2994 (1995) PUBMED 7555724 REFERENCE 8 (bases 1 to 1653) AUTHORS Kelly GM, Greenstein P, Erezyilmaz DF and Moon RT. TITLE Zebrafish wnt8 and wnt8b share a common activity but are involved in distinct developmental pathways JOURNAL Development 121 (6), 1787-1799 (1995) PUBMED 7600994 REFERENCE 9 (bases 1 to 1653) AUTHORS Strahle U and Jesuthasan S. TITLE Ultraviolet irradiation impairs epiboly in zebrafish embryos: evidence for a microtubule-dependent mechanism of epiboly JOURNAL Development 119 (3), 909-919 (1993) PUBMED 8187646 REFERENCE 10 (bases 1 to 1653) AUTHORS Joly JS, Maury M, Joly C, Duprey P, Boulekbache H and Condamine H. TITLE Expression of a zebrafish caudal homeobox gene correlates with the establishment of posterior cell lineages at gastrulation JOURNAL Differentiation 50 (2), 75-87 (1992) PUBMED 1354191 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from BX247946.6. On Aug 16, 2023 this sequence version replaced NM_131109.2. 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. ##Evidence-Data-START## Transcript exon combination :: BC154241.1, GDQQ01001020.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2168448, SAMEA3505370 [ECO:0000348] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-636 BX247946.6 42195-42830 637-782 BX247946.6 44543-44688 783-1653 BX247946.6 44791-45661 FEATURES Location/Qualifiers source 1..1653 /organism="Danio rerio" /mol_type="mRNA" /strain="Tuebingen" /db_xref="taxon:7955" /chromosome="14" /map="14" gene 1..1653 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="caudal type homeobox 4" /db_xref="GeneID:798281" /db_xref="ZFIN:ZDB-GENE-980526-330" exon 1..636 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /inference="alignment:Splign:2.1.0" misc_feature 84..86 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="upstream in-frame stop codon" CDS 201..1013 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="caudal homeobox 1; caudal type homeo box transcription factor 4" /codon_start=1 /product="homeobox protein CDX-4" /protein_id="NP_571184.2" /db_xref="GeneID:798281" /db_xref="ZFIN:ZDB-GENE-980526-330" /translation="
MYVGYLLEKEASMYHQGAVRRSGISLPPQNFVSTPQYSDFTGYHHVPNMETHAQSAGAWGAPYGAPREDWGAYSLGPPNSISAPMSNSSPGPVSYCSPDYNTMHGPGSAVLPPPPENIPVAQLSPERERRNSYQWMSKTVQSSSTGKTRTKEKYRVVYTDHQRLELEKEFHFNRYITIRRKSELAVNLGLSERQVKIWFQNRRAKERKLIKKKLGQSDGSGGSVHSDPGSVSPLPVPGSLSPSDIHGSLYPAQMNALPSMRNIQQVTVTQ"
misc_feature 237..638 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="Caudal like protein activation region; Region: Caudal_act; pfam04731" /db_xref="CDD:428094" misc_feature order(657..668,672..674,723..725,741..743,780..782, 786..791,798..803,807..815,819..824) /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:238039" misc_feature order(660..662,669..671,789..791,798..803,810..812) /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="specific DNA base contacts [nucleotide binding]; other site" /db_xref="CDD:238039" misc_feature 663..821 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /note="Homeobox domain; Region: Homeobox; pfam00046" /db_xref="CDD:425441" exon 637..782 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /inference="alignment:Splign:2.1.0" exon 783..1653 /gene="cdx4" /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215; id:ibd2812; id:ibd5107; kgg; kugelig" /inference="alignment:Splign:2.1.0" ORIGIN
agactcacatcatgtttgattgaagcacgtcaaggactacgtcgcgtgacccggagctccttttggactattacacttccagataaatagtattgaagaaaaagtttttgagtcgggccttggatccaagtgatatttggcttgatgcatggctggcatgttgccttaaaaaaagttattttaggggtttcttccaaatcatgtacgttggataccttttggagaaagaggcaagcatgtatcaccaaggagcggttcgtcgatctggcatcagtcttccaccacagaactttgtttccacacctcagtattcagattttacaggataccatcatgtgcccaatatggagacacacgcacagtcggcaggggcatggggcgctccttatggcgctccgagagaggactggggcgcctacagcctcggacctccaaattctatttctgcacctatgagcaattcatctccgggaccagtttcctattgctcgcccgattataacaccatgcacggccctggatcggcggttcttcctccaccacctgaaaatattcctgtggcccaactatccccagagagagaaaggcgtaattcctatcagtggatgagcaaaaccgtccagtcgtcatcaaccggcaaaacgagaacgaaggagaaataccgagtggtatacacagatcaccaaaggctggagctggagaaagagtttcattttaatcgctatatcacaatcagaagaaaatccgaacttgctgtaaacctcgggctttcagagagacaggttaagatctggtttcagaaccgcagagctaaggaaaggaaattaatcaaaaagaaattgggtcagtctgacggaagcggagggtcagtgcacagcgacccaggctccgtcagtcctctaccggtaccagggtcactgagtccttcagatatacacggttctctgtatccagcacaaatgaacgccttgccgtccatgaggaacatacagcaagttactgtcactcagtgaactcgaacttggaacatccaactttaactgagcactccaacacgctgaaaggacagaaccaaacgtggtcaaaaaggattacaaactattaatgaataaatgaatgaataaataaataagaggcgtgggttgtggattacaaccgaagaatcacgtctgaaatgcgacgaaatgctggaggctcttcaaatattgttttaatagaatagtttttaaaattaagaaaaaaaactacaaaaaccttgttcgtctgatccagagactaaatattttaatggtttgtgttttctcgaataagatataaatatcttttttctgtatgtggtgagtgtatctaaatgtttgtttgtatataaaatgagaactacaggtacggagtttcatgggacgtgtaatgatccttaccctggaactgttaaacttttattgtctgtgaaaaccaatgacctgcgatgtcaggctgttttatgcgccagtttgtgtccaaagcgcacgtcgttcactttcttttcacaggggtgatgtgcaggtgtcacataccagatacgggtataacgtttgatttcagcaatgtgtaaataaatgttttgcaataacttttattgtgtcttcatgtatcattaaacaaatggcaatagca
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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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