LOCUS       NM_131717               2511 bp    mRNA    linear   VRT 16-OCT-2021
DEFINITION  Danio rerio SIX homeobox 4b (six4b), mRNA.
ACCESSION   NM_131717 XM_009294646
VERSION     NM_131717.2
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 2511)
  AUTHORS   Talbot JC, Teets EM, Ratnayake D, Duy PQ, Currie PD and Amacher SL.
  TITLE     Muscle precursor cell movements in zebrafish are dynamic and
            require Six family genes
  JOURNAL   Development 146 (10) (2019)
   PUBMED   31023879
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2511)
  AUTHORS   Hu P, Liu M, Liu Y, Wang J, Zhang D, Niu H, Jiang S, Wang J, Zhang
            D, Han B, Xu Q and Chen L.
  TITLE     Transcriptome comparison reveals a genetic network regulating the
            lower temperature limit in fish
  JOURNAL   Sci Rep 6, 28952 (2016)
   PUBMED   27356472
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2511)
  AUTHORS   Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M,
            Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD,
            Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov
            GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W and
            Hertzano R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2511)
  AUTHORS   Ogawa Y, Shiraki T, Kojima D and Fukada Y.
  TITLE     Homeobox transcription factor Six7 governs expression of green
            opsin genes in zebrafish
  JOURNAL   Proc Biol Sci 282 (1812), 20150659 (2015)
   PUBMED   26180064
REFERENCE   5  (bases 1 to 2511)
  AUTHORS   Gomez-Marin C, Tena JJ, Acemel RD, Lopez-Mayorga M, Naranjo S, de
            la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E,
            Bovolenta P, Nobrega MA, Carvajal J and Gomez-Skarmeta JL.
  TITLE     Evolutionary comparison reveals that diverging CTCF sites are
            signatures of ancestral topological associating domains borders
  JOURNAL   Proc Natl Acad Sci U S A 112 (24), 7542-7547 (2015)
   PUBMED   26034287
REFERENCE   6  (bases 1 to 2511)
  AUTHORS   Phillips BT, Kwon HJ, Melton C, Houghtaling P, Fritz A and Riley
            BB.
  TITLE     Zebrafish msxB, msxC and msxE function together to refine the
            neural-nonneural border and regulate cranial placodes and neural
            crest development
  JOURNAL   Dev Biol 294 (2), 376-390 (2006)
   PUBMED   16631154
REFERENCE   7  (bases 1 to 2511)
  AUTHORS   Whitlock KE, Smith KM, Kim H and Harden MV.
  TITLE     A role for foxd3 and sox10 in the differentiation of
            gonadotropin-releasing hormone (GnRH) cells in the zebrafish Danio
            rerio
  JOURNAL   Development 132 (24), 5491-5502 (2005)
   PUBMED   16291787
REFERENCE   8  (bases 1 to 2511)
  AUTHORS   Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly
            PD, Chu F, Postlethwait JH and Talbot WS.
  TITLE     The zebrafish gene map defines ancestral vertebrate chromosomes
  JOURNAL   Genome Res 15 (9), 1307-1314 (2005)
   PUBMED   16109975
REFERENCE   9  (bases 1 to 2511)
  AUTHORS   Glavic A, Maris Honore S, Gloria Feijoo C, Bastidas F, Allende ML
            and Mayor R.
  TITLE     Role of BMP signaling and the homeoprotein Iroquois in the
            specification of the cranial placodal field
  JOURNAL   Dev Biol 272 (1), 89-103 (2004)
   PUBMED   15242793
REFERENCE   10 (bases 1 to 2511)
  AUTHORS   Bebenek IG, Gates RD, Morris J, Hartenstein V and Jacobs DK.
  TITLE     sine oculis in basal Metazoa
  JOURNAL   Dev Genes Evol 214 (7), 342-351 (2004)
   PUBMED   15221378
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BX649231.4, EH591208.1, EH592927.1 and EH608698.1.
            
            On or before Jun 23, 2015 this sequence version replaced
            XM_009294646.1, NM_131717.1.
            
            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.
            
            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 :: AF030283.1, GDQH01032690.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2168446, SAMEA2168447
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-225               BX649231.4         71286-71510
            226-1161            EH591208.1         29-964
            1162-1856           EH592927.1         121-815
            1857-2348           EH608698.1         167-658             c
            2349-2361           EH608698.1         153-165             c
            2362-2362           BX649231.4         78576-78576
            2363-2415           EH608698.1         99-151              c
            2416-2511           BX649231.4         78630-78725
FEATURES             Location/Qualifiers
     source          1..2511
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="20"
                     /map="20"
     gene            1..2511
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="SIX homeobox 4b"
                     /db_xref="GeneID:65232"
                     /db_xref="ZFIN:ZDB-GENE-010201-1"
     exon            1..841
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    69..71
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="upstream in-frame stop codon"
     CDS             108..1955
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="sine oculis homeobox homolog 4a; etID17314.20; sine
                     oculis homeobox homolog 4.1; sine oculis homeobox homolog
                     8; sine oculis homeobox homolog 4b"
                     /codon_start=1
                     /product="homeobox protein SIX4b"
                     /protein_id="NP_571792.2"
                     /db_xref="GeneID:65232"
                     /db_xref="ZFIN:ZDB-GENE-010201-1"
                     /translation="

MCCLKPRGVTYQDAFKMSSSSSEVISADEIKRESRGSVKLSVLDPAELPMENAELLDCSPASLAFSPEQVACVCEALMQGGNVDRLARFLWSLPQSDLLRGNESILKAQAIVAFHHARYQELYCILENHSFSPSNHSSLQDMWYKARYTEAEKARGRPLGAVDKYRLRRKYPLPRTIWDGEETVYCFKERSRNALKDMYKRNRYPSPAEKRNLAKMTGLSLTQVSNWFKNRRQRDRNPSEAQSKSESDGNHSTEDESSKGQEDLSPRPLSSGSSSSVPHGTAPPTVYSDGGTTVIQQIGDVKMPSHSGGGMSYNGDLASVNAHYINSGAYGHSHSSNALLNGLGATGGHFLTFDPQRVSHHSQERLLGGSSVSYAPFSMGVSETASGKIDTMQTLVSNGEDGVISSVVSFASAPSTPSTTSGGLHLSSYSVVNLPGNESTMGLPPLMLPPSSTSSTHGSAPLGNVVSDSSQHSSQTLLYSQTVKQEPLDVPGSYAYPSDMPLDQGSNLGYTASLFLSSSSSSGSLPSTITATVTSTLSNSDVHHALNQAGRGLQEDGVALSSDYRSQDIHLPNSLQVVSREGEGPVRVVCGDLDMEGKELAKLQTVQMDDDGSDL"

     misc_feature    300..629
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="Transcriptional regulator, SIX1, N-terminal SD
                     domain; Region: SIX1_SD; pfam16878"
                     /db_xref="CDD:465293"
     misc_feature    660..824
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="Homeodomain; DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:238039"
     misc_feature    order(663..665,783..785,792..797,804..806)
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            842..1479
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /inference="alignment:Splign:2.1.0"
     exon            1480..2511
                     /gene="six4b"
                     /gene_synonym="six4.1; six4a; six8; wu:fj32d01"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gtggagttaaacttgtggtagaacgggggacgccagatcttatccactccacgcagcggccagatacctgatcgtgcttggatggaggggcgaaacccgatcgcctgatgtgctgcctgaaacccagaggagtgacttatcaggacgcgttcaaaatgtcttcttcctcaagcgaggtcattagtgccgatgagatcaagagggagagtcgtgggagtgtcaagctgtcagtgctggaccccgcggagttgccgatggagaatgccgaacttttggactgctcgccggcctccctggccttttcccccgagcaggtcgcgtgcgtctgcgaggcgctgatgcagggtgggaacgtggaccgcctggccaggttcctgtggtcactaccgcagagtgacctcctgcgggggaacgagagcatcctgaaggcgcaagcgatagtcgccttccaccatgcccgctaccaagagctctactgcatcttggagaaccactctttcagcccgtcgaaccactcgtctctgcaggatatgtggtacaaggcgcgctacaccgaggcggagaaggcgcgaggcagaccgctgggtgccgtggacaagtatcgcttacgcaggaaatatccgctgcctcggactatctgggacggagaagagaccgtgtattgtttcaaagagaggtctcggaacgcgctgaaggatatgtacaagcggaaccggtacccatctccagccgagaagcgaaatctggcaaaaatgacaggactttccttgacgcaggtcagcaactggttcaaaaacaggaggcagagagacagaaatccatcagaagcgcaatcgaagagtgagtcggatggcaatcacagtacagaagatgagtccagtaaaggccaagaggacttgtcaccacgtcccctctcaagcggctcttccagctcagtcccacacggaacagccccccctacagtttactcagacggaggaacaacagtcatccaacaaataggagatgtcaaaatgccctcacactcaggtggaggaatgagttataatggtgaccttgcgagcgtcaatgctcactacatcaacagtggagcttatggtcactcacacagcagcaatgctctcctgaacggacttggcgccacaggtggccatttcttgacctttgatcctcagagggtctcccatcacagtcaggaaaggctgttaggtgggtcttccgtgtcttatgctccattctcaatgggagtttctgaaacagcctctggaaagatagataccatgcagactttagtttccaatggtgaggatggagtcatttcttcagtggtgtcctttgcttcggccccctccacaccatccactacctcagggggccttcatctcagcagttacagcgtggtcaatctccctggaaatgaatctacaatgggtcttcctcctctaatgctgcctccatcatcaacatcatccactcacggatctgctcctttgggcaacgtagtcagtgactcttcccagcactcaagccaaactctgctctactcccagactgtgaagcaggagcccctggatgtgcctggaagctatgcttatccttctgatatgcccctggaccaaggtagcaacctgggctatacagcctcccttttcctctcgtcgtcctccagtagtggttctcttccctctaccatcacagctacagtcacctcaaccctctccaactccgatgtccaccatgctctgaatcaagcaggacgtggcctccaagaggatggtgtagctctgtcttcagactacaggtctcaagacatccatctgcccaacagcctgcaggttgtttctagggaaggagaaggtccagtcagggttgtttgtggggatttggatatggaggggaaagagctggccaagctgcagactgtacagatggacgatgatggaagcgacctctgatgatgtcaataatgcatttcactcgtgctggactggttttgtcacgccgcattgtgcccttatggacgctttaagcacaaatcattctcatatgaaccctagcgatggatgtaaaaatgcgaacagtgccttcctgtcctgatatatcccaacttgcactaagagggctgcagaacttaccaggcaatgcactgacttttggaagattatttagctgcagtctttatactgtcacctcaaaaacaaaatactaaatacctgttaaaaagcacaactgtgctctgaatcaaataatgcagctttatagtgattgttttcttttaacaggattttattgatgcacagatgcatttttgttgttgttgttgttgtttatggtctttttgtatttaatttttttgtgtgtgaagatgcaaacgtgataaagcttattttgttatgcttgacttgaggaattttatgttacagaatttttttaattcaaactgacaagtctctttctacatatccaagcgtggacttgtgtggaagctagataacaagccatttatttgaa

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