RetrogeneDB ID: retro_obra_16

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 9:10875445..10876450(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB09G21570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB02G15500
• Aliases: None
• Description: None

Sequence

>retro_obra_16
ATGTTTTCCCGAATTCTCGAGGGCTTCGGATACAATGGAGAGAAAAGGTTCGAGCAGACGTACCGCTGCTGCTCGCCAGC
GACCATTAACAAGCCGCACCTGGAAAGCGGGGACAAGGTGATCATGCCGGCGTCGGCGCTGCACCGCCTCACCTCCCTCG
ACGTCGAGTTCCCGATGCTGTTCGAGCTCTCGCGCCACAGCAGCTACGCCGCCGCTGCCGCCGGCGCCGCTCGCCGGGTC
TCCCACTGCGGCGTGCTGGAGTTCGTGGCGGAGGACGGCGTGGTGGTCATCCCGGGGTGGATGATGCGCAACATGGGCGT
CAGGGAGGGCGACCTCGTCGGCGTCAAGAGCGTCAGCCTCCCCAAGGGCACCTACGTGAAGCTGCAGCCTCACACCGGCG
ACTTCCTCGACACGGCCAACCCCAAGGCCGTCCTGGAGAAGACGCTGAGGAACTTCACCTGCCTGACCACCGGCGACACT
ATCATGGTGGCTTACAACAACAACGAGTATCACATCGACATCGTGGAGACGAAGCCGGCACCAGCTGTTTGCATCATCGA
CACGGATTGTGAGGTGGATTTTGCACCTCCTCTCGATTACAGAGAACCTGAAAAAGTTGAGCGGCAGGAACCATCAGTTC
CTGCAAGCAAGGTGACTTCTGAAGCTAAAGATGATGCTGTCAAAGATGAACCAAAATTCAGAGCATTCCCTGGCTTAGGG
AATCGGTTGGATGGCAAGGCCTTAAAACCACAAGCAGCAAAAATCCCTCCTCCTGCTGCTGCAAGTTCAGGCTCAAACAA
GAAGGTGAATCAGCAGACAGTGGCTCCTGCATCTTCAGGAGCTAGCAACTCCACTACACGTCAGAAAAAAGGGAAGGTTG
TTTTCGGTTCGAACACAAGCAGTAGCAAACAACCAGAAAAGGCTCCTGATCGAGCTGATCAACCTCCAAAGAAGGAGAAG
CCCAAGTTCCAAGCATTTTCTGGGAAAAGCTACTCATTGAAATGA

Alignment

ORF - retro_obra_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAERTSHCGVLEFIAEEGMIYMPYWMMQNLLLQEGDMVFIKNANLPKGTYVKLQPHTTDFLDISNPKAIL
          AA.R.SHCGVLEF.AE.G....P.WMM.N....EGD.V..K...LPKGTYVKLQPHT.DFLD..NPKA.L
Retrocopy AARRVSHCGVLEFVAEDGVVVIPGWMMRNMGVREGDLVGVKSVSLPKGTYVKLQPHTGDFLDTANPKAVL

Parental  EKTLRNYSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIETDCEVDFAPPLDYKEPEPPIAAVP--PS
          EKTLRN..CLTTGD.IMVAYNN..Y.IDIVETKP..A..II.TDCEVDFAPPLDY.EPE......P..P.
Retrocopy EKTLRNFTCLTTGDTIMVAYNNNEYHIDIVETKPAPAVCIIDTDCEVDFAPPLDYREPEKVERQEPSVPA

Parental  AAPTAE---EAAEEEPKFIPFTGSGRRLDGKASKDKDVSASSPAKRQANSTNGVQPST----ASTSQGSS
          ...T.E....A...EPKF..F.G.G.RLDGKA.K........PA.....S...V...T.....S....S.
Retrocopy SKVTSEAKDDAVKDEPKFRAFPGLGNRLDGKALKPQAAKIPPPAAASSGSNKKVNQQTVAPASSGASNST

Parental  SRKTSGKLVFGPGGNRPSKEADKVPEKEPKEDPKKDEPKFSAFTGRKYSLK
          .R...GK.VFG......SK...K.P.......PKK..PKF.AF.G..YSLK
Retrocopy TRQKKGKVVFG-SNTSSSKQPEKAPDR-ADQPPKKEKPKFQAFSGKSYSLK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza brachyantha was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_16 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB02G15500	1 retrocopy	retro_obra_16 ,
Prunus persica	PRUPE_ppa008670mg	1 retrocopy	retro_pper_9,