RetrogeneDB ID: retro_bdis_3

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:31588165..31589530(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G31650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G14140
• Aliases: None
• Description: None

Sequence

>retro_bdis_3
ATGTCGTCGCGGGAATCGGATATCATGGAGGAGTACGCGGAGACGGTGAAGGAGCGGAGAACAGAGGAGAAGCTCAAGGA
CGTGAACCTGGACGACTGGCTCCCGATCACGTCGTCGCGCACGGCCAAGTGGTACTACTCGGCGTTCCACAACGTGACGG
CCATGGTGGGCGCCGGCGTGCTGGGCCTCCCCTTCGCCATGGCCCAGCTCGGCTGGGGCCCAGGAGTGGCCGTCATCGTC
GCCTCCTTCGTCATCACGCTCTACACGCTGTGGCAGCTGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTCGACCG
GTACCACGAGCTCGGCCAGCACGCCTTCGGCGACAAGCTGGGCCTCTGGATCATCGTCCCGCAGCAGCTCATCGTCGAGG
TCGGCACCGACATCGTGTACATGGTCACGGGCGGCCAGTCGCTCAAGAAGTTCCACGACCTCGTCTGCAACGGCAGGTGC
AAGGACATCCGCCTCACCTTCTTCATCATGATCTTCGGCGCCGTCCACTTCGTGCTCTCCCAGATGCCCAACTTCAACTC
CATCTCTGGCGTGTCAGCCGCCGCCGCCGTCATGTCCTTGTGTTACTCCATGGTCGCCTTCTTCACGTCGGCGGTCAAGG
GCCACGTGGGCGCGGCCGTTGACTACGGGCTGAAGGCGACGACCACGGTGGGGCAGGTCTTCGGCATGCTGAACGGGCTA
GGGGCGGTGGCCTTCGCGTTCGCGGGCCACAGCGTGGTGCTGGAGATCCAAGCGACGATCCCTTCGACGCCGGAGCAGCC
ATCGAAGAAGCCGATGTGGCGCGGGGTGGTCGTCGCCTACGCCGCCGTGGCGCTCTGCTACTTCTGCGTCGCCTTCGGGG
GCTACTACGCCTTCGGGAACTCCGTCGACCCCAACGTGCTCATCACGCTGGAGAAGCCACGCTGGCTCATCGCGGCCGCC
AACATGATGGTGGTCGTCCACGTCATCGGCAGCTACCAGGTGTTCGCCATGCCGGTCTTCGACATGATGGAGACGGTGCT
GGTGAAGAAGCTCAAGTTCGCGCCCGGACTACCGCTCCGCCTCGTCGCCCGCTCCGCCTACGTGGCGCTCACCATGTTCG
TCGGCATGACCTTCCCGTTCTTCGACGGCCTGCTGGGTTTCTTCGGAGGCTTCGCGTTTGCGCCCACCACCTACTTCCTT
CCCTGCGTCATCTGGCTCATGCTGCGCAAGCCCGCCAGGTTCAGCGCCACGTGGATCGTCAACTGGGTGTTGATCGTCCT
CGGGGTCCTGCTCATGCTGCTGGCCCCCATCGGTGGACTGCGCCAAATCATCCTTGATGCCAAGACTTTCAAGTTCTACT
CTTAA

Alignment

ORF - retro_bdis_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.61 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENHSSPAKDVRTEQEKK---IDDWLPITSSRNAKWWYSAFHNVTAMVGAGVLSLPYAMSELGWGPGIAVL
          E......K..RTE...K....DDWLPITSSR.AKW.YSAFHNVTAMVGAGVL.LP.AM..LGWGPG.AV.
Retrocopy EEYAETVKERRTEEKLKDVNLDDWLPITSSRTAKWYYSAFHNVTAMVGAGVLGLPFAMAQLGWGPGVAVI

Parental  VISWVITLYTLWQMVEMHEMVPGKRFDRYHELGQHAFGEKLGLWIVVPQQLIVEVGVNIVYMVTGGKSLK
          V.S.VITLYTLWQ.VEMHEMVPGKRFDRYHELGQHAFG.KLGLWI.VPQQLIVEVG..IVYMVTGG.SLK
Retrocopy VASFVITLYTLWQLVEMHEMVPGKRFDRYHELGQHAFGDKLGLWIIVPQQLIVEVGTDIVYMVTGGQSLK

Parental  KFHDVICDGKCKDIKLTYFIMIFASVHFVLSQLPNLNSISGVSLAAAVMSLSYSTIAWGASVDKGQV-AN
          KFHD..C.G.CKDI.LT.FIMIF..VHFVLSQ.PN.NSISGVS.AAAVMSL.YS..A...S..KG.V.A.
Retrocopy KFHDLVCNGRCKDIRLTFFIMIFGAVHFVLSQMPNFNSISGVSAAAAVMSLCYSMVAFFTSAVKGHVGAA

Parental  VDYSIRATTTPGKVFGFFGALGDVAFAYAGHNVVLEIQATIPSTPEKPSKKPMWKGVVVAYIVVAICYFP
          VDY...ATTT.G.VFG....LG.VAFA.AGH.VVLEIQATIPSTPE.PSKKPMW.GVVVAY..VA.CYF.
Retrocopy VDYGLKATTTVGQVFGMLNGLGAVAFAFAGHSVVLEIQATIPSTPEQPSKKPMWRGVVVAYAAVALCYFC

Parental  VALIGYWAFGNGVDDNILITLSKPKWLIALANMMVVIHVIGSYQIYAMPVFDMIETVLVKKLHFPPGLTL
          VA..GY.AFGN.VD.N.LITL.KP.WLIA.ANMMVV.HVIGSYQ..AMPVFDM.ETVLVKKL.F.PGL.L
Retrocopy VAFGGYYAFGNSVDPNVLITLEKPRWLIAAANMMVVVHVIGSYQVFAMPVFDMMETVLVKKLKFAPGLPL

Parental  RLIARTLYVALTMFIAITFPFFGGLLGFFGGFAFAPTTYFLPCIMWLAIYKPKRFSLSWFTNWVCIILGL
          RL.AR..YVALTMF...TFPFF.GLLGFFGGFAFAPTTYFLPC..WL...KP.RFS..W..NWV.I.LG.
Retrocopy RLVARSAYVALTMFVGMTFPFFDGLLGFFGGFAFAPTTYFLPCVIWLMLRKPARFSATWIVNWVLIVLGV

Parental  CLMILSPIGGLRQIIMDSKTYKFYS
          .LM.L.PIGGLRQII.D.KT.KFYS
Retrocopy LLMLLAPIGGLRQIILDAKTFKFYS

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_3 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	BRADI3G14140	1 retrocopy	retro_bdis_3 ,