RetrogeneDB ID: retro_bdis_29

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:74573342..74574215(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G78697
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G02680
• Aliases: None
• Description: None

Sequence

>retro_bdis_29
ATGGAGCTTGGCAGGATCAAGATGAAGCGGTTCGCGGACGGGGAGCTGTACGTGCAGCTGCAGGAGAGCGTCCGGGGGTG
CGACGTGTTCCTGGTGCAGCCGACGTGCCCTCCCGCCAACGAGAACCTGATGGAGCTCCTCATCATGATCGACGCCTGCC
GCCGCGCCTCCGCCAAGACCATCACCGCCGTCATCCCCTACTTTGGCTACGCCAGGGCCGACCGCAAGATGCAGGGCCGC
GAGTCCATCGCCGCCAAGCTCGTCGCCAACCTAATCACCCACGCCGGCGCCCACCGCGTGCTCGCCTGCGACCTCCACTC
GGGCCAGTCCATCGGCTACTTCGACATCCCCGTCGACCACGTCTATGGCCAGCCCGTCATTCTCGACTACCTGGCCAGCA
AGACCATCTGCCCCAACGACGTCGTCGTCGTCTCGCCCGACGTGGGGGGAGTCGCCAGGGCGCGCGCCTTCGCCAAGAAG
CTGTCCGACGCGCCGCTGGCCATCGTCGACAAAAGGCGGCTGGGCCACAACCAGGCGGAGGTGATGAATCTCATCGGCGA
CGTCAAGGGGAAAGTGGCCGTGATGGTGGACGACATGATCGACACGGCGGGGACCATGGCCAAGGGGGCAGAGCTGCTGC
ACAGGGAAGGGGCCAGAGCCGTGTACGCCTGCAGCACCCACGCCGTGCTCAGCCCTCCCGCTGTCGAGAGGCTCTCCGGT
GGCCTCTTCCAGGAGGTGATCATCACCAACACCGTCCCAGTGCCGGAACACCAACGCTTCCCGCAGCTCACCGTCCTCTC
CGTCGCCAACCTCCTCGGCGAAACCATATGGCGTGTGCACGACGATTCCTCTGTCAGCAGCATCTTCCAATGA

Alignment

ORF - retro_bdis_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 71.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LELGKINIKRFADGEIYVQLQESVRGCDVFLVQPSCPPANENLMELLIMIDACRRASAKNITAVIPYFGY
          .ELG.I..KRFADGE.YVQLQESVRGCDVFLVQP.CPPANENLMELLIMIDACRRASAK.ITAVIPYFGY
Retrocopy MELGRIKMKRFADGELYVQLQESVRGCDVFLVQPTCPPANENLMELLIMIDACRRASAKTITAVIPYFGY

Parental  ARSDRKSQGRESIAAKLVANMITEAGANRVLVSDLHSSQAMGYFDIPVDHVYGQPVILDYLASKTICSND
          AR.DRK.QGRESIAAKLVAN.IT.AGA.RVL..DLHS.Q..GYFDIPVDHVYGQPVILDYLASKTIC.ND
Retrocopy ARADRKMQGRESIAAKLVANLITHAGAHRVLACDLHSGQSIGYFDIPVDHVYGQPVILDYLASKTICPND

Parental  LVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRHGHNVAEVMNLIGDVKGKVAVMMDDMIDTAGTIAKGA
          .VVVSPDVGGVARARAFAKKLSDAPLAIVDKRR.GHN.AEVMNLIGDVKGKVAVM.DDMIDTAGT.AKGA
Retrocopy VVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRLGHNQAEVMNLIGDVKGKVAVMVDDMIDTAGTMAKGA

Parental  ELLHQEGAREVYACCTHAVFSPPAIERLSSGLFQEVITTNTIPLKEDKNFPQLTILSVANLLGETIWRVH
          ELLH.EGAR.VYAC.THAV.SPPA.ERLS.GLFQEVI.TNT.P..E...FPQLT.LSVANLLGETIWRVH
Retrocopy ELLHREGARAVYACSTHAVLSPPAVERLSGGLFQEVIITNTVPVPEHQRFPQLTVLSVANLLGETIWRVH

Parental  DDCSV
          DD.SV
Retrocopy DDSSV

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_29 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G02680	1 retrocopy	retro_bdis_29 ,
Leersia perrieri	LPERR02G02000	1 retrocopy	retro_lper_21,
Oryza brachyantha	OB02G12100	1 retrocopy	retro_obra_24,
Oryza barthii	OBART02G02200	1 retrocopy	retro_obar_2,
Oryza glumaepatula	OGLUM02G02060	1 retrocopy	retro_oglu_34,
Oryza punctata	OPUNC02G01640	1 retrocopy	retro_opun_20,
Oryza sativa japonica	OS02G0127700	1 retrocopy	retro_osat_35,
Triticum aestivum	Traes_6AS_88F0CBEC0	1 retrocopy	retro_taes_35,