RetrogeneDB ID: retro_obra_28

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 2:26987180..26988323(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB02G45430
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB03G12440
• Aliases: None
• Description: None

Sequence

>retro_obra_28
ATGAACTGCTTCTCGTGGAACCCCCGGCTGTCGTGGGCGTGCTCGCAACGCAACAAGGATGGTGGCAGCCCGTGCAGCCC
GTCCAGCTATGCGGCGGAAAGCTCCATGGGCATGCGCCGCCGGTCGGAGCAGCAGGCGGCGGGCGGCACCACCCGCAAGT
TCACGCTGGCGCAGCTGTGGGCGGCGACGGACGGCTTCCACGAGTCCAACCTGGTGGGCGAGGGCGGCTTCGGCAGGGTG
TACAGGGGGCGGCTCCTGCTGGACGGGCTCGGGGTCGGCCCCGGCCCCGTAGCCGTGAAGCAGCTCTGCCGCGGCGGCGC
GCAGGGAACCCCCGAGTTCCTGGTGGAATGCATGATGCTCATGATGCTCCACCACCCCAACCTCGTCTCCCTCGTCGGCT
ACTGCTCCGAATCCACCGGCGAGCGCCTGCTCGTCTACGAGTTCCTGCCCCGCGGCAGCCTGGACGCGCACCTCTTCCCC
GGCGGCAGGAGGCACGACCCGCTGTGCTGGGACGCGCGCGTCAGGATCGCCCTCGGCGCTGCCAGGGGGCTGCGCTACCT
GCACGAGGTTGTCACGCCGCCGGTGATCTACCGCGACCTCAAGTCATCCAACATTCTCCTCGCCGACGACCTCACCCCCA
AGCTGTCCGACTTTGGCCTCGCCAAGCTTGGCCCCGTCGGCGACGACACCCACGTCTCCACGCGCGTCATGGGCACCTAC
GGCTACTGCGCGCCCGACTACGCCATGAGCGGCAAGCTCAACGTCAAGTCCGACGTCTACAGCTTTGGCGTCGTGCTCCT
CGAGCTCATCACGGGCCGCAGGGCCTTCGACGCCGCCCGCTCCCCCCCGGAGGAGCAGCGCCTCCTCGTCTGGGCACGGC
CCTACCTCGCCGGCGACCGCAAGAGGTGCTTCGCCCTGGCCGACCCGCTGCTGCAGGGCCGCTACCCCCGTCGCGCCTTC
TACCAGCTCGCCGTCGTCACCTCGCTCTGCCTCCGTGACAACCCCAACCTCCGCCCCTCCATGACAGACGTCACCCAAGC
CCTCGAGCACGTCGCCTCCCAGCCATGGCAACATCATCATAACCAACGACCCACGCCCGATGTCCTCCGCTCCACCTCCT
CTTCCTCGCCTCATGCTTCCTAG

Alignment

ORF - retro_obra_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.31 %
• Parental protein coverage: 67.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAVKQLTQDGVQGRNEFLVEVLMLTVLNHPHLVSLVGFCAQGD-ERLLVYEYMPFGSLESHLFDVPVGKQ
          VAVKQL...G.QG..EFLVE..ML..L.HP.LVSLVG.C.....ERLLVYE..P.GSL..HLF.......
Retrocopy VAVKQLCRGGAQGTPEFLVECMMLMMLHHPNLVSLVGYCSESTGERLLVYEFLPRGSLDAHLFPGGRRHD

Parental  PLDWNTRMRIAVGVAEGLSYLHNVADPPIIYRDMKAANILLDEDYKPKLSDFGLAKVGPVGDRTHVSTRV
          PL.W..R.RIA.G.A.GL.YLH.V..PP.IYRD.K..NILL..D..PKLSDFGLAK.GPVGD.THVSTRV
Retrocopy PLCWDARVRIALGAARGLRYLHEVVTPPVIYRDLKSSNILLADDLTPKLSDFGLAKLGPVGDDTHVSTRV

Parental  MGTYGYCAPDYVLSGKLTMKSDIYSFGVLLLELITGRRIYDASR-PKPEQSLLTWSRPFL-HDKRKFHRL
          MGTYGYCAPDY..SGKL..KSD.YSFGV.LLELITGRR..DA.R.P..EQ.LL.W.RP.L..D......L
Retrocopy MGTYGYCAPDYAMSGKLNVKSDVYSFGVVLLELITGRRAFDAARSPPEEQRLLVWARPYLAGDRKRCFAL

Parental  ADPALQGCYPTSALNQLVVISIMCLQDQPHVRPIISDVVIGLNHVASQPY
          ADP.LQG.YP..A..QL.V....CL.D.P..RP...DV...L.HVASQP.
Retrocopy ADPLLQGRYPRRAFYQLAVVTSLCLRDNPNLRPSMTDVTQALEHVASQPW

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_28 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB03G12440	1 retrocopy	retro_obra_28 ,