ZFIN

ZFIN ID: ZDB-GENE-030708-2

ZFIN ID: ZDB-GENE-030708-2

CITATIONS (55 total)

Gene Name:	zic family member 3 heterotaxy 1 (odd-paired homolog, Drosophila)
Gene Symbol:	zic3

Farmer, D.T., Dukov, J.E., Chen, H.J., Arata, C., Hernandez-Trejo, J., Xu, P., Teng, C.S., Maxson, R.E., Crump, J.G. (2024) Cellular transitions during cranial suture establishment in zebrafish. Nature communications. 15:6948

Pandey, S., Moyer, A.J., Thyme, S.B. (2023) A single-cell transcriptome atlas of the maturing zebrafish telencephalon. Genome research. 33(4):658-671

Li, H., Xu, W., Xiang, S., Tao, L., Fu, W., Liu, J., Liu, W., Xiao, Y., Peng, L. (2022) Defining the Pluripotent Marker Genes for Identification of Teleost Fish Cell Pluripotency During Reprogramming. Frontiers in genetics. 13:819682

Talbot, C.D., Walsh, M.D., Cutty, S.J., Elsayed, R., Vlachaki, E., Bruce, A.E.E., Wardle, F.C., Nelson, A.C. (2022) Eomes function is conserved between zebrafish and mouse and controls left-right organiser progenitor gene expression via interlocking feedforward loops. Frontiers in cell and developmental biology. 10:982477

Sun, Y., Yang, F., Liu, Y., Yu, M., Wu, F., Wang, G. (2021) Di-2-ethylhexyl phthalate induces heart looping disorders during zebrafish development. Toxicology and industrial health. 37(7):391-397

Sarmah, S., Srivastava, R., McClintick, J.N., Janga, S.C., Edenberg, H.J., Marrs, J.A. (2020) Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects. Scientific Reports. 10:3951

Kumar, A., Anuppalle, M., Maddirevula, S., Huh, T.L., Choe, J., Rhee, M. (2019) Peli1b governs the brain patterning via ERK signaling pathways in zebrafish embryos. Gene. 694:1-6

Minhas, R., Paterek, A., Łapiński, M., Bazała, M., Korzh, V., Winata, C.L. (2019) A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Developmental Dynamics : an official publication of the American Association of Anatomists. 248(9):837-849

Li, S., Liu, S., Chen, W., Yuan, Y., Gu, R., Song, Y., Li, J., Cao, Y., Lin, Y., Xu, J., Wang, H., Ma, D., Ma, X., Sheng, W., Huang, G. (2018) A novel ZIC3 gene mutation identified in patients with heterotaxy and congenital heart disease. Scientific Reports. 8:12386

Nakayama, Y., Inomata, C., Yuikawa, T., Tsuda, S., Yamasu, K. (2017) Comprehensive analysis of target genes in zebrafish embryos reveals gbx2 involvement in neurogenesis. Developmental Biology. 430(1):237-248

Rabinowitz, J.S., Robitaille, A.M., Wang, Y., Ray, C.A., Thummel, R., Gu, H., Djukovic, D., Raftery, D., Berndt, J.D., Moon, R.T. (2017) Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 114(5):E717-E726

Ota, S., Taimatsu, K., Yanagi, K., Namiki, T., Ohga, R., Higashijima, S.I., Kawahara, A. (2016) Functional visualization and disruption of targeted genes using CRISPR/Cas9-mediated eGFP reporter integration in zebrafish. Scientific Reports. 6:34991

Biswas, G., Kinoshita, S., Kono, T., Hikima, J.I., Sakai, M. (2015) Evolutionary evidence of tumor necrosis factor super family members in the Japanese pufferfish (Takifugu rubripes): Comprehensive genomic identification and expression analysis. Marine genomics. 22:25-36

Elkon, R., Milon, B., Morrison, L., Shah, M., Vijayakumar, S., Racherla, M., Leitch, C.C., Silipino, L., Hadi, S., Weiss-Gayet, M., Barras, E., Schmid, C.D., Ait-Lounis, A., Barnes, A., Song, Y., Eisenman, D.J., Eliyahu, E., Frolenkov, G.I., Strome, S.E., Durand, B., Zaghloul, N.A., Jones, S.M., Reith, W., Hertzano, R. (2015) RFX transcription factors are essential for hearing in mice. Nature communications. 6:8549

Moreno-Mateos, M.A., Vejnar, C.E., Beaudoin, J.D., Fernandez, J.P., Mis, E.K., Khokha, M.K., Giraldez, A.J. (2015) CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nature Methods. 12:982-8

Nelson, A.C., Cutty, S.J., Niini, M., Stemple, D.L., Flicek, P., Houart, C., Bruce, A., Wardle, F.C. (2014) Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biology. 12:81

Drummond, D.L., Cheng, C.S., Selland, L.G., Hocking, J.C., Prichard, L.B., and Waskiewicz, A.J. (2013) The role of Zic transcription factors in regulating hindbrain retinoic acid signaling. BMC Developmental Biology. 13:31

Fodor, E., Zsigmond, A., Horváth, B., Molnár, J., Nagy, I., Tóth, G., Wilson, S.W., and Varga, M. (2013) Full transcriptome analysis of early dorsoventral patterning in zebrafish. PLoS One. 8(7):e70053

Winata, C.L., Kondrychyn, I., Kumar, V., Srinivasan, K.G., Orlov, Y., Ravishankar, A., Prabhakar, S., Stanton, L.W., Korzh, V., and Mathavan, S. (2013) Genome wide analysis reveals zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genetics. 9(10):e1003852

Bogdanovic, O., Fernandez-Minan, A., Tena, J.J., de Lacalle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S.J., Veenstra, G.J., and Gomez-Skarmeta, J.L. (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome research. 22(10):2043-2053

Cast, A.E., Gao, C., Amack, J.D., and Ware, S.M. (2012) An essential and highly conserved role for Zic3 in left-right patterning, gastrulation and convergent extension morphogenesis. Developmental Biology. 364(1):22-31

Garnett, A.T., Square, T.A., and Medeiros, D.M. (2012) BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border. Development (Cambridge, England). 39(22):4220-4231

Robles, V., Martí, M., and Belmonte, J.C. (2011) Study of Pluripotency Markers in Zebrafish Embryos and Transient Embryonic Stem Cell Cultures. Zebrafish. 8(2):57-63

Christen, B., Robles, V., Raya, M., Paramonov, I., and Izpisúa Belmonte, J.C. (2010) Regeneration and reprogramming compared. BMC Biology. 8:5

Kaslin, J., Ganz, J., Geffarth, M., Grandel, H., Hans, S., and Brand, M. (2009) Stem cells in the adult zebrafish cerebellum: initiation and maintenance of a novel stem cell niche. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29(19):6142-6153

Keller, M.J., and Chitnis, A.B. (2007) Insights into the evolutionary history of the vertebrate zic3 locus from a teleost-specific zic6 gene in the zebrafish, Danio rerio. Development genes and evolution. 217(7):541-547

Okuda, Y., Yoda, H., Uchikawa, M., Furutani-Seiki, M., Takeda, H., Kondoh, H., Kamachi, Y. (2006) Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(3):811-825

Woods, I.G., Wilson, C., Friedlander, B., Chang, P., Reyes, D.K., Nix, R., Kelly, P.D., Chu, F., Postlethwait, J.H., and Talbot, W.S. (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome research. 15(9):1307-1314

Lo, J., Lee, S., Xu, M., Liu, F., Ruan, H., Eun, A., He, Y., Ma, W., Wang, W., Wen, Z., and Peng, J. (2003) 15,000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome research. 13(3):455-466

Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903

Grinblat, Y. and Sive, H. (2001) zic gene expression marks anteroposterior pattern in the presumptive neurectoderm of the zebrafish gastrula. Developmental Dynamics : an official publication of the American Association of Anatomists. 222(4):688-693

Additional Citations (24):

ZFIN Staff (2023) Automated Curation of UniProt Database Links. Automated Data Submission.

ZFIN Staff (2020) Addition of links from ZFIN to Expression Atlas. Semi-automated Curation.

ZFIN Staff (2017) Curation of PANTHER Gene IDs. Automated Data Submission.

ZFIN Staff (2017) Curation of Alliance of Genome Resources Database Links. Automated Data Submission.

Varshney, G.K., Zhang, S., Burgess, S.M., ZFIN Staff (2015) Automated Data Load From CRISPRz. ZFIN Direct Data Submission.

Busch-Nentwich, E., Kettleborough, R., Dooley, C. M., Scahill, C., Sealy, I., White, R., Herd, C., Mehroke, S., Wali, N., Carruthers, S., Hall, A., Collins, J., Gibbons, R., Pusztai, Z., Clark, R., and Stemple, D.L. (2013) Sanger Institute Zebrafish Mutation Project mutant data submission. ZFIN Direct Data Submission.

ZFIN Staff (2013) Semi-automated association of ENSDARG identifiers with ZFIN genes for the ZMP project. Semi-automated Curation.

UniProt-GOA (2011) Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries. Manually curated data.

Gaudet, P., Livstone, M.S., Lewis, S.E., Thomas, P.D. (2010) Annotation inferences using phylogenetic trees. Automated Data Submission. 12:449-62

ZFIN Staff (2007) Microarray Expression to Gene Association in ZFIN. Semi-automated Curation.

Ensembl curators, GOA curators (2006) Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara. Manually curated data.

ZFIN Staff (2006) Curation of Ensembl Database Links. Automated Data Submission.

ZFIN Staff (2004) ZGC Data Curation and Association in ZFIN by ZFIN Staff. Semi-automated Curation.

Rauch, G.J., Lyons, D.A., Middendorf, I., Friedlander, B., Arana, N., Reyes, T., and Talbot, W.S. (2003) Submission and Curation of Gene Expression Data. ZFIN Direct Data Submission.

ZFIN Staff (2003) Curation of VEGA Database Links. Automated Data Submission.

ZFIN Staff (2003) Curation of orthology data. Manually curated data.

ZFIN Staff (2003) Curation of unpublished nucleotide sequence accession numbers. Manually curated data.

ZFIN Staff (2003) Computational Sequence to Gene Association in ZFIN. Semi-automated Curation.

ZFIN Staff (2002) Gene Ontology Annotation Through Association of UniProt Keywords with GO Terms. Automated Data Submission.

ZFIN Staff (2002) Curation of NCBI Gene Data Via Shared RNA Sequence IDs. Automated Data Submission.

ZFIN Staff (2002) Scientific Curation. Manually curated data.

ZFIN Staff (2002) Gene Ontology Annotation Through Association of InterPro Records with GO Terms. Automated Data Submission.

Kudoh, T., Tsang, M., Hukriede, N.A., Chen, X., Dedekian, M., Clarke, C.J., Kiang, A., Schultz, S., Epstein, J.A., Toyama, R., and Dawid, I.B. (2001) A gene expression screen in zebrafish embryogenesis. ZFIN Direct Data Submission.

Thisse, B., Pflumio, S., Fürthauer, M., Loppin, B., Heyer, V., Degrave, A., Woehl, R., Lux, A., Steffan, T., Charbonnier, X.Q. and Thisse, C. (2001) Expression of the zebrafish genome during embryogenesis (NIH R01 RR15402). ZFIN Direct Data Submission.