LOCUS       XM_005168976            2360 bp    mRNA    linear   VRT 08-SEP-2024
DEFINITION  PREDICTED: Danio rerio iroquois homeobox 6a (irx6a), transcript
            variant X1, mRNA.
ACCESSION   XM_005168976
VERSION     XM_005168976.5
DBLINK      BioProject: PRJNA13922
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_007118.7) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Sep 8, 2024 this sequence version replaced XM_005168976.4.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_000002035.6-RS_2024_08
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.3
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 08/15/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..2360
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="7"
     gene            1..2360
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="iroquois homeobox 6a; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 1
                     mRNA, 4 ESTs, 3 Proteins, and 100% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     61 samples with support for all annotated introns"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
     misc_feature    1
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /experiment="COORDINATES: cap analysis [ECO:0007248]"
                     /note="transcription start site"
     CDS             305..1822
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /codon_start=1
                     /product="Iroquois homeobox protein 6a isoform X1"
                     /protein_id="XP_005169033.1"
                     /db_xref="GeneID:474317"
                     /db_xref="ZFIN:ZDB-GENE-040712-5"
                     /translation="

MVTKEAAMSFSQFGYPYNATSQFFVSATPSTTCCDSISRSVTEGSSASQTAASFCCPSYENRLLASTRTELNAALGMYGSPYAAAAAAAGQNYANYFPYSADPSAIYSSLNPQYEIKEGSGSLHSTITQPATYYPYDHSLGQYQYDRYGTVDFNGSTRRKNATRETTSTLKTWLYEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWSPKNKAGDDRKEDLGKSDPDITKDSKDSKDEQDLQFSDLDDMEDEDCDKLDSDCEKSGQDDLPTSSPPKRDCNPDIPLHSNFPSFPCGLKSLGPLNPDYLDHLGSKPQQQQPSPQSTSINTVALSHFESSEKPRIWSLARTAAAGVVLGTQHVGDVRTGPVDCQMQGVRLPTVGAVQCGELKGLQDPTNLSNTESLFQEGLQGIHKAYSSGSFKTLQLHSSSYPGLTESCQYSSMEGFPSAGKTETESSELSDTCPTIQEAKTTAFRPVMKRTMEMPINMGKFL"

     misc_feature    order(776..784,788..790,848..850,866..868,905..907,
                     911..916,923..928,932..940,944..949)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(776..778,785..787,914..916,923..928,935..937)
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    824..940
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:428673"
     polyA_site      2360
                     /gene="irx6a"
                     /gene_synonym="zgc:109993; ziro6a"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      

agaggcacaaataatagcacaaccacaagttcatatcttgcaagtcttacgttatcctttaagctttctacagctgtttaacaacaatatttttgtacttgatgaagcttaactctaatttctcatttccttaaggggattatctatacatataaaactagggctggcgtaaacatcctcagtgcttcccagttaagtgcagtcatctattattgagcgaaaggccgagtgtggaaatgtgtgtaagacggtggatttgaagtagatttggtttcaatcgatcagcaggagaagaatattgcttatggtaacaaaagaagcagctatgtccttctctcagtttggatatccttacaatgcaacttctcagtttttcgtgtcggcaacccccagtacgacttgctgcgattcgatatccaggtcggtgacagaaggatcgagcgcatcgcagaccgcagcctccttctgctgtccctcctatgagaaccggctgctggcgagtacacggacggagctcaacgccgcgctcgggatgtacggctccccttacgcagcagcagcggccgcagccgggcagaactacgccaactactttccgtatagcgccgacccctccgccatctactccagcctgaacccacaatatgaaatcaaagaggggtcaggcagtcttcatagcactataacacaaccagccacttactatccatatgaccactcactcggacagtaccagtatgacaggtatgggacagttgattttaatggatcaacacggagaaagaacgccacacgtgagacaacaagtacgcttaaaacatggctttatgagcaccgcaaaaacccttatcctacaaagggtgaaaagatcatgctggccattatcaccaaaatgaccctcacgcaagtgtctacctggtttgccaatgctagaagacgactaaaaaaagaaaacaagatgacttggtcccccaaaaacaaagcaggcgatgacaggaaggaagacctcggtaagagtgacccagacattaccaaagactccaaagacagtaaggatgagcaggacctgcagttcagtgacctggatgatatggaggatgaggactgtgacaagctggacagtgactgtgaaaaatcaggtcaggatgacctcccgacctcctcccctccaaagagagactgtaaccctgacatccctctccactccaacttcccatcttttccctgtggtctgaagagtttggggcctctgaacccagactacctagatcatctgggctccaaaccacagcagcaacagccctcacctcagtccacctccataaacactgtggcactctctcactttgagtcatcggagaagccccggatctggtcgttggcacgtacggccgcagcaggggttgtactaggcacacagcatgttggggatgtacggactgggcctgtggactgtcagatgcagggagtccggttacccacagtcggagcagtgcagtgtggggagctgaagggccttcaggaccctacaaacctcagcaatactgaaagcctttttcaagaaggactacaggggatacacaaggcatacagtagcgggagcttcaagacactacaacttcactcttcatcatatcctggactgacagaatcctgccagtactcctcaatggaaggcttccccagtgcaggaaagacagagacagaatccagtgagctcagtgacacatgcccaacaatccaggaggctaagaccactgcattcagacctgtgatgaagaggactatggaaatgccaataaacatggggaagtttttatgatctacattatgcactatggaatggagtcaatgaggaactttaagcccatggcagcagacacttgaaatagtagcgcaatgactttgtgtgccctttctggaactgtgaaaactggaggcagccataattttgcacaatatgatttaatggtgtcaataactttatgcaatgttttgtgtatgtatgagaataaattgtgattttttatgtctgcattggcaatcgtaggtttagtaattctatttatctatttattgttttatcatccatctgctttatttatctgttaccatgtgtcctctcaaggtttttttgtgtgtgttaagtttaattctctgtggttatgtgcttaatgttatgtgatttacttttttttggaagctggtgtaaaatttagtcagtcttttaacttttatttacttctcaaaaataaatgaggtgcgatactgtgctcctgcggagtgtgatatgtttatataaaaaaaaagttgtgtataaatgtcatgttgttatttataaaatattttataagaactcg

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