RetrogeneDB ID: retro_obra_14

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 1:33800826..33801435(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB01G55000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB03G45940
• Aliases: None
• Description: None

Sequence

>retro_obra_14
ATGGCCTCTCTGGTGTTGAAGGATCTGAACAAGCGCTTCCTGGGCCTCTCCTGCTCCTCCGCCGCCTCCCCCCCCCCCCC
CCCCCCCGCCCGCCACTCGCCGCCGCACCTCCGAGACCCAGCTCGCACGCCAAGCAAGAAGCCGAAGAAGAGCAAGCAGC
AGCTAGTTAGCCCCGCAAGCTCCTCCAGGTTCCTCCTCAACTCTTCGCGGATGCAACCCGCGGATGATAGTATAATCATC
CGTAACGACCGCGAGTTGGAGTTGGCGCCGCCAGTTACTGCTGCGGCGGAAGAGGAGAAAGAGATAGCAGCAGCCGGAGC
CGGAGACGGGAGAGAGACGTCGCAGCCGCAGGTGCAGGTGGTGGTGCTGCGGGTGTCCCTGCACTGCAAGGGGTGCGCCG
GCAAGGTGAAGAAGCACATCTCCAGGATGGAGGGCGTCACCTCCCTGGACATCGACATCGCCACCAAGAAGGTCACGGTG
GTCGGAGACGTCACGCCGCTAGCCGTGCTCAGCACCGTCTCCAAGATCAAGCCCGCCCAGTTCTGGCCCACGACGCCCAC
CCTATCATCGCCATCGCCTGCGCCGCCCCGCGCCTCCGCCTCCTTCTGA

Alignment

ORF - retro_obra_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 53. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIQEVEASAAPAVDAKVVGEVQAGDVKNT-QTQEQVVVLKVSLHCKACAGKVKKHLSKMEGVTSFNIDFA
          E........A.A...K......AGD...T.Q.Q.QVVVL.VSLHCK.CAGKVKKH.S.MEGVTS..ID.A
Retrocopy ELELAPPVTAAAEEEKEIAAAGAGDGRETSQPQVQVVVLRVSLHCKGCAGKVKKHISRMEGVTSLDIDIA

Parental  AKKVTVVGDVTPLGVLNSVSKVKNAQFWAATTPAMAA
          .KKVTVVGDVTPL.VL..VSK.K.AQFW..TTP....
Retrocopy TKKVTVVGDVTPLAVLSTVSKIKPAQFW-PTTPTLSS

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_14 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	OB03G45940	1 retrocopy	retro_obra_14 ,