GGRNA ver.2 Home | Help | Advanced search    Previous release (v1)

2024-03-29 21:30:08, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       XM_009860412            1392 bp    mRNA    linear   INV 22-OCT-2018
DEFINITION  PREDICTED: Ciona intestinalis homeobox protein Hox-A2 (LOC778789),
            mRNA.
ACCESSION   XM_009860412
VERSION     XM_009860412.3
DBLINK      BioProject: PRJNA187185
KEYWORDS    RefSeq; includes ab initio.
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_020170.2) annotated using gene prediction method: Gnomon,
            supported by mRNA and EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Oct 22, 2018 this sequence version replaced XM_009860412.2.
            
            ##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##
            
            ##RefSeq-Attributes-START##
            ab initio :: 22% of CDS bases
            ##RefSeq-Attributes-END##
FEATURES             Location/Qualifiers
     source          1..1392
                     /organism="Ciona intestinalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:7719"
                     /chromosome="5"
     gene            1..1392
                     /gene="LOC778789"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Gnomon. Supporting evidence
                     includes similarity to: 2 mRNAs, 2 ESTs, 2 Proteins, and
                     78% coverage of the annotated genomic feature by RNAseq
                     alignments, including 40 samples with support for all
                     annotated introns"
                     /db_xref="GeneID:778789"
     CDS             52..1392
                     /gene="LOC778789"
                     /codon_start=1
                     /product="homeobox protein Hox-A2"
                     /protein_id="XP_009858714.1"
                     /db_xref="GeneID:778789"
                     /translation="
MNMFLSNPFLQMCYPSAISGQIKPETQVPPGFIKNNQTSPPYSLPYLFHSSSTESDKMSSSATECFSPVFTRRSTDTSYKTEMTSDASLSHQLPSDLWARNSFLSQCILQNSKEANSTDFYDDDSAENQQNKRRRTRTNFSTWQLEELEKAFGNSHYPDVYMREALALRLDLVESRVQVWFQNRRAKWRKREHTKKGPGRPPHNAQLTLCSGEPMDPSEIERREKMKQERKKRKQDCNCKSSLNEKQGRKTSNNQDSISPHNDSCKDRNIIQKTCCDSLNAKNNILLPWLVNQPPQSINHELKISENETLGSPLSIENDNQMTDGRKEMSDANPMTPGSRNSHSIENILYKNKIAKPQFFNHVPGTSGTLTSPSSSFGNLPMQSSPLFAEFIRRSSIFSLFPNIPKELQESTAADLNNYTRLYQQYQLQLRVFSDSFSNALNKGKQ"
     misc_feature    order(451..465,469..471,520..522,538..540,577..579,
                     583..588,595..600,604..612,616..621)
                     /gene="LOC778789"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    457..618
                     /gene="LOC778789"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(457..459,466..468,586..588,595..600,607..609)
                     /gene="LOC778789"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
ORIGIN      
taattttttcatatttttcctatagggcttttctattttgcgacttgaaatatgaatatgtttttaagcaacccgtttcttcaaatgtgctatccgtccgcaatatcgggacagataaaaccagagacacaagttccaccaggattcatcaaaaacaaccaaacatcacctccatattctctgccgtatttattccactcttcatcgacggaaagcgacaaaatgtcgtcatcagccaccgagtgtttttctcctgtatttactcggcgatctacggatacttcgtacaaaacggaaatgacgtcagatgcaagtttgtcgcatcagttacctagtgatttatgggcacgaaactcatttttatcccaatgtattctgcaaaactcgaaagaagcaaacagcacggatttttacgacgatgattcggcagaaaaccaacaaaataaacgacgacgtacaagaacaaacttcagcacttggcagttagaagagttggaaaaagctttcggaaattctcactatccagatgtatacatgcgagaggcactggcacttcgtcttgatctagtggagtcacgtgtccaggtttggttccaaaaccgacgagcaaaatggaggaagcgtgaacacacgaagaaagggccgggtcgtcctccacataatgctcaactcacgttatgttcaggtgagccgatggacccaagtgaaatcgagcgacgagaaaaaatgaaacaagaaagaaaaaagcgaaaacaagattgcaattgtaaaagcagcttgaatgagaagcaaggcagaaaaacatcaaataaccaagattcgatctcacctcacaacgattcatgtaaagatagaaatattattcaaaaaacatgttgcgactcactgaatgcaaaaaacaacattttgcttccgtggttggtaaatcaacctccacaaagtatcaatcatgagttgaagatcagtgagaatgaaaccttaggttcgcccctttcaatcgaaaacgataatcagatgaccgacggacgtaaagaaatgtctgatgcaaatcccatgacgcctggttcacgaaattcccactcaattgaaaatattctttacaaaaacaaaatcgcaaaacctcaattctttaaccacgtgccaggtacgagtggtacccttacgtcaccaagtagcagtttcgggaatttacccatgcaaagttcccctttgttcgctgagtttatacggagaagcagcatattctcactcttcccaaacatcccgaaagagcttcaggaaagcacagctgcagatttaaacaactatacgcgactctaccagcaataccaattacaattacgtgtattctctgactcgttttccaacgcgcttaacaaaggcaagcaatga
//

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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]