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2024-03-29 00:16:53, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_018811998            3015 bp    mRNA    linear   INV 22-OCT-2018
DEFINITION  PREDICTED: Ciona intestinalis homeobox-containing protein 1
            (LOC778606), transcript variant X3, mRNA.
ACCESSION   XM_018811998
VERSION     XM_018811998.2
DBLINK      BioProject: PRJNA187185
KEYWORDS    RefSeq.
SOURCE      Ciona intestinalis (vase tunicate)
  ORGANISM  Ciona intestinalis
            Eukaryota; Metazoa; Chordata; Tunicata; Ascidiacea; Phlebobranchia;
            Cionidae; Ciona.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_020166.2) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Oct 22, 2018 this sequence version replaced XM_018811998.1.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI
            Annotation Status           :: Full annotation
            Annotation Name             :: Ciona intestinalis Annotation
                                           Release 104
            Annotation Version          :: 104
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 8.1
            Annotation Method           :: Best-placed RefSeq; Gnomon
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..3015
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="1"
     gene            1..3015
                     /gene="LOC778606"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Gnomon. Supporting evidence
                     includes similarity to: 7 ESTs, and 100% coverage of the
                     annotated genomic feature by RNAseq alignments, including
                     80 samples with support for all annotated introns"
                     /db_xref="GeneID:778606"
     CDS             81..1619
                     /gene="LOC778606"
                     /codon_start=1
                     /product="homeobox-containing protein 1 isoform X3"
                     /protein_id="XP_018667543.1"
                     /db_xref="GeneID:778606"
                     /translation="
MRDTRLSPHPEEMGEPDPPKFTVNQILLLQKLKQSGLTKSQIIKGLDEMERFDDVGLGSPGASVSSSTQQVPNGNSPSSVGSTNSGNTVTSCANAGARRNSTSPQSPHLPQVKTNTVIPHPQPIPNHLMFGAHMQNASQLSLIPPVAAWPNTSQAVAVATAASILQNGFAHGNVPHSVYPSLINGRGLLQRGPAMSGTGSTVVEVDGEKIDITEELEDLFRRDQASVKEDIRKFISERHISQSAIAKATRNAISQSYISQWLAQPQDISGQKKKAMYTWYIVERRKPPGLTNGMSSVPPVVFRHNEIENDCISPMMMKSKRGARFTWPKECLSILENYYNANSYPDECKREEIAHACNAIIQSQKPGSMLTELDKVTTVKVYNWFANRRKDDKRRRHIEHVEAMDQHHLIMSPRRNSATSPSPSCHSNDSSQGVESNERCMVIPKKENPMQLALEMAAVNHSIMALVNPHQVDDPMREDEEDDLGESSSEEIQRPEERRPFERLPDNRSYAG"
     misc_feature    153..923
                     /gene="LOC778606"
                     /note="Hepatocyte nuclear factor 1 (HNF-1), N-terminus;
                     Region: HNF-1_N; pfam04814"
                     /db_xref="CDD:428137"
     misc_feature    1041..1241
                     /gene="LOC778606"
                     /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(1047..1049,1056..1058,1227..1229,1236..1241)
                     /gene="LOC778606"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
ORIGIN      
cccagtttgtttatttcactttccagcatattagatttaaaaaccgtgcaacataaaactgaaccttaagtttcgactgaatgcgcgacactagactctcgccccatcccgaagaaatgggggaaccggacccccccaagttcacagtcaaccagatccttctcctgcaaaagttaaagcaaagtggtctcaccaagtcgcagattataaaaggacttgatgagatggaaagattcgatgatgtgggactcgggagcccaggagcaagcgtatcatcatccactcagcaagtaccgaacggcaattcccctagcagtgtagggtcgactaacagtggcaatacagtgacatcatgtgctaacgctggagcacgacgcaacagcacaagtcctcagtcgccccatttaccacaggtaaagacgaatacagtgattcctcatccccagcctatccccaaccatttgatgtttggagctcatatgcagaatgcaagccagctctcgcttataccgcctgttgctgcgtggccaaatacgtcacaagccgttgccgtagcaacagcagccagtatcctgcaaaacggttttgctcacgggaatgtccctcattctgtgtatccgagccttatcaacggcagaggacttcttcaaagaggacccgcgatgtcgggaacagggagcacagtcgtagaagtggatggtgagaagattgacatcacagaggagcttgaagatctcttccgacgggatcaagcttccgttaaagaggacatccgaaaatttatcagcgaacgtcacatttcccaatccgcaatcgcaaaagcgacaagaaatgctatcagccaaagctacatctcacaatggttagcccaaccccaagatatcagcgggcagaagaagaaagccatgtacacttggtacatcgtggaacgtagaaaaccaccaggccttactaacggcatgagctcggtcccccctgtagtgtttcgtcacaacgagattgagaatgattgcataagccctatgatgatgaagtcgaaacgaggagcaaggttcacctggccaaaggaatgcctgtcaatacttgagaattattacaacgcaaactcctatcctgatgaatgtaaacgtgaggagatagcacatgcttgcaatgcgatcatacaaagtcaaaaaccaggcagcatgcttacagaactggacaaagtgaccactgttaaagtttataattggtttgcaaaccgacgcaaagacgataaacgtcgtcgtcacatagaacacgtggaggcaatggaccaacaccatctcattatgagccctcgtcgtaactcggccacttcaccttccccatcttgtcattcaaacgacagctcacaaggggttgaaagcaacgaacgctgcatggtgatacccaagaaagaaaatcctatgcagctagcacttgaaatggcggctgttaaccattcaatcatggcgctcgtcaacccgcatcaggtcgacgatccgatgcgagaagacgaggaagacgaccttggagaatcttcctcggaggaaatccaacgaccagaggagcgtagaccgtttgaacgcttaccggacaaccgaagctacgccggctgagtctttccaaactccccgtttaattccgatctcttgcgccaccgatggagcatgcttcgccttgcccgccgtcgagctgtccccccctccttgccttcagcgctatttatgttcagtattccaatattattgcgaaatacgaacctttaaagtcgtcttacgactcgttccacgccttagtttctcgccctgccttgcgcggcgtcggtcgctttttttcgtcccctatcggtgctaggggtgtctgttttccttattgcgctctaaccaacgtaaactgtgccattctacatgtccgctataaaacagtatacaacacaacctaaatgcaggtaattttccaacttaagcaaacgataacatttcctatagtaaccggttccaaatacccggccatctccaccatataaagtattcctttacctttttcacccccaaagcaaagggttcgttccttctctatatagtactgactcgcccgagcttgttcgttttattctttctttcttttaccttatacgcgtcgcggacgagcgttttttcaaataccccccagcagtgttagcttattgttctgtcctctttgcacgtccgtatttcccgttttccgaggcccgctaacgcagtaatgttgcccacacacatataaacggcttcgaatactccattttcgtctaacgatttataacaatttctccatataaaactacccaaagctagactgcaacgtaacagcacccagacagcccaatagcagtgctacccacaacatatctgtattctccactgttaaaaaagaccccagcgcttgacttttcacgaggcttctccgccactgccaagtgcttttttggtattctgactgctcccgctgggtcacgaacccggaactcctgttcctgcaaaccagtttcacgttcagtattgtgtccgccttttttatcgcacttacagaacttaaatttcggcaataacgtgtgtaaatattgttcctatccttatacacgctgtggactttgcagcgctggcgttttattttattttattctatcctatacattatcccataggcgccaaacctggggtttcaggctaggcaggcctgccgtgaaattttttcctctaaattaatcagtaaacattaaaacaaaaatcgttttgagaaattcgcatccagcaatttctgccttccctgcagtttcaaaactttggcgcctatacattatctatatattcaatatatgtatttaaatttttgtcgctgatgccctccttaacggtttggtgctgaagtcacgtgcatgctgtaccattgtgacgtcgatacatgtgacgtgtttctttttacaatcaagcccgaatgatgtaaattaaataaacggcattaccgttgtaa
//

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]