RetrogeneDB ID: retro_bdis_44

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:6406419..6408018(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G08230
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G37470
• Aliases: None
• Description: None

Sequence

>retro_bdis_44
ATGGCGGCAAGAGCTCGTCTGGTCGCATTTCTTATCGGCATGGCCAGCTTCCTCTCCATCGTAGCCGCCGGTCAGATCCG
GCCACTGCCATCCGGTGGCCAGCTCCCCAGTGGCCTCTTCGTCCACAGCATCGCTTCAATGATTCGCACAGATCGCAACG
CGACGACAAAGGCATCATCGGATTTTGGCCGCATCGTGGAGGCTGCTCCAGAGGCTGTCCTCCACCCGGCAACGCCCGCC
GACATCGCCGCTCTGATCCGATTCTCAGCGTCCTCAAAGGCCCCGTTCCCCGTGGCGCCGCGCGGGCAGGGCCACTCCGC
CCGCGGGCAGTCGCTCGCTCCAGGCGGCGTCGTCGTGGACATGCGCGCTCTGGGGCGCGGTCACCGCCGCATCAACGTGT
CCGCGGGCGCGGGCTACGTCGACGCCGGCGGCGAGCAGCTGTGGATCGACGTCCTCCGGGCGACGCTAGAGCACGGCCTG
GCGCCGCGCGCGTGGACGGACTACCTCCGACTCACCGTCGGCGGCACGCTCTCCAATGCCGGCATCGGCGGGCAGGCGTT
CCGGCATGGCCCGCAGATCGCCAACGTGCGGGAGCTCGACGTGGTCACCGGGACGGGTGAGCTGGTGACGTGCTCCCGTG
AGGAGAGCTCTGACCTGTTCTTCGCGGTGTTGGGCGGGCTGGGCCAGTTCGGGGTCATAACTCGGGCTCGGATCGCGCTG
GAGCCGGCCCCGAAGCGGGCGCGATGGGTCCGGCTCGCCTACACGGATGTGACTGTGTTCACCGGGGACCAAGAGCTGCT
CATTTCCAAGAAGGCGAGCGAAGCCGGGTTCGACTACGTGGAAGGCCAGGTCCAGCTCAACCGAACGCTGATCGATGGTC
CGGAGTCCACACCGTTCTTCTCCGGTGCTGATATCAACAGGCTTGCCGGGCTCGTCTCCAGGTCTGGGTCCGGAGCCATA
TATTTCATCGAAGCCGCCATGTACTACGACGAAGCAACCGCCTCCTCGGTGGACCAAAAATTGGAGGCGGTGCTAGAGCA
GCTAAGCTTCACTCCAGGATTCGTGTTCACCAAGGACGTAACTTACGTGCAGTTCCTCGACCGTGTTCGCGTGGAGGAGG
AGGTGCTCCGATCGGTCGGGGTGTGGGATGTGCCGCACCCGTGGCTGAACCTTTTCATCCCCCGGTCACGAATCATTGGC
TTCGATACCGGCGTTCTTAAGGGCATCCTTGGGGGTACCAACCCTGTTGGGGTCATCCTTATGTACCCCATGAACACCAA
CAAGTGGGACGACCGGATGACGGCAGTGACGCCCCAAACCGAGGAAGATGTGTTCTATGCCGTGAGTCTTCTCCGGTCCG
CCGTGGCCGTTGGAGATGTGGAGCGTCTCGAAAGGGAGAACGAGGCGGTTCTGGCGTTTTGTACCAGGGAAGCCATCCGG
TGCAAACAATACCTGCCGCACTACACAAGTGAGGATGGATGGCGACGACATTTCGGGACTAAGTGGGAGAGAATTGCCGA
GCTTAAGGCCAAATACGACCCCCAAACGATAATGGCACCAGGACAGAGGATTTTTCAGTCAAGCATCGCAAGTGCATAA

Alignment

ORF - retro_bdis_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.04 %
• Parental protein coverage: 98.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASLATFLIVTSLFST---ASHLGTLASGAQPDEDLSALDVVSKIRTDWGSIVRASLDFGHIVETTPMGV
          RA.L..FLI....F.....A.....L.SG.Q....L......S.IRTD......AS.DFG.IVE..P..V
Retrocopy RARLVAFLIGMASFLSIVAAGQIRPLPSGGQLPSGLFVHSIASMIRTDRNATTKASSDFGRIVEAAPEAV

Parental  FHPASPSDISALIRFSLSQPAPFTVSPRGQGHSSRGQALASGGIVVDMPSLQGHNGGDHGRRVNVSVDGM
          .HPA.P.DI.ALIRFS.S..APF.V.PRGQGHS.RGQ.LA.GG.VVDM..L....G..H.R..NVS....
Retrocopy LHPATPADIAALIRFSASSKAPFPVAPRGQGHSARGQSLAPGGVVVDMRAL----GRGHRR-INVSAGAG

Parental  YVDVGGEQLWIDVLAATLRHGGGLAPRVWTDYLRITVGGTLSNAGIGGQAFRHGPQISNVQELDVVTGTG
          YVD.GGEQLWIDVL.ATL.H..GLAPR.WTDYLR.TVGGTLSNAGIGGQAFRHGPQI.NV.ELDVVTGTG
Retrocopy YVDAGGEQLWIDVLRATLEH--GLAPRAWTDYLRLTVGGTLSNAGIGGQAFRHGPQIANVRELDVVTGTG

Parental  DMITCSRSQNSDLFFATLGGLGQFGVITRARVGLEPAPKRVKWVRLAYSDVRLFTADQELLISKAA---G
          ...TCSR...SDLFFA.LGGLGQFGVITRAR..LEPAPKR..WVRLAY.DV..FT.DQELLISK.A...G
Retrocopy ELVTCSREESSDLFFAVLGGLGQFGVITRARIALEPAPKRARWVRLAYTDVTVFTGDQELLISKKASEAG

Parental  FDYVEGQVQLNRTLTEGRRSSSFFSASELARLAGLTLDTGSAAIYYIEGAMYYDGYSAATVDQKLEALLE
          FDYVEGQVQLNRTL..G..S..FFS.....RLAGL....GS.AIY.IE.AMYYD...A..VDQKLEA.LE
Retrocopy FDYVEGQVQLNRTLIDGPESTPFFSGADINRLAGLVSRSGSGAIYFIEAAMYYDEATASSVDQKLEAVLE

Parental  ELSFLPGLVFIRDVAYVQFLDRVGQEEQKLRSAGAWDVPHPWLNLFVPKSRIHEFDAGVFKGILKDAKPV
          .LSF.PG.VF..DV.YVQFLDRV..EE..LRS.G.WDVPHPWLNLF.P.SRI..FD.GV.KGIL....PV
Retrocopy QLSFTPGFVFTKDVTYVQFLDRVRVEEEVLRSVGVWDVPHPWLNLFIPRSRIIGFDTGVLKGILGGTNPV

Parental  GLLLMYPMNKNKWDNQMTAMTP--DEDVFYAVGLLRSAMGPGDLERLEKENEAVLGFCDRAGIGCKQYLP
          G..LMYPMN.NKWD..MTA.TP...EDVFYAV.LLRSA...GD.ERLE.ENEAVL.FC.R..I.CKQYLP
Retrocopy GVILMYPMNTNKWDDRMTAVTPQTEEDVFYAVSLLRSAVAVGDVERLERENEAVLAFCTREAIRCKQYLP

Parental  HYASMDAWRQHFGNKWSWVAELKAKYDPKAILSPGQGIFPSARTSS
          HY.S.D.WR.HFG.KW...AELKAKYDP..I..PGQ.IF.S...S.
Retrocopy HYTSEDGWRRHFGTKWERIAELKAKYDPQTIMAPGQRIFQSSIASA

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_44 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	BRADI1G37470	1 retrocopy	retro_bdis_44 ,