RetrogeneDB ID: retro_bdis_33

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:41374790..41375585(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G41070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G52110
• Aliases: None
• Description: None

Sequence

>retro_bdis_33
ATGTCGTCCTCGTCCATGCTGCCGGCAGCCGCGACCGCGGCCTCGAAGCGGCTGATCCTGGTGCACGGCACGGGCCACGG
CGGCTGGTGCTGGTACAAGGTGGCCACGCTGCTCCGCGCCGCGGGCCACCGCGTGGACGCGCCGGACATGGCCGCCTCCG
GGGCCGACGCGCGCCCGCTCCGGGACGCGCCCACCTTCGAGGACTACTCGCGCCCGCTCCTCGACGCCCTCCGAGCCCTT
CCCCCGGGCGAAAAGGCGGTGCTCGTCGGCCACAGCTTCGGCGGGATGAGCGTGGCGCTGGCCGCCGAGGAGTTTCCCGA
CAAGGTGGCCGCGGCCGTGTTCCTCACGGCCTTCATGCCGGACTGCGCACACCCGCGCACGCACACCATCGAGGCGCTCC
CCGCGGGGCTGGACTGGATGGACAGCGTGACGGACGAAGGGCACGCCCCGCCGTCCGTGTTCCTCGGGCCGCAGTTCCTG
CGGAGGATGCTGTACCAGCTCTGCCCGGAGGAGGATTATACTCTGTCGCAGAGCCTGGCCAGGGTGAGCTCCTACTACGT
GGCCGACCAGCGGCGCCGGCCGCCGTTCAGCGCGGACCGGTACGGCGCCGTGAGCAAGGTGTACGTGGTCGCCAAGCAGG
ACCTGGCCATGGTGGAGCAGTACCAGAGGCAGATGATCGCTAGCGTCCCCGTGGCGGAGGTCAGGGAGATGGCTGGAGCT
GACCACATGGCCATGCTCTCGGCGCCCGAGGTGCTGGCGGGACACCTCGCCGACATCGCCAACACCTACGCTTGA

Alignment

ORF - retro_bdis_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.79 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASSCKGNKHIVLVHGACHGGWSWFKVATRLRAAGHRVSTPDLAASGVDPRPLREVPTFRDYTRPLLDLLE
          A......K...LVHG..HGGW.W.KVAT.LRAAGHRV..PD.AASG.D.RPLR..PTF.DY.RPLLD.L.
Retrocopy AAATAASKRLILVHGTGHGGWCWYKVATLLRAAGHRVDAPDMAASGADARPLRDAPTFEDYSRPLLDALR

Parental  SLPPAGEKVVLVGHSLGGISVALAAELFPEKIAAAVFLSAFMPDHKSPPSHVLEKFVEGRTLDWKDTEMK
          .LPP.GEK.VLVGHS.GG.SVALAAE.FP.K.AAAVFL.AFMPD...P..H..E....G..LDW....M.
Retrocopy ALPP-GEKAVLVGHSFGGMSVALAAEEFPDKVAAAVFLTAFMPDCAHPRTHTIEALPAG--LDW----MD

Parental  PQDPEGKLPISMLFGPVVTRSNFYQLCSPEDFTLGRSLMRVGSMFVEDLKLQRPYSEARYGCVRKVFIVC
          ....EG..P.S...GP...R...YQLC..ED.TL..SL.RV.S..V.D.....P.S..RYG.V.KV..V.
Retrocopy SVTDEGHAPPSVFLGPQFLRRMLYQLCPEEDYTLSQSLARVSSYYVADQRRRPPFSADRYGAVSKVYVVA

Parental  KDDLAIVEGFQRWMIRNNPVDEVKEIDGADHMAMLSTPTQLTQCLSDIAETYA
          K.DLA.VE..QR.MI...PV.EV.E..GADHMAMLS.P..L...L.DIA.TYA
Retrocopy KQDLAMVEQYQRQMIASVPVAEVREMAGADHMAMLSAPEVLAGHLADIANTYA

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_33 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	BRADI2G52110	1 retrocopy	retro_bdis_33 ,
Aegilops tauschii	F775_21190	1 retrocopy	retro_atau_7,