RetrogeneDB ID: retro_bdis_10

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 4:33448574..33449666(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI4G28100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G54810
• Aliases: None
• Description: None

Sequence

>retro_bdis_10
ATGTCGATGGCGCAGGTGTGCTGTGATACCGCGGTGGTTGTTGGGGCGGAGGCCGAGGCCAGGGCGCGGGCGCGCGCCGG
CAGGCGGCGCCGAGCCGCCGGGGACGCCGCCACGGGGCGGTGGAAGGTCGCGCCGGAGGTTCCGCAGGGCGCGGAAGAGG
CCGCCGCGGCCACCAGGAAGCGCCGCGCGGCCGGAGCCGAGGCGGGTGCGGCGAAGCGGCATGGGGTGGCTTCTGTCGCC
GGCCGTAGGAGGGAGATGGAGGACGCGGTCTCCGTCCGCGAGGCGTTCGCCGCCGCTCCGGCTGAGGAGGAGGAGGAGGG
GAAGGAGCCCGGAAAAGCCGGACGCGACTTCTACGGGGTGTTCGACGGGCACGGCTGCTCGCACGTGGCGGACGCGTGCC
GGGACCGGATGCACGAGCTGGTCGCCGAGGAGCTGCCCGGCGCCGGCGCCTCCCCCGATTCCTGGACCACCGCGATGGAG
CGGAGCTTCTCGAGGATGGACGCCGAGGTGATGGCTGCGGGCGGGCGCGAGCGCGACGACAGCGCGAGCTGCCGGTGCGA
GGCGCACAAGTGCGACCACGTCGGGTCAACGGCGGTCGTGGCCGTCGTGGAGGCCCGGCGCGTCGTCGTGTCCAACTGCG
GCGACTCCCGCGCCGTCCTCTGCCGCGACGGCGCCCCGGTGCCCCTCTCCTCCGACCACAAGCCCGACAGACCGGACGAG
CTGGAGCGGATCGAGTCCGCCGGCGGGCGCGTCATATTCTGGGAGGGCGCGAGGGTGCTGGGCGTGCTGGCCATGTCGCG
CGCCATCGGGGACGGGTACCTGAAGCCGTTCGTATCGGCTGTCCCGGAGGTGACGGTGACCGAGAGGCTCGACGGCGACG
AGTGCCTGATCCTGGCCAGCGACGGGCTTTGGGACGTGGTCAGCAACCAGACCGCGTGCGATGTGGCGCGAGCCTGCCTC
CGGAGGGGCAGAGACAGGTGGTGCGCCGAGGCGGCGGCCATGCTCACTAAGATGGCTCTAACCAAGGGCAGCTCCGACAA
CATCTCTGTCGTCGTCGTCGATCTACGGCCGAGGAATCCGTTGCCATTGTAG

Alignment

ORF - retro_bdis_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.3 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGSAESHFFGVFDGHGCSHVATTCQDSMHEAVADEHSKAAGSSSEEVPAWKGVMERSFARLDEKARNWAT
          PG.A...F.GVFDGHGCSHVA..C.D.MHE.VA.E....AG.S......W...MERSF.R.D........
Retrocopy PGKAGRDFYGVFDGHGCSHVADACRDRMHELVAEE-LPGAGASPD---SWTTAMERSFSRMDAEVMAAGG

Parental  NRSGEEPKCRCEQQMPSRCDHVGSTAVVAVVSPTQLVVGNAGDSRAVLSRAGVPIELSVDHKPDRPDELE
          ........CRCE......CDHVGSTAVVAVV.....VV.N.GDSRAVL.R.G.P..LS.DHKPDRPDELE
Retrocopy RERDDSASCRCEAH---KCDHVGSTAVVAVVEARRVVVSNCGDSRAVLCRDGAPVPLSSDHKPDRPDELE

Parental  RIQAAGGRVIYWDGARVLGVLAMSRAIGDGYLKPFVTAEPEVTVTERADDDECLILASDGLWDVVTNEMA
          RI..AGGRVI.W.GARVLGVLAMSRAIGDGYLKPFV.A.PEVTVTER.D.DECLILASDGLWDVV.N..A
Retrocopy RIESAGGRVIFWEGARVLGVLAMSRAIGDGYLKPFVSAVPEVTVTERLDGDECLILASDGLWDVVSNQTA

Parental  CGVVRACFR
          C.V.RAC.R
Retrocopy CDVARACLR

Legend:

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

Expression

RNA-Seq

Brachypodium distachyon was not studied using RNA-Seq expression data.

ChIP-Seq

Brachypodium distachyon was not studied using ChIP-Seq data.

EST

Brachypodium distachyon was not studied using EST data.

TSS

Brachypodium distachyon was not studied using FANTOM5 data.

Lab

retro_bdis_10 was not experimentally validated.

Homology

Retrocopy orthology:

Brachypodium distachyon 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
Brachypodium distachyon	BRADI2G54810	1 retrocopy	retro_bdis_10 ,
Triticum aestivum	TRAES3BF069100050CFD_g	1 retrocopy	retro_taes_29,