LOCUS       NM_152940               2385 bp    mRNA    linear   VRT 06-APR-2025
DEFINITION  Danio rerio cone-rod homeobox (crx), mRNA.
ACCESSION   NM_152940
VERSION     NM_152940.1
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 2385)
  AUTHORS   Volkov,L.I., Ogawa,Y., Somjee,R., Vedder,H.E., Powell,H.E.,
            Poria,D., Meiselman,S., Kefalov,V.J. and Corbo,J.C.
  TITLE     Samd7 represses short-wavelength cone genes to preserve
            long-wavelength cone and rod photoreceptor identity
  JOURNAL   Proc Natl Acad Sci U S A 121 (47), e2402121121 (2024)
   PUBMED   39531499
REFERENCE   2  (bases 1 to 2385)
  AUTHORS   Chiang,H.J., Nishiwaki,Y., Chiang,W.C. and Masai,I.
  TITLE     Male germ cell-associated kinase is required for axoneme formation
            during ciliogenesis in zebrafish photoreceptors
  JOURNAL   Dis Model Mech 17 (7) (2024)
   PUBMED   38813692
REFERENCE   3  (bases 1 to 2385)
  AUTHORS   Wang,W., Yang,N., Wang,L., Zhu,Y., Chu,X., Xu,W., Li,Y., Xu,Y.,
            Gao,L., Zhang,B., Zhang,G., Sun,Q., Wang,W., Wang,Q., Zhang,W. and
            Chen,D.
  TITLE     The TET-Sall4-BMP regulatory axis controls craniofacial cartilage
            development
  JOURNAL   Cell Rep 43 (3), 113873 (2024)
   PUBMED   38427557
REFERENCE   4  (bases 1 to 2385)
  AUTHORS   Jing,Y., Luo,Y., Li,L., Liu,M. and Liu,J.X.
  TITLE     Deficiency of copper responsive gene stmn4 induces retinal
            developmental defects
  JOURNAL   Cell Biol Toxicol 40 (1), 2 (2024)
   PUBMED   38252267
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2385)
  AUTHORS   Neil,G.J., Kluttig,K.H. and Allison,W.T.
  TITLE     Determining Photoreceptor Cell Identity: Rod Versus Cone Fate
            Governed by tbx2b Opposing nrl
  JOURNAL   Invest Ophthalmol Vis Sci 65 (1), 39 (2024)
   PUBMED   38261312
REFERENCE   6  (bases 1 to 2385)
  AUTHORS   Babb,S.G., Kotradi,S.M., Shah,B., Chiappini-Williamson,C.,
            Bell,L.N., Schmeiser,G., Chen,E., Liu,Q. and Marrs,J.A.
  TITLE     Zebrafish R-cadherin (Cdh4) controls visual system development and
            differentiation
  JOURNAL   Dev Dyn 233 (3), 930-945 (2005)
   PUBMED   15918170
REFERENCE   7  (bases 1 to 2385)
  AUTHORS   Perkins,B.D., Nicholas,C.S., Baye,L.M., Link,B.A. and Dowling,J.E.
  TITLE     dazed gene is necessary for late cell type development and retinal
            cell maintenance in the zebrafish retina
  JOURNAL   Dev Dyn 233 (2), 680-694 (2005)
   PUBMED   15844196
REFERENCE   8  (bases 1 to 2385)
  AUTHORS   Shen,Y.C. and Raymond,P.A.
  TITLE     Zebrafish cone-rod (crx) homeobox gene promotes retinogenesis
  JOURNAL   Dev Biol 269 (1), 237-251 (2004)
   PUBMED   15081370
REFERENCE   9  (bases 1 to 2385)
  AUTHORS   Stenkamp,D.L. and Frey,R.A.
  TITLE     Extraretinal and retinal hedgehog signaling sequentially regulate
            retinal differentiation in zebrafish
  JOURNAL   Dev Biol 258 (2), 349-363 (2003)
   PUBMED   12798293
REFERENCE   10 (bases 1 to 2385)
  AUTHORS   Stenkamp,D.L., Frey,R.A., Mallory,D.E. and Shupe,E.E.
  TITLE     Embryonic retinal gene expression in sonic-you mutant zebrafish
  JOURNAL   Dev Dyn 225 (3), 344-350 (2002)
   PUBMED   12412019
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF503443.1.
            
            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 :: AF503443.1, CN510104.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505372
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2385
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="5"
                     /map="5"
     gene            1..2385
                     /gene="crx"
                     /note="cone-rod homeobox"
                     /db_xref="GeneID:81881"
                     /db_xref="ZFIN:ZDB-GENE-010403-1"
     misc_feature    375..377
                     /gene="crx"
                     /note="upstream in-frame stop codon"
     CDS             411..1256
                     /gene="crx"
                     /codon_start=1
                     /product="cone-rod homeobox protein"
                     /protein_id="NP_694419.1"
                     /db_xref="GeneID:81881"
                     /db_xref="ZFIN:ZDB-GENE-010403-1"
                     /translation="

MMSYIKQPHYAVNGLTLSASGMDLLHTAVGYPATPRKQRRERTTFTRTQLDILEALFTKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQTSGQPKPRPPKKKSSPPPDLTSDPGTSSSVVAAPTPTVPPSVSAGTAPVSVWSPTSLSPLPDPLCGSGTPCVQRPAPYPMSYGQPSSYSQGYGSSPYFSGLDCSPYLSPMTTQLSASGGALSPLTVPSMGGSLSQSPSLSSQGYSTASLGFSSVDCLDYKDQQAWKLNFSTVDCLDHKFQVL"

     misc_feature    522..701
                     /gene="crx"
                     /note="Region: homeodomain"
     misc_feature    555..692
                     /gene="crx"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    864..1100
                     /gene="crx"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
ORIGIN      

cggcacgaggctcatagtgtcccgctcctgtccggtcttacccaagggacacgcgcctttaccaacgccaaaactctgaccaagagccagcaacttttctcgcatatagacatttatttgttctttaactcacattagggtctattattggatatttagagcgatagtaatggtagattcctacttaaacttgggcaaaagtgtaagcttattgaagacagcgagtagcgcgcgcgcgagcatctacagctgtttgaggagcacagacacgcgccaggcgcgagcacagacacgcgacccccgacccgtaaaacagcgtcgcagagaaaaaagagagtgagagggggtgagagagggagggagagagagagcaatagagagagtgtgcgagagacgcggccgtcccaagaatgatgtcctacataaagcagccccattatgctgtgaacgggttaacactgtccgcctcaggaatggacctgctccacaccgccgtcggctacccagccactccgaggaagcagcgtcgagagcgcaccaccttcactcgcacccagctggacattctggaagctttgttcaccaaaacacgctatccagacatatttatgagagaagaggtagctctgaaaatcaaccttcccgagtccagagttcaggtgtggtttaagaaccgtcgtgctaaatgccgccagcagcagcagcagaccagcggtcagcccaagccccgtccccccaaaaagaagtcctcccctccccctgatctgacctctgaccctggcactagctcctcggtggtggctgccccgaccccgaccgtgccccctagtgtgagcgcaggcacagcaccagtttctgtatggagtcccacttctctttcccccctccctgatccactgtgtggttcaggcaccccctgcgtgcagcgtcctgctccatatcccatgagctacggtcagccctcttcctacagccagggctatggctcttctccttacttcagcggattggattgcagcccgtacctttctcccatgaccacccagctgtcagcaagtggaggcgccctctcccccctcaccgtgccctccatgggcggctcgctcagccagtcgccctctctctcctcccagggatacagcactgcgtcgttgggcttcagttcggtagactgccttgactacaaggaccagcaggcctggaagctcaacttcagcactgtggactgcctcgaccacaaattccaggtgctgtagaaaagaaagtgagagagagagagtgaagcgcaagagggaaggaaagatgcgtgaagaagaaatgatgcagaactattgccggagacattgtgatgatgaacaggactgaatcagcgtgattcatgtgatcttagaggtgaaaaaaggagcacccattttggaacaggtgaagactgttcctctgtaatccagatctgctctgtgattggctgagattgaagggactcttcaagtctactgatcagtcatcattattaaccatttacctcacacatgcacacaccattgactaactttcacaatgcatacacacaaacacacattggtattaatggtttataaggacatgccattggcattatgtattttatacagttaaaaccatttttatatgaccccacccctaaatctgacccttccaagaaatctgtggcacatttgaaatgtcaatttaagcattttgaattacaaggacataagaaatgtcctcataaaccacagcaatgttgtaattcctaggtcatacccatgtcattatacatttctgtccttgtaaaccacaaaaaccagtacacacagaaacaaagacatgcacataactggaggggaatctgtgtttgtttgtttttttgcagatacagttagcttattgttggacaaagttgttctttctacttttttcatgagtttggtttggtttgtctgtactgggagacattaggagttcttgtgtcgtgcttttagcttgctgttatttatgtatcgttaaattatgttaacttataacaaataatgttgttttctgttagtttgagttaatcgttactaattaaacttcatttaatggcatcgtatgcatgctatcgacatatgttttctatttgggtgaccttgtgtggaaaaatgttggtgtttacaaatgtcattatgttgctttgactgaacacgtacagaggggagctgaaggttttcatttttaattagtattactattccattaattgtggctttgtttaacaacgtctgtctaacaagagttgtctgaactcgcttcttgttgattatggcaagaataaagtatcactgtaattaactaaaaacagggctggaaaaaaaaaaaaaaaaaaaa

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