RetrogeneDB ID: retro_obra_10

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 1:8693384..8694305(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB01G22230
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB05G12230
• Aliases: None
• Description: None

Sequence

>retro_obra_10
ATGGACGCGCGGTGTGGGTGGACGGCGGCGGCGGCGGAGATGGCGGAGGAGCTGGAGGATGGTTTCCGGAGAGGGCCGTG
GGCGGCGGAGGAGGACGCGGTGCTGGCCGGGCACGTGGCGGCGCACGGGGAGGGGCGGTGGAACGAGGTGGCGCGGGCGG
CGGGGCTGAGGCGGACCGGGAAGAGCTGCCGGCTCCGGTGGCTCAACTACCTCCGCCCCGACGTGCGGCGCGGGGACTTC
ACCCCGCAGGAGCAGCTGCTCATCCTGGAGCTCCACTCCCGGTGGGGGAACCGCTGGTCCAGGATCGCGCAGCACCTGCC
CGGGAGGACGGACAACGAGATCAAGAACTACTGGCGGACCCGGGTGCAGAAGCACGCCAAGCAGCTCGGCTGCGACGTCA
ACAGCGGCCAGTTCAGGGACGTCATGAGGCACCTCTGGATGCCACGCCTCGTCGAGAGGATCCAGGCGGCCGCCGCCGCC
GCAACGGCGCTGGCCACCTCGCCGGACGAGCACGCCGCGCCGGCTGTTGCTCACGGCGACATGTGCCACTCACCCGACCC
GTCAACGACGACGATGTCGAGCACCGGCACCTCCGCGGGGTCGTCTTCAACGTCGTCGTCGATAACGTCCACGTCGGTGC
CGCGCGGCGAGCAGTTCCCGTCGTCGACGAACCAGGAGCACCTGGCCATGGCCAGCGTCACCGCCGTGGCGGCGGCGGAT
TGGTCGAGCGAGCAATACGGCAGCGCGAGCACCGGGTTCGGTGCTGATGACATGTTCGAGGGGAGCTGGTCGGAGCTCCT
CGCTCGCGCCTACGACGACGACGGCGCTGATTCTTCGCTGCTGCCGGACTTCCAAACGGCAGAAACCGGAGACAATTGGT
GGAGTTTGGAGGACGACATCTGGTCGCAGAGGCCGTACTGA

Alignment

ORF - retro_obra_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.85 %
• Parental protein coverage: 50.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAAAVASEDEGDLRRGPWTVEEDALLVDYIATHGEGRWNSLARCAGLRRTGKSCRLRWLNYLRPDVRRGN
          .AA..A.E.E...RRGPW..EEDA.L....A.HGEGRWN..AR.AGLRRTGKSCRLRWLNYLRPDVRRG.
Retrocopy AAAEMAEELEDGFRRGPWAAEEDAVLAGHVAAHGEGRWNEVARAAGLRRTGKSCRLRWLNYLRPDVRRGD

Parental  ITAEEQLLILDLHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLRCDVNSKQFRDVVRHVWMPR
          .T..EQLLIL.LHSRWGNRWS.IAQ.LPGRTDNEIKNYWRTRVQKHAKQL.CDVNS.QFRDV.RH.WMPR
Retrocopy FTPQEQLLILELHSRWGNRWSRIAQHLPGRTDNEIKNYWRTRVQKHAKQLGCDVNSGQFRDVMRHLWMPR

Parental  LVERIQAADSSAA--AESDDVPVAPPV
          LVERIQAA...A...A.S.D...AP.V
Retrocopy LVERIQAAAAAATALATSPDEHAAPAV

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_10 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB05G12230	1 retrocopy	retro_obra_10 ,
Oryza glumaepatula	OGLUM05G02350	1 retrocopy	retro_oglu_19,
Oryza nivara	ONIVA05G02220	1 retrocopy	retro_oniv_30,
Oryza punctata	OPUNC05G02190	1 retrocopy	retro_opun_37,
Oryza glaberrima	ORGLA05G0022200	1 retrocopy	retro_ogla_43,
Oryza rufipogon	ORUFI05G02420	1 retrocopy	retro_oruf_21,