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2024-03-28 23:55:35, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_131333               1587 bp    mRNA    linear   VRT 09-DEC-2023
DEFINITION  Danio rerio visual system homeobox 1 homolog, chx10-like (vsx1),
            mRNA.
ACCESSION   NM_131333
VERSION     NM_131333.1
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 1587)
  AUTHORS   Hickey GJ, Wike CL, Nie X, Guo Y, Tan M, Murphy PJ and Cairns BR.
  TITLE     Establishment of developmental gene silencing by ordered polycomb
            complex recruitment in early zebrafish embryos
  JOURNAL   Elife 11, e67738 (2022)
   PUBMED   34982026
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1587)
  AUTHORS   Itoh T, Inoue S, Sun X, Kusuda R, Hibi M and Shimizu T.
  TITLE     Cfdp1 controls the cell cycle and neural differentiation in the
            zebrafish cerebellum and retina
  JOURNAL   Dev Dyn 250 (11), 1618-1633 (2021)
   PUBMED   33987914
REFERENCE   3  (bases 1 to 1587)
  AUTHORS   Mukaigasa K, Sakuma C and Yaginuma H.
  TITLE     The developmental hourglass model is applicable to the spinal cord
            based on single-cell transcriptomes and non-conserved
            cis-regulatory elements
  JOURNAL   Dev Growth Differ 63 (7), 372-391 (2021)
   PUBMED   34473348
REFERENCE   4  (bases 1 to 1587)
  AUTHORS   Lahne M, Brecker M, Jones SE and Hyde DR.
  TITLE     The Regenerating Adult Zebrafish Retina Recapitulates Developmental
            Fate Specification Programs
  JOURNAL   Front Cell Dev Biol 8, 617923 (2021)
   PUBMED   33598455
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1587)
  AUTHORS   Guo R, Ge K, Wang Y, Lu M, Li F, Tian L, Gan L and Sheng D.
  TITLE     LIM Homeobox 4 (lhx4) regulates retinal neural differentiation and
            visual function in zebrafish
  JOURNAL   Sci Rep 11 (1), 1977 (2021)
   PUBMED   33479361
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1587)
  AUTHORS   D'Autilia S, Decembrini S, Casarosa S, He RQ, Barsacchi G, Cremisi
            F and Andreazzoli M.
  TITLE     Cloning and developmental expression of the Xenopus homeobox gene
            Xvsx1
  JOURNAL   Dev Genes Evol 216 (12), 829-834 (2006)
   PUBMED   17103185
REFERENCE   7  (bases 1 to 1587)
  AUTHORS   Wan L, Almers W and Chen W.
  TITLE     Two ribeye genes in teleosts: the role of Ribeye in ribbon
            formation and bipolar cell development
  JOURNAL   J Neurosci 25 (4), 941-949 (2005)
   PUBMED   15673675
REFERENCE   8  (bases 1 to 1587)
  AUTHORS   Shen YC and Raymond PA.
  TITLE     Zebrafish cone-rod (crx) homeobox gene promotes retinogenesis
  JOURNAL   Dev Biol 269 (1), 237-251 (2004)
   PUBMED   15081370
REFERENCE   9  (bases 1 to 1587)
  AUTHORS   Kurtzman AL and Schechter N.
  TITLE     Ubc9 interacts with a nuclear localization signal and mediates
            nuclear localization of the paired-like homeobox protein Vsx-1
            independent of SUMO-1 modification
  JOURNAL   Proc Natl Acad Sci U S A 98 (10), 5602-5607 (2001)
   PUBMED   11331779
REFERENCE   10 (bases 1 to 1587)
  AUTHORS   Kurtzman AL, Gregori L, Haas AL and Schechter N.
  TITLE     Ubiquitination and degradation of the zebrafish paired-like
            homeobox protein VSX-1
  JOURNAL   J Neurochem 75 (1), 48-55 (2000)
   PUBMED   10854246
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF025348.2.
            
            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 :: AF025348.2 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505392, SAMEA4476733
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1587
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="17"
                     /map="17"
     gene            1..1587
                     /gene="vsx1"
                     /note="visual system homeobox 1 homolog, chx10-like"
                     /db_xref="GeneID:30598"
                     /db_xref="ZFIN:ZDB-GENE-990415-205"
     misc_feature    10..12
                     /gene="vsx1"
                     /note="upstream in-frame stop codon"
     CDS             31..1065
                     /gene="vsx1"
                     /note="transcription factor VSX1; visual system homeobox 1
                     protein; etID309864.17; paired-like homeobox protein"
                     /codon_start=1
                     /product="visual system homeobox 1"
                     /protein_id="NP_571408.1"
                     /db_xref="GeneID:30598"
                     /db_xref="ZFIN:ZDB-GENE-990415-205"
                     /translation="
MTGREEATDEKPKVKLYPSFGIDKSRLNGSGFRSKGFAITDLLGLESELQPHQSGPGAGPNGEGQSAAVGGFSFPGGSLPLGLGFLCSLAAQQPPGAPCFLPSHIPLLQSRTESHFMQNLEQQRDVYSDDDCLSGDRNDGKNSGNSQKRKKRRHRTVFTSHQLEELEKAFNEAHYPDVYAREMLAMKTELPEDRIQVWFQNRRAKWRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESIINSAKSGMMGSCAPWLLGEPAGMHKKSMEIVKKAPGTPESTHSDTYSEEHKGKDSDTTWSSGANGADDSEDMAIDLSSTSKQENKSTLKRSPPRTENSSDSENES"
     misc_feature    139..162
                     /gene="vsx1"
                     /note="propagated from UniProtKB/Swiss-Prot (O42250.2);
                     Region: Octapeptide motif"
     misc_feature    175..240
                     /gene="vsx1"
                     /note="propagated from UniProtKB/Swiss-Prot (O42250.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    331..>693
                     /gene="vsx1"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    409..498
                     /gene="vsx1"
                     /note="propagated from UniProtKB/Swiss-Prot (O42250.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    469..483
                     /gene="vsx1"
                     /note="propagated from UniProtKB/Swiss-Prot (O42250.2);
                     Region: Nuclear localization signal.
                     /evidence=ECO:0000269|PubMed:11331779"
     misc_feature    order(484..498,502..504,553..555,571..573,610..612,
                     616..621,628..633,637..645,649..654)
                     /gene="vsx1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    490..651
                     /gene="vsx1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(490..492,499..501,619..621,628..633,640..642)
                     /gene="vsx1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    847..1062
                     /gene="vsx1"
                     /note="propagated from UniProtKB/Swiss-Prot (O42250.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
ORIGIN      
ggcacgaggtgaattaaagaaactgccaccatgacgggaagagaagaagctacagatgaaaaacctaaagttaaactttacccttcgttcggaatcgacaaatcacgtctgaatggatctggatttcggtccaaagggttcgcaatcacagatctcctgggtctggagtcggaacttcagccgcaccagtcaggtccaggcgcggggcccaatggagagggccagagcgcggcggttggaggattttctttcccgggaggatctttgcccttgggcttggggtttctgtgtagtttggcggcgcaacagcctcctggagccccgtgttttctcccgagccacatccctctgttgcagtcacggacggagagccacttcatgcagaatctggagcagcaaagggacgtttactccgatgatgactgcctttccggtgatcgcaatgatggaaaaaactcagggaactctcaaaagaggaaaaagagaaggcacaggacagttttcacctcccatcaacttgaggaactagagaaagccttcaatgaagcacactatccagacgtttacgcgagagaaatgctggcaatgaagacagagctaccagaggacaggatacaggtatggtttcaaaaccggcgtgcaaagtggaggaaaagggaaaagtgctggggccgtagcagcgtgatggcagagtatgggctgtatggagccatggtgcgccactccattccactcccagaatccatcatcaactctgccaagagcgggatgatgggctcatgcgctccctggcttctaggtgagccagcaggaatgcacaaaaagtctatggaaattgtgaagaaagctcctggcacgcctgaatcgacacattcagatacatattcagaggaacacaaagggaaagacagcgacacgacatggtcaagcggagctaatggagcggacgattcagaagacatggcaatagatttgtctagcacttcaaaacaagagaacaaaagcactttgaaaagatctccgcctcgcacagaaaacagcagcgattctgaaaatgagagttaaaaatggacctcaatatatggacagttttgaagagcacgtgctgtacaaggactatcagttaataggatgtctcaccttttgtttgtttgcatttctgtgtcatttaagggtttttatgttgttgcttatcaaataattgaatactagagactgttttattctgaattattttatgtttcatgtaaatagtgtttaaaaagtttgcatttatgggcattatccatctaattttaagtaagttcccatattttattttttctctgtcaaaaaaatgctgtaaggtgattacttgttcaccgctactgtgaatgtcatatttccctgttaaaatacagcatgtgtctgggtaacagaaatgattttaaagcactttacctgctgtgatgatgaatgttttgcattgataagtgtcatcaacagagcaatataatgccagcaaaaaaagaaatccacatcaccacacacacaaaaaataataactaaataaacatattttatgcttttgaaaaaaaaaaaaaaaaa
//

by @meso_cacase at DBCLS
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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. [Full Text]