RetrogeneDB ID: retro_bdis_48

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:48590943..48591701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G10302
• Aliases: None
• Description: None

Sequence

>retro_bdis_48
GGACACTGGGAGGTGGAGGCCCTCAACCTCGGTACCGGGAAGGAAGAGAAGCACGCGGCGAGGTTCCTGGTGGTGGCGGC
GGGGGAGTTCGACGAGAAGGCGATCCCGGCGGTGCCAGGGCTCGACACTTTCCCCGGGAAAGCCATCCACTCTAGCGAGT
ACCGCTCCGCGAAGGGGCTGGAAGGGAAAGCCGTGCTGGTGGTCGGGTGCGGCAACTCGGGGATGGAGATCGCGCTGGAC
CTGGCCGAGTCCGGCGCCGCCGCGTCCGTCGTGGTCCGCGGCGAGGCGCACCTGCTGACGCGGCGCATCATGAGCCTCTC
CACCTCCCTCTTCGCCTACCTCCCGCTCTGGGCCATCGACAACCTCGCGCTCTTCATGTGCTACCTCGCCTTCCGCGGCG
ACACGGCCAAGCACGGCGTCCCCCGGCCCGCGCTCGGCCCCTTCGCCAGGAAGCTCCAGAAGAACGCGTACCCGGTCATC
GACGTCGGCACCTACGCAAGATCAAAACCGGCCAGATCCGGGTCCTCCCTGCCAGGGAGAGGATAGAGGGTAACATGGTC
GAGTTCGCCGACGGCAAGCGGCACCCGTTCGATGTCATCGTCTTCGCCACCGGCTACCGCAGCGGCGTCAACAAGTGGCT
CCGGGGCGAGCCGGGCGGCGGGCTGATCGGGGAAGACGGGATGGCGAAGGGAAGGAGCCCCAAGGGGGAGAATGGGCTGT
ACCGGGCCGGGCTCGCCCGGAGAGGGATCTATGGCAGC

Alignment

ORF - retro_bdis_48 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.08 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLWAVDAVDAATGKSERYVARRLVAAAGENDRMVLPEGLPGMETFPGTVMHAGEYRNGKGFEGKRVLVVG
          G.W.V.A....TGK.E...AR.LV.AAGE.D....P...PG..TFPG...H..EYR..KG.EGK.VLVVG
Retrocopy GHWEVEALNLGTGKEEKHAARFLVVAAGEFDEKAIP-AVPGLDTFPGKAIHSSEYRSAKGLEGKAVLVVG

Parental  SGNSGMEIAYDLAVAGAAASVVVRSELHLVTKEIWNVAMTLYRYLPVWLIDRIVLLLCAVVL-GDTSRYG
          .GNSGMEIA.DLA..GAAASVVVR.E.HL.T..I......L..YLP.W.ID...L..C.....GDT...G
Retrocopy CGNSGMEIALDLAESGAAASVVVRGEAHLLTRRIMSLSTSLFAYLPLWAIDNLALFMCYLAFRGDTAKHG

Parental  LRRPAIGPFSMKLQTPAYPVVDVGTYA-KIKTGEIQVLPAMKSVDRDVVEFADGKRHPFDAIVFATGYRS
          ..RPA.GPF..KLQ..AYPV.DVGTYA.KIKTG.I.VLPA........VEFADGKRHPFD.IVFATGYRS
Retrocopy VPRPALGPFARKLQKNAYPVIDVGTYA<KIKTGQIRVLPARERIEGNMVEFADGKRHPFDVIVFATGYRS

Parental  TTKQWLKDD---GLIGEDGMAKRSYPGHWKGENGLYCAGMVRRGIYGS
          ....WL......GLIGEDGMAK...P...KGENGLY.AG..RRGIYGS
Retrocopy GVNKWLRGEPGGGLIGEDGMAKGRSP---KGENGLYRAGLARRGIYGS

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_48 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	BRADI1G28967	1 retrocopy	retro_bdis_22,
Brachypodium distachyon	BRADI2G10302	1 retrocopy	retro_bdis_48 ,