2024-11-01 07:55:50, GGRNA.v2 : RefSeq release 226 (Sep, 2024)
LOCUS NM_001326290 2460 bp mRNA linear VRT 30-JUN-2024 DEFINITION Danio rerio homer scaffold protein 1b (homer1b), transcript variant 2, mRNA. ACCESSION NM_001326290 XM_005157295 VERSION NM_001326290.1 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 2460) AUTHORS Gabellini,C., Pucci,C., De Cesari,C., Martini,D., Di Lauro,C., Digregorio,M., Norton,W., Zippo,A., Sessa,A., Broccoli,V. and Andreazzoli,M. TITLE CRISPR/Cas9-Induced Inactivation of the Autism-Risk Gene setd5 Leads to Social Impairments in Zebrafish JOURNAL Int J Mol Sci 24 (1), 167 (2022) PUBMED 36613611 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 2460) AUTHORS Ikeda,A., Yamasaki,C., Kubo,Y., Doi,Y., Komamizu,M., Komatsu,M. and Shiozaki,K. TITLE Alteration of the neuronal and glial cell profiles in Neu1-deficient zebrafish JOURNAL Glycoconj J 39 (4), 499-512 (2022) PUBMED 35877057 REFERENCE 3 (bases 1 to 2460) AUTHORS Deng,J., Wang,Y., Hu,M., Lin,J., Li,Q., Liu,C. and Xu,X. TITLE Deleterious Variation in BR Serine/Threonine Kinase 2 Classified a Subtype of Autism JOURNAL Front Mol Neurosci 15, 904935 (2022) PUBMED 35754711 REMARK Publication Status: Online-Only REFERENCE 4 (bases 1 to 2460) AUTHORS Gao,L., Penglee,R., Huang,Y., Yi,X., Wang,X., Liu,L., Gong,X. and Bao,B. TITLE CRISPR/Cas9-induced nos2b mutant zebrafish display behavioral abnormalities JOURNAL Genes Brain Behav 20 (5), e12716 (2021) PUBMED 33200539 REFERENCE 5 (bases 1 to 2460) AUTHORS Tang,W., Davidson,J.D., Zhang,G., Conen,K.E., Fang,J., Serluca,F., Li,J., Xiong,X., Coble,M., Tsai,T., Molind,G., Fawcett,C.H., Sanchez,E., Zhu,P., Couzin,I.D. and Fishman,M.C. TITLE Genetic Control of Collective Behavior in Zebrafish JOURNAL iScience 23 (3), 100942 (2020) PUBMED 32179471 REFERENCE 6 (bases 1 to 2460) AUTHORS Frank,D.F., Miller,G.W., Connon,R.E., Geist,J. and Lein,P.J. TITLE Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95 JOURNAL PeerJ 5, e4106 (2017) PUBMED 29201571 REMARK Publication Status: Online-Only REFERENCE 7 (bases 1 to 2460) AUTHORS Bayes,A., Collins,M.O., Reig-Viader,R., Gou,G., Goulding,D., Izquierdo,A., Choudhary,J.S., Emes,R.D. and Grant,S.G. TITLE Evolution of complexity in the zebrafish synapse proteome JOURNAL Nat Commun 8, 14613 (2017) PUBMED 28252024 REMARK Publication Status: Online-Only REFERENCE 8 (bases 1 to 2460) AUTHORS Pasquier,J., Cabau,C., Nguyen,T., Jouanno,E., Severac,D., Braasch,I., Journot,L., Pontarotti,P., Klopp,C., Postlethwait,J.H., Guiguen,Y. and Bobe,J. TITLE Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database JOURNAL BMC Genomics 17, 368 (2016) PUBMED 27189481 REMARK Publication Status: Online-Only REFERENCE 9 (bases 1 to 2460) AUTHORS Lin,C.Y., Chen,J.S., Loo,M.R., Hsiao,C.C., Chang,W.Y. and Tsai,H.J. TITLE MicroRNA-3906 regulates fast muscle differentiation through modulating the target gene homer-1b in zebrafish embryos JOURNAL PLoS One 8 (7), e70187 (2013) PUBMED 23936160 REMARK GeneRIF: Results indicate that miR-3906 controls [Ca(2+)]i homeostasis in fast muscle through fine tuning homer-1b expression during differentiation Publication Status: Online-Only REFERENCE 10 (bases 1 to 2460) AUTHORS Baraban,S.C., Dinday,M.T. and Hortopan,G.A. TITLE Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment JOURNAL Nat Commun 4, 2410 (2013) PUBMED 24002024 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from CT033828.6 and EH491241.1. On May 13, 2016 this sequence version replaced XM_005157295.2. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## RNAseq introns :: mixed/partial sample support SAMEA2168446, SAMEA2168447 [ECO:0000350] ##Evidence-Data-END## PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-13 CT033828.6 32678-32690 14-429 EH491241.1 30-445 430-430 CT033828.6 44976-44976 431-836 EH491241.1 447-852 837-837 CT033828.6 70714-70714 838-985 EH491241.1 854-1001 986-1056 CT033828.6 82158-82228 1057-1167 CT033828.6 83956-84066 1168-1248 CT033828.6 84167-84247 1249-2460 CT033828.6 87491-88702 FEATURES Location/Qualifiers source 1..2460 /organism="Danio rerio" /mol_type="mRNA" /strain="Tuebingen" /db_xref="taxon:7955" /chromosome="5" /map="5" gene 1..2460 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="homer scaffold protein 1b" /db_xref="GeneID:436769" /db_xref="ZFIN:ZDB-GENE-040801-44" exon 1..359 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" misc_feature 253..255 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="upstream in-frame stop codon" CDS 355..1437 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="isoform 2 is encoded by transcript variant 2; homer homolog 1; homer homolog 1b; homer scaffolding protein 1b" /codon_start=1 /product="homer protein homolog 1b isoform 2" /protein_id="NP_001313219.1" /db_xref="GeneID:436769" /db_xref="ZFIN:ZDB-GENE-040801-44" /translation="
MGEQPIYSTRAHVFQIDPSTKKNWMPTSKHAVTVSYFYDSTRNVYRIISLDGSKAIINSTITPNMSFTKTSQKFGQWADSRANTVYGLGFSSEHHLAKFADKFAEYKEAARIAKEKSLEKMELASSPSQESPADIHSPLTPPVTADLCRINGTGDDVTLSDVSPNSMLQSDLSPTTPTLAHSPTTNKHWEAELAALKSNNAKLTAALLESTANVKQWKQQLAAYQEEAERLHKRVSELESQSSQTNVIKSQKTELNQTIEELECTLRAKEEEMMRLKEEVENAKQLQAQKDELTKKLEDTDMRNKELEEQLSDLEQRLESSQVDQENLRKNLKTLLEILDGKIFELTELRDNLAKLIEDS"
misc_feature 361..687 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="Homer/Vesl family proteins EVH1 domain; Region: EVH1_Homer_Vesl; cd01206" /db_xref="CDD:269917" misc_feature order(424..426,562..564,574..576,619..621) /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="proline-rich peptide binding site [polypeptide binding]; other site" /db_xref="CDD:269917" misc_feature <922..>1431 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /note="Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Region: Smc; COG1196" /db_xref="CDD:440809" exon 360..516 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 517..648 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 649..741 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 742..899 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 900..1056 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 1057..1167 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 1168..1248 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" exon 1249..2460 /gene="homer1b" /gene_synonym="homer1; zgc:100854; zgc:92844" /inference="alignment:Splign:2.1.0" ORIGIN
tagattcatctttagagccacacgcccaccgagagagaggcagcggctcgttattcacccctgcgccaccgttacctcacgctcttcaacgaatacaatattcacaccgcagagatgcgaggtgagcccgtcgtgtgccaaagcagctgaaattgggcagtattagtgggcaattcgccgtgggatccattcagtgaatctgacagcctacatacagagcgcgtaacgagagacgcagaatgccgctgctcataatgtgaccgaccgcatccagagccgcttcattcagctggaagaacaaactcgctgatcaacaaatcctatctcgtctcaggagggaaaaacaacagcaacatgggggagcagcccatctacagcacccgggcacacgtcttccagatagaccccagcactaagaaaaactggatgcccaccagcaaacatgcggtcactgtatcttacttctacgacagtaccaggaacgtgtacagaatcatcagcttggatggatcgaaggcaataataaacagcactatcaccccgaacatgtccttcacaaagacatctcaaaagtttggccagtgggctgacagccgtgccaacacagtgtatgggctgggtttctcctccgagcatcatctggccaagttcgcagataaatttgcagagtacaaagaagcagccagaatagccaaggagaagtctctagaaaagatggagctggcaagttcgccctctcaggaatcgcctgctgacattcattcccctctgactccaccggtcactgcggacctctgccgaatcaacggcactggtgatgatgtcactctgtctgacgtgtcacccaactctatgcttcaatcagatctttctcccaccacgccgactcttgcacacagcccaactaccaacaaacactgggaggcagagctagcagcactaaagagcaacaatgctaagctcacagctgctctgctggagtccacagccaacgtcaaacaatggaaacagcagctcgccgcttatcaggaggaggctgaaaggctacacaaacgggtttcagaattggaaagtcaaagtagtcaaaccaacgtgatcaaatcccagaaaactgagctgaaccaaacaatagaggagctggaatgcactctgagggcaaaggaagaggaaatgatgcgattgaaagaagaagtagaaaacgccaagcagcttcaagctcaaaaagatgaactcaccaaaaaattagaggacacggatatgcggaacaaggagctagaggaacagttgtctgacctggagcagcgcctagagtccagtcaggtggaccaggagaacctgcgcaagaacctcaaaactctgctggagatcctggatggaaagatcttcgagctgaccgagctgagagacaacctagccaaactcatcgaagacagctagactcgcatctctactagacatttttacagaaaaattaaataaaaaccacacagtgtccaattcaggcccagagagagtctgactttcacagtcggactctccttcactcacttacatggaatgattaacctttggttgcacttgattttgtattttagttttttcgaggtacgtttattctcttcagtgccactgctaccgactgagttttattgtttcaaacactacattttctttcattcttgatgtttccttgaattcccctccccgaaataggcagcctgcaaagactacggctgcagataggctcctactctttaacggtgctggttttgtgtgcctggctgttggcgtaaaatggacgttacctatgctgctgaggacacttacatgaattacactgactggatcttcagtcgcattttaagactggatattcagagccatatgttgtagccaaacgttattggctcgcctcttccccttcatggaaactgcctcaatgttaagtaagtcaaagtttcaggatactcaaccgctgacctaaaaatctcttgacatttagcagacgctgagatgtagatgtggcgtaaacgctttaggcctgtaatatacactgagcaatattagtgtgagcgtctgtatggcagattagtgtgagccacctcaatgcatccgtcaggtactcaaacgctcgaaaggacgaatttacggtcatctttcggatttctccagcgatcagtgtattgcttttggatcgtattggccttattatatccactatctatacatttttcaggattttttcttgaagacgaggatcttccttttgtttgttaacttaccaaatgcaattatgtattcgattccttacgattttcaataacgctattattgtaatatttaaaaggtccatcctgctgatggctgttacggtacatagatcactgtcagtatgattgtatttatatgtggggaaaattctgtttttgatttcccaatgttaataaagactatttaaag
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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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