RetrogeneDB ID: retro_obra_25

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 10:8919515..8920286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB10G18630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB03G14280
• Aliases: None
• Description: None

Sequence

>retro_obra_25
ATGGGTATGGCTAAGACGATCCTGGCTGTGTGCACCGTCCTCGCGGCGCGCGTGGCGGTCGGCGCCGCCGGCGGTGGCGG
CTGGACTCCGGCGACGGCGACGTTCTACGGCGGGGGCGACGGGGCCGGGACGATGGGCGGCGCGTGCGGGTACGGGAACC
TGTACGTCCAGGGGTACGGCATCGACAACGCGGCGCTGAGCTCGGAGCTGTTCGCCGACGGCGCGGCGTGCGGGCAGTGC
TACCTCATCATCTGCGACACCGGCAAGACGCCGGAGTGGTGCAAGGCCGGCCGCGCGGTCACCGTCACGGCCACCAACCT
GTGCCCGCCCAACTGGGACCTGCCCAGCGACAACGGCGGCTGGTGCAACGCGCCCCGGCACCACTTCGACATGTCGCAGC
CGTCGTGGGAGCAGATCGGCGTCTACCGCGCCGGCATCGTGCCGGTGCTCTACCAGCGCATCAAGTGCTGGCGCCGCGGC
GGCGTCCGCTTCACCGTCAGCGGCTTCAACTACTTCGAGCTCGTGCTCATCACCAACGTCGCCGGCAGCGGCTCCGTCGC
CGCCGTGTCCATCAAGGGCACCAAGACGGGCTGGCTCCGGATGTCGCGCAACTGGGGCGCCAATTGGCAGTCGCTCGCCG
GCCTCGCCGGCCAGGCGCTCAGCTTCGCCGTCACCTCCTCCGGCGGGCAGTACCTGGAGTTCAACGGCATCACGCCGGAC
GGGTGGACGTTCGGCCAGACCTTCTCCACCTACAAGCAGTTCGACTACTGA

Alignment

ORF - retro_obra_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.98 %
• Parental protein coverage: 91.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WPPGPATFYGGADGSGTMGGACGYGNLYDQGYGINNAALSTALFNGGASCGQCYLIICDSSKAPNWCRLG
          W.P..ATFYGG.DG.GTMGGACGYGNLY.QGYGI.NAALS..LF..GA.CGQCYLIICD..K.P.WC..G
Retrocopy WTPATATFYGGGDGAGTMGGACGYGNLYVQGYGIDNAALSSELFADGAACGQCYLIICDTGKTPEWCKAG

Parental  KAVTVTATNFCPPNWDLPSDKGGWCNPPRPHFDMSQPAWENIGIYQAGIVPILYQQVKCWKSGGVRFTIN
          .AVTVTATN.CPPNWDLPSD.GGWCN.PR.HFDMSQP.WE.IG.Y.AGIVP.LYQ..KCW..GGVRFT..
Retrocopy RAVTVTATNLCPPNWDLPSDNGGWCNAPRHHFDMSQPSWEQIGVYRAGIVPVLYQRIKCWRRGGVRFTVS

Parental  GFNYFELVLVTNVAGSGSVASMSVKGSSTGWIQMSRNWGANWQCLAGLAGQALSFTVTSTGGQTIVFDSV
          GFNYFELVL.TNVAGSGSVA..S.KG..TGW..MSRNWGANWQ.LAGLAGQALSF.VTS.GGQ...F...
Retrocopy GFNYFELVLITNVAGSGSVAAVSIKGTKTGWLRMSRNWGANWQSLAGLAGQALSFAVTSSGGQYLEFNGI

Parental  VPAGWSFGQTYSTYKQFDY
          .P.GW.FGQT.STYKQFDY
Retrocopy TPDGWTFGQTFSTYKQFDY

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_25 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	OB03G14280	1 retrocopy	retro_obra_25 ,