RetrogeneDB ID: retro_bdis_40

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:37309706..37310729(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G34920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G28240
• Aliases: None
• Description: None

Sequence

>retro_bdis_40
ATGGGAGAAGCTGCAGCCGATGTGGCCGCGTCGTACGAAGGGTTCTTCGGCGTGGGAGAGTGCAAGGGGCAGGTGGTGAT
CGACGGCGAGCAGGTGCCGTTGGTCCTGACTCCGGCCCAGGCCCAGGCCCAGGACCAAGGCGTCGACCACTCGGCCCTGG
TAGCGGCCCTGAAGGCCCAGCGCGGGTGGGTGGAGGAGAAGGTGATTGCCAACAGCGGCGTGCTCCTGCGCGGGTTCGGC
GTGCGCGACGCGGCGGAGTTCGACGCCGTCGTGGACGCGCTGGGCTGGGCCGACATCCGCTACGTGGGCCCGGCTCCCCG
CACCCACGTCCACGGCCGGATCTGGACCGCCAACGAGGGCCCACTGGAGGAGTTCATCTACTACCACCACGAGATGGTCC
TCATCAAGGAGTTCCCAGGGTTCGTCATCCTCTTCTGCGAGACCCCGCCGCCGGAGGGCGGGGAGACCCCCTTTGTGCCC
AGCTTCCGCGTCACGGAGCGCGCGCTCCAGGAGTTCCCGGACATGGTGGAGCAGCTGGATTCCAAGGGCCTGCGGTACAC
GTTCACGGCGCTGAGCAAGGACGACACCAAGTCGATGCGGGGACGCGGGTGGGAGGACGCCTTCGCCACCACCGACAAGG
CCGTCGCCGAGCAGCGGGCGAGGGCGCTGGGGATGGACGTGGAGTGGCTCCCCGAGAATGGAGGCGTCAGGACGATCCTC
GGGCCGAGGAAGCTCACCAGGGTTTTCCCCGGGAGGAAGGGCCGGAGGATGTGGTTCAACACCGTGGTCGGGATGCACGG
CAAGGAGCTCAGCTCGGCGGCGTTCGCCGACGGGTCGGAGATCCCGGCGGACTTCGTGAAGCGGTGCGGGGAGATCATCG
AGGAGGAGAGCATCCAGTTCCGGTGGGAGAAGGGCGACGTGCTCATCCTCGACAACCTCGCCACGCTCCACGGCCGCCGG
CCCTCGCTGCCGCCCCGGAGGGTCCTCGTCGCCACCTGCAAGGTCACTACCCCGCTCGATTGA

Alignment

ORF - retro_bdis_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.64 %
• Parental protein coverage: 75.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSSYEALVAALEAEREWLEAKVVANSAVLLRGFDVRDAVEFDAVVEALGWADIRYVGPAPRTHVHGRVWT
          G....ALVAAL.A.R.W.E.KV.ANS.VLLRGF.VRDA.EFDAVV.ALGWADIRYVGPAPRTHVHGR.WT
Retrocopy GVDHSALVAALKAQRGWVEEKVIANSGVLLRGFGVRDAAEFDAVVDALGWADIRYVGPAPRTHVHGRIWT

Parental  ANEGPLEQSVYFHHEMVLIKDFPGKVILFCEVPPPEGGETPFVPSFRVTERILEEFPEMVEELDAKGLRY
          ANEGPLE...Y.HHEMVLIK.FPG.VILFCE.PPPEGGETPFVPSFRVTER.L.EFP.MVE.LD.KGLRY
Retrocopy ANEGPLEEFIYYHHEMVLIKEFPGFVILFCETPPPEGGETPFVPSFRVTERALQEFPDMVEQLDSKGLRY

Parental  TFVAPSNNDTKSMRGRGWEDAFATSDKAEAEKRAKALGMDVEWLPD-GGAKTILGPRTLTRVFPGRKGRR
          TF.A.S..DTKSMRGRGWEDAFAT.DKA.AE.RA.ALGMDVEWLP..GG..TILGPR.LTRVFPGRKGRR
Retrocopy TFTALSKDDTKSMRGRGWEDAFATTDKAVAEQRARALGMDVEWLPENGGVRTILGPRKLTRVFPGRKGRR

Parental  MWFNTLVGMHGKELSSAIVADGAEIPASFVRRCEETIEEESIQFRWRKGDILILDNLATLHGRRPSLPPR
          MWFNT.VGMHGKELSSA..ADG.EIPA.FV.RC.E.IEEESIQFRW.KGD.LILDNLATLHGRRPSLPPR
Retrocopy MWFNTVVGMHGKELSSAAFADGSEIPADFVKRCGEIIEEESIQFRWEKGDVLILDNLATLHGRRPSLPPR

Parental  RVLVATCK
          RVLVATCK
Retrocopy RVLVATCK

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_40 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G28240	1 retrocopy	retro_bdis_40 ,