RetrogeneDB ID: retro_bdis_23

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:2701230..2702502(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G03807
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G49781
• Aliases: None
• Description: None

Sequence

>retro_bdis_23
ATGGGCAATCAACAAGATGATCGTCATCGTCTTCTTCTTCTCCATAGATGGCTGCTAATTACACTGGTAGTAGTAACAGC
ATTGCATATGCATACGGCGGAGGCGGCGCCGGCGCCGGAGAAGAAGAAGCAGCAGAAGCAGATGGTGCCGTGCATGTACA
TCTTCGGCGACTCGCTGGTGGACAACGGCAACAACAACAACATCCTCAGCCTGGCCAGGGCCAACTACCGCCCCTACGGC
GTCGACTTCCCTTCCTCCGCCGCTTCCCCGCCGGGCCGCTTCACCAACGGCCGCACCGTGGTGGACATCCTCGCGGGCCT
CCTGGGCTTCCAGCCGCCCTTCATCCCGGCCCACGCCATGGCGGCCCAGGACGAGTACGCGCGCGGGCTCAACTTCGCCT
CGGGCGCCGCGGGCGTCCGGCCGGAGACCGGCAACAACCTCGGCGGACATTACCCGCTGGCCGACCAGGTGGAGCACTTC
CGGGCCGTGGCCGACCAGCTGACTTCGTCATCCTCGCCGGAGGGGAAGAAGAAGATGACGAACCAGTTGGGGAAGTGCAT
CTACTATGTTGGCATGGGCAGCAACGACTACCTCAACAACTACTTCATGCCGGACTACTACAGCACGGCCCGGGACTACG
ACCCGGCCGCCTACGCCGCGGCGTTGCTGCAGGAATATTCCCGACAGATCAACGTGTTGTACGACCTCGGCGCACGGAAG
ATCGTCGTCGCCGGCGTCGGCCAGATCGGGTGCATCCCCTACGAGCTCGCCAGGATCAACGACGGCTCACCTCCTCCTAA
TACCGTCGGCAATGGCGCCGGCATCGGCATTGCCGTTCCTGGCATCACCATCTCCCTCGGCGGTGCCAATCGCCGCAGAA
GCAACAACAATGTCTGCAACGAGGAGATCAACAACGCGATCGCCATCTACAACAAGGGGTTACTCTCCATGGTGAAGCGG
CTGAACCGGCAACTGCCTGGTGCCAAGCTCGTCTTCCTCGACGCCGTGAGCGGCGGGAGGGACCTTGTGGTGAACGCCGG
GAAGTACGGGTTCACGGTGGTGGACAAAGGGTGTTGCGGCGTGGGGCGGAACAACGGGCAGATCACGTGCCTTCCCATGC
AGCGGCCCTGCGAGGACCGGAGCCAGTACATCTTCTGGGACGCGTTCCACCCGACAGAGGCCGCCAACAGGATCATTGCT
GCTAGGGCATTTGGATCAGCCCCCGGCAACGACGCGTACCCCTTCAACATCAGCCGCCTCGCCACCTTATGA

Alignment

ORF - retro_bdis_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.99 %
• Parental protein coverage: 71.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPCYFVFGDSLVDNGNNNDIASLARANYPPYGIDFPGGAT---GRFSNGLTTVDAISRLLGFDD-YIPAY
          VPC...FGDSLVDNGNNN.I.SLARANY.PYG.DFP..A....GRF.NG.T.VD....LLGF....IPA.
Retrocopy VPCMYIFGDSLVDNGNNNNILSLARANYRPYGVDFPSSAASPPGRFTNGRTVVDILAGLLGFQPPFIPAH

Parental  AGANNDQLLTGVNFASAAAGIRDETGQQLGQRISFGGQLQNYQAAVQQLVSILGDEDSA--ANHLSQCIF
          A.A..D....G.NFAS.AAG.R.ETG..LG.......Q.....A...QL.S....E......N.L..CI.
Retrocopy AMAAQDEYARGLNFASGAAGVRPETGNNLGGHYPLADQVEHFRAVADQLTSSSSPEGKKKMTNQLGKCIY

Parental  TVGMGSNDYLNNYFMPAVYSSSRQYTPEQYADVLINQYSQQLTTLYNNGARKVALMGVGQVGCSPNELAQ
          .VGMGSNDYLNNYFMP..YS..R.Y.P..YA..L...YS.Q...LY..GARK....GVGQ.GC.P.ELA.
Retrocopy YVGMGSNDYLNNYFMPDYYSTARDYDPAAYAAALLQEYSRQINVLYDLGARKIVVAGVGQIGCIPYELAR

Parental  QSD
          ..D
Retrocopy IND

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_23 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	BRADI2G49781	1 retrocopy	retro_bdis_23 ,
Brachypodium distachyon	BRADI3G28100	1 retrocopy	retro_bdis_35,