RetrogeneDB ID: retro_bdis_18

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:32828380..32829922(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G37000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G78400
• Aliases: None
• Description: None

Sequence

>retro_bdis_18
ATGGCGGTCGGCGTCGGCGTCCTCTCCGGGAGCTCCGGCGGCGGCAACGGGAGGGTCACCGCCTTCGTGGTGCTCTCGTG
CATCACCGCGGGCATGGGCGGCGTCATCTTCGGCTACGACATCGGGATCGCAGGCGGCGTGTCGTCGATGGAGCCGTTCC
TGAAAAAGTTCTTCCCGGAGGTGTACCGGCGGATGAAGGGCGACGGTAGCATCAGCAACTACTGCAAGTTCGACAGCCAG
CTGCTGACTGCCTTCACTTCCTCGCTCTACGTCGCCGGCCTCCTCACCACTTTCCTCGCGTCCACGGTCACAGCCCGGCG
CGGCCGCCGCCCGTCCATGCTCCTGGGCGGCGCCAGCTTCCTCGCGGGCTCGGCCGTGGGCGCCGCGGCCGTGGACATCT
ACATGGTCATCCTCGGCCGGGTGCTCCTCGGGGTCGGCCTGGGCTTCGCGAACCTGGCCGTGCCGCTGTACCTGTCGGAG
ATGGCGCCGTCGCGGCACCGCGGCGCGTTCAGCAACGGCTTCCAGCTGAGCGTCGGGGTCGGCGCGCTCGCGGCCAATTT
GATCAACTTCAGCACGCAGAAGATCAGGGGCGGGTGGGGGTGGCGCGTGTCGCTGGCACTCGCCGCCGTCCCCGCTGCGC
TTCTGCTCGTCGGCGCCATCTTCCTCCCGGAGACGCCCAACAGCCTGATCCAGCAAGGCAGAGACCGTCAGGACGTGGCC
GTGCTGCTGCGGAAGATCCGCGGCACGGATGACGTGGACGCCGAGCTGGACGACATCGTGGCCGCCGCGGCAGCTAACAG
CGAAGGGGCAGCCGGAAGTGGCCTGCGGATGCTGCTCACTCAGCGTAAATACCGGCCTCAGCTGGCGATGGCCGTGATGA
TACCCTTCTTCCAGCAGGTGACGGGGATCAACGCGATCGCGTTCTACGCGCCGGTGCTGCTGCGCAGCATCGGCATGGGC
GAGTCGGCGTCGCTGCTGTCGGCGGTCGTCACGGGCGTCGTCGGCGCGGGCTCCACCTTCCTCTCCATGTTCCTCGTCGA
CCGGTTCGGGCGCCGCACGCTCTTCCTGGCGGGGGGCGCGCAGATGCTGGCGTCGCAGGTGCTCATCGGCGGCATCATGG
CCGCGAAGCTCGGGGACGACGGAGGGGTGAGCAAGGCGTGGGCCGGGGTGCTCGTGCTGCTCATCGCCGTCTACGTGGCC
GGGTTCGGGTGGTCGTGGGGCCCGCTGGGGTGGCTCGTGCCCAGCGAGATCTTCCCGCTGGAGGTGCGCTCGGCGGGGCA
AGGGGTGACGGTGGCCGTGAGCTTCGTGTTCACGGTGGTCGTGGCGCAGGCGTTCCTGGCCATGCTGTGCCACATGAGGG
CCGGGATATTCTTCTTCTTCGCGGCGTGGCTGGCGGCCATGACGGCGTTCGTGTACCTCCTCCTGCCGGAGACGAAAGGG
GTGCCGATGGAGCAGATGGCTGCCTTGTGGGCCGAGCACTGGTTCTGGAAGCGGGTCCTCCTGGGCTCCGAGGAGGCGCC
AACAGCGAGCGGGAAACTCTGA

Alignment

ORF - retro_bdis_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.72 %
• Parental protein coverage: 92.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAAGYNGRVTSFVVLSCIVAGSGGILFGYDLGISGGVTSMESFLKKFFPEVYHQMKGDKVDVSNYCRF
          .....G.NGRVT.FVVLSCI.AG.GG..FGYD.GI.GGV.SME.FLKKFFPEVY..MKGD....SNYC.F
Retrocopy SGSSGGGNGRVTAFVVLSCITAGMGGVIFGYDIGIAGGVSSMEPFLKKFFPEVYRRMKGDG-SISNYCKF

Parental  DSELLTVFTSSLYVAGLVATLFASSVTTRYGRRASILIGGSVFIAGSVFGGAAVNVYMLLLNRILLGIGL
          DS.LLT.FTSSLYVAGL..T..AS.VT.R.GRR.S.L.GG..F.AGS..G.AAV..YM..L.R.LLG.GL
Retrocopy DSQLLTAFTSSLYVAGLLTTFLASTVTARRGRRPSMLLGGASFLAGSAVGAAAVDIYMVILGRVLLGVGL

Parental  GFTNQSIPLYLSEMAPPQYRGAINNGFELCISIGILIANLINYGVAKIEGGWGWRISLSMAAVPAAFLTV
          GF.N...PLYLSEMAP...RGA..NGF.L....G.L.ANLIN....KI.GGWGWR.SL..AAVPAA.L.V
Retrocopy GFANLAVPLYLSEMAPSRHRGAFSNGFQLSVGVGALAANLINFSTQKIRGGWGWRVSLALAAVPAALLLV

Parental  GAIFLPETPSFLIQRGGGNTDAAKAMLQRLRGTAGVQKELDDLVAAAGA---GQQGRPLRTLLGKKKYRP
          GAIFLPETP..LIQ.G....D.A...L...RGT..V..ELDD.VAAA.A...G..G..LR.LL...KYRP
Retrocopy GAIFLPETPNSLIQQGRDRQDVA-VLLRKIRGTDDVDAELDDIVAAAAANSEGAAGSGLRMLLTQRKYRP

Parental  QLAMAILIPFFNQVTGINVINFYAPVMFRTIGLKESASLMSAVVTRLCATAANVVAMVVVDRSGRRKLLL
          QLAMA..IPFF.QVTGIN.I.FYAPV..R.IG..ESASL.SAVVT...........M..VDR.GRR.L.L
Retrocopy QLAMAVMIPFFQQVTGINAIAFYAPVLLRSIGMGESASLLSAVVTGVVGAGSTFLSMFLVDRFGRRTLFL

Parental  AGGVQMILSQFAVGAILAAKFKDHGAMDKEYAYLVLVIMCVFVAGFAWSWGPLTYLVPTEICPLEIRSAG
          AGG.QM..SQ...G.I.AAK..D.G...K..A........V.VAGF.WSWGPL..LVP.EI.PLE.RSAG
Retrocopy AGGAQMLASQVLIGGIMAAKLGDDGGVSKAWAGVLVLLIAVYVAGFGWSWGPLGWLVPSEIFPLEVRSAG

Parental  QSVVIAVIFLATFVIGQTFLAMLCHLRSGTFFLFGGWVCLMTLFVFFFLPETKQLPMEQMEQVWRRHWFW
          Q.V..AV.F..T.V..Q.FLAMLCH.R.G.FF.F..W...MT.FV...LPETK..PMEQM...W..HWFW
Retrocopy QGVTVAVSFVFTVVVAQAFLAMLCHMRAGIFFFFAAWLAAMTAFVYLLLPETKGVPMEQMAALWAEHWFW

Parental  RRV-VGTEE
          .RV..G.EE
Retrocopy KRVLLGSEE

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_18 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	BRADI1G24820	1 retrocopy	retro_bdis_38,
Brachypodium distachyon	BRADI1G78400	1 retrocopy	retro_bdis_18 ,