RetrogeneDB ID: retro_bdis_2

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:46739263..46740673(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G44780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G37290
• Aliases: None
• Description: None

Sequence

>retro_bdis_2
ATGGAGACGGAAGGGCACTCTCTGCGGTCGGCGTCGTGCGTGGACGGCGGCAAGAGGCGCGTGAGCTACTACTACGACCC
GGGCATCGCCAACGTGGACTACGGCGAGGGCCACGTCATGGTGCCCCGCCGCGTGGCCATGACGCACGCCCTCGTGTCCT
CCTACGGCCTGCTCCCGGACATGAAGCGCCTCCGCACCAGGCCCGCCACCGAAAGCGACCTGCGCGCCTTCCACGGCGCC
TCCTACGTCGAGCTCCTCCGCTCCATCAACCCGGAATCCTACCGCCTCAACCTCGACCAGGCCAAGACGCGGGCCGAGGA
GCGCGGCGTCGGCCGCGTGAAGACCAAGGAGAACGGCGACAACTACGACAACCCCGTCATCGACGGCCTCTGGGACTACT
GCCTCAGCTACGCCGGCGGGTCCCTGGCCGCGGCGCGCGCGCTGGCCTGCGGCGAGTCCGACGTGGCCATCAACTGGTCC
GGCGGGATGCACCACGCGTGCCGGGCCAAGGCCAGCGGCTTCTGCTACGTCAACGACATCGTGCTCGCCATCCAGCGGCT
CCTCGCCCGCTTCCGCCGCGTGCTCTACGTCGACATCGACGTGCACCACGGCGACGGCGTCGAGCACCGCTTCCGGAGGG
AGCCCCGGGTCATGACGGTCTCCTTCCACCGCTACGACGGCGTCTTCTTCCCCACCACCGGCGAGGCTGCGGACGTCGGC
CAAGGCGAGGGGCTCTACCACGCGCTCAACGTGCCGATGAAGGCCGGCATGGACGACGAGGGCTACCTCAACGTCCTCTT
CCGGCCCATCATGGCCCGGGTCATGGAGGTGTTCGCGCCGGACGCCGTCGTGCTGCAGTGCGGGGCCGACTCGCTCTCGG
GCGACGCGATCGGCGGGTTCCACCTGTCAGTCAAGGGCCACGCCGCCTGCGTCGCCTTCCTCCGCAGCTTCAACGTGCCG
CTGCTCCTGCTCGGCGGCGGCGGCTACACCATCAACCACGTCGCCTCCTGCTGGTGCTACGAGACGGCGGTGGCCGTCGG
CAAGGAGAAGGAGATCCCCGACGACATACCCTACCACGGTTACGAGCACTACTACAAGGACCAGGGATACAAGCTCCATT
ATGCAGTGGACAAGAAGAACGGCAGGAAGGATGTCTCTGGCCTGGAGAAGATAAAGCAGGACGCTCTGAAGAACCTCTCC
ATGCTCAGGCCGCCGCCCACATTGCTGCTCCAGGAGCCCGCCGGTGGGGACATCAACGTGAATGACCTCTACGACAACGA
CTACAGTAATCCCAAGAGAAGAAGAGAGGAAGACGACCCCATGGAGAGGCTGCACCGGCTCTGCGGCGTCGAGGACCTAA
AAGGTTTCTTCACTGGGATCGGCAGGAGAAAGAAACTAGGACAACTATAG

Alignment

ORF - retro_bdis_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.89 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DCPVFDGLYSFCQTYAGGSVGGAVKLNHGH-DIAINWAGGLHHAKKCEASGFCYVNDIVLAILELLKYHQ
          D.PV.DGL...C..YAGGS...A..L..G..D.AINW.GG.HHA....ASGFCYVNDIVLAI..LL....
Retrocopy DNPVIDGLWDYCLSYAGGSLAAARALACGESDVAINWSGGMHHACRAKASGFCYVNDIVLAIQRLLARFR

Parental  RVLYVDIDIHHGDGVEEAFYTTDRVMTVSFHKF-GDYFPGTGDIRDVGHSKGKYYSLNVPLDDGIDDESY
          RVLYVDID.HHGDGVE..F....RVMTVSFH...G..FP.TG...DVG...G.Y..LNVP...G.DDE.Y
Retrocopy RVLYVDIDVHHGDGVEHRFRREPRVMTVSFHRYDGVFFPTTGEAADVGQGEGLYHALNVPMKAGMDDEGY

Parental  QS-LFKPIMGKVMEIFRPGAVVLQCGADSLSGDRLGCFNLSIKGHAECVRFMRSFNVPVLLLGGGGYTIR
          ...LF.PIM..VME.F.P.AVVLQCGADSLSGD..G.F.LS.KGHA.CV.F.RSFNVP.LLLGGGGYTI.
Retrocopy LNVLFRPIMARVMEVFAPDAVVLQCGADSLSGDAIGGFHLSVKGHAACVAFLRSFNVPLLLLGGGGYTIN

Parental  NVARCWCYETGVALG--HELTDKMPLNEYYEYF-GPDYTLHVAPSNMENKNTNRQLDEIRSRLLDNLTKL
          .VA.CWCYET.VA.G...E..D..P...Y..Y.....Y.LH.A............L..I....L.NL..L
Retrocopy HVASCWCYETAVAVGKEKEIPDDIPYHGYEHYYKDQGYKLHYAVDKKNGRKDVSGLEKIKQDALKNLSML

Parental  RHAPSVQFQERPPEAELPEQD---EDQENPDERHHADSDVE
          R..P....QE.P........D....D..NP..R...D...E
Retrocopy RPPPTLLLQE-PAGGDINVNDLYDNDYSNPKRRREEDDPME

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_2 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	BRADI1G37290	1 retrocopy	retro_bdis_2 ,
Ostreococcus lucimarinus	OSTLU_119545	1 retrocopy	retro_oluc_1,