RetrogeneDB ID: retro_bdis_30

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:4546768..4548784(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G06050
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G01477
• Aliases: None
• Description: None

Sequence

>retro_bdis_30
ATGGCCCGAGGGACGTCGACGACGGCGTTGCTTCTGGGGCTGTTCCTCGTGGGGTTTCTGGTGGCTCCGTCGGCCGCGGC
GGCGGACTCGAAGGGGGATCAGCAGCCGGCGAACAAGGCGTCTGGCGGTCCGGTGATCGGCATCGACCTGGGCACGACCT
ACTCGTGCGTGGGCGTGTACCGGAACGGCCACGTGGAGATCATTGCCAACGACCAAGGCAACCGCATCACCCCCTCCTGG
GTCGCCTTCACCGACTCCGGCGAGCGCCTCATCGGCGAGGCCGCCAAGAACCAGGCCGCCTCCAACCCCCTCCGCACCAT
CTACGACGCCAAGCGCCTCATCGGCCGACAGTACGGCGACGCGGAGGTGCACAAGGACATGAAGCACCTGCCGTACAAGA
TCGTGGAGAAGCGCGGGAAGCCGCACATGGAGGTTGAGGTGAAGGACGGCGACGTGCGGACGCTGAGCCCGGAGGAGGTG
AGCGCCATGGTGCTGACGCGGATGAAGGAGACGGCGGAGGCGTTCCTGGGGGAACCGGTGAAGGACGCCGTGATCACCAT
CCCGGCCTACTTCAACGACGCGCAGCGCCAGGCCACCAAGGACGCCGGCGCCATCGCCGGCCTCAACGTCGTCCGCCTCA
TCAACGAGCCCACCGCCGCCGCCATCGCCTACGGCCTCGACAACAAGGCCAAGGACGCCAAGGAGGAGAGGAACGTGCTC
GTCTTCGACCTCGGCGGCGGCACCTTCGACGTCAGCGTGCTCACCATCGACAACGGCGTCTTCGAGGTGCTGGCCACCAA
CGGCGACACCCACCTCGGCGGCGAGGACTTCGACCACCGCCTCATGGACTACCTCGTCAAGCTTGTCAAGCGCAAGCACG
GCAAGGACGTCTCCCACGACGCCCGCGCGCTGGGGAAGCTCCGGCGCGAGTGCGAGCGCGCCAAGCGCGCGCTCAGCAGC
CAGCACCAGGTCCGGGTGGAGATCGAGTCGCTCTTCGACGGCGTCGACCTGTCGGAGCCGCTCACCAGGGCCCGGTTCGA
GGAGCTCAACTCGGACCTCTTCCGCAAGACGATGACCCCCGTCAAGAAGGCCATGGCGGACGCCGGGCTCGCCAAGGGCG
ACATCCACGAGGTCGTGTTAGTCGGCGGCAGCACCCGGATCCCCAAGATCCAGCAGTTCCTCAAGGACTACTTCGACGGC
AAGGAGCCCAGCAAAGGCGTCAACCCTGACGAGGCCGTGGCGTACGGCGCGGCCGTGCAGGGGAGCATCGTGCGTGGGGA
CAACGCCGAGAAGCTCGTGGTGCTCGACGTGACGCCGCTCACGCTCGGCATCGAGACGGCCGGCGGCGTCATGACGCCCC
TGATCCCGCGCGGCACGGTGATCCCCACGAGGAAGACCAAGACGTTCACCACGTACCAGGACCGGCAGACCACGGTGAGC
GTCGTGGTGTTCGAGGGCGAGCGGAGCATGACCAAGGACAACAAGCAGCTCGGCAAGTTCGACCTGACCGGCATCGCGCC
GGCGCCCCGGGGCACGCCGCAGATCGAGGTCACCTTCGAGGTGGACGTCAATGGCATCCTCCATGTTAAGGCGGCGGACA
AGGGCACGGGTAAGTCGGAGAAGATCCAGATCACGAGCGCCGCCGACCGCCGGATCACGCAGGAGGAGATCGACCGGATG
GTGCGCGAGGCGGAGGAGTTCGCCGAGGAGGACAGGAAGGTGAGGGAGAGGGTCGACGCGAGGAACAGGATGGAGGCGTA
CGTGTACCACGTCCGGACCACGGTGGACGGCGAGGCTGGGCAAGGGATGGACGGCGGGGATAAGGAGAGGGTCCGGGAGG
CGGCCAGGGAGGCCAGCGAGTGGATCGACGAGAACCCGGAAGCGGATAAGGATGAGTACGTGGAGAAGCTCAAGGAGCTC
GAGGACCTCTGCAACCCTGTCTTCGCCGCCGCGGACTCCCACAAGTCCGGTGGCGGGCATGACGAAGCCGAGGAAGACGA
CCACGACGAGCTTTAG

Alignment

ORF - retro_bdis_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.67 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTVIGIDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVGFTDS-ERLIGEAAKNQAAVNPERTIFDVKR
          G.VIGIDLGTTYSCVGVY.NGHVEIIANDQGNRITPSWV.FTDS.ERLIGEAAKNQAA.NP.RTI.D.KR
Retrocopy GPVIGIDLGTTYSCVGVYRNGHVEIIANDQGNRITPSWVAFTDSGERLIGEAAKNQAASNPLRTIYDAKR

Parental  LIGRKFEDKEVQRDMKLVPYKIVNRDGKPYIQVKIKDGENKVFSPEEISAMILGKMKETAEAYLGKKIND
          LIGR...D.EV..DMK..PYKIV...GKP...V..KDG.....SPEE.SAM.L..MKETAEA.LG....D
Retrocopy LIGRQYGDAEVHKDMKHLPYKIVEKRGKPHMEVEVKDGDVRTLSPEEVSAMVLTRMKETAEAFLGEPVKD

Parental  AVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKGGE----KNILVFDLGGGTFDVS
          AV.T.PAYFNDAQRQATKDAG.IAGLNV.R.INEPTAAAIAYGLD.K........N.LVFDLGGGTFDVS
Retrocopy AVITIPAYFNDAQRQATKDAGAIAGLNVVRLINEPTAAAIAYGLDNKAKDAKEERNVLVFDLGGGTFDVS

Parental  ILTIDNGVFEVLATNGDTHLGGEDFDHRIMEYFIKLIKKKYSKDISKDNRALGKLRREAERAKRALSNQH
          .LTIDNGVFEVLATNGDTHLGGEDFDHR.M.Y..KL.K.K..KD.S.D.RALGKLRRE.ERAKRALS.QH
Retrocopy VLTIDNGVFEVLATNGDTHLGGEDFDHRLMDYLVKLVKRKHGKDVSHDARALGKLRRECERAKRALSSQH

Parental  QVRVEIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKSQIHEIVLVGGSTRIPKVQQ
          QVRVEIESLFDG.D.SEPLTRARFEELN.DLFRKTM.PVKKAM.DAGL.K..IHE.VLVGGSTRIPK.QQ
Retrocopy QVRVEIESLFDGVDLSEPLTRARFEELNSDLFRKTMTPVKKAMADAGLAKGDIHEVVLVGGSTRIPKIQQ

Parental  LLRDYFEGKEPNKGVNPDEAVAFGAAVQGSILSGEGGDETKDILLLDVAPLTLGIETVGGVMTKLIPRNT
          .L.DYF.GKEP.KGVNPDEAVA.GAAVQGSI..G...D.......LDV.PLTLGIET.GGVMT.LIPR.T
Retrocopy FLKDYFDGKEPSKGVNPDEAVAYGAAVQGSIVRG---DNAEKLVVLDVTPLTLGIETAGGVMTPLIPRGT

Parental  VIPTKKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPPAPRGTPQIEVTFEVDANGILNV
          VIPT.K...FTTYQD.QTTVS..VFEGERSMTKD...LGKFDL.GI.PAPRGTPQIEVTFEVD.NGIL.V
Retrocopy VIPTRKTKTFTTYQDRQTTVSVVVFEGERSMTKDNKQLGKFDLTGIAPAPRGTPQIEVTFEVDVNGILHV

Parental  KAEDKGTGKSEKITITNEKG-RLSQEEIDRMVKEAEEFAEEDKKVKERIDARNQLETYVYNMKNTVGDKD
          KA.DKGTGKSEKI.IT.....R..QEEIDRMV.EAEEFAEED.KV.ER.DARN..E.YVY....TV....
Retrocopy KAADKGTGKSEKIQITSAADRRITQEEIDRMVREAEEFAEEDRKVRERVDARNRMEAYVYHVRTTV--DG

Parental  KLADKLESEEKEKVEEALKEALEWLDENQSAEKEDYEEKLKEVEAVCNPIVSAVYQRSGGAPGGEDGAGG
          ..........KE.V.EA..EA.EW.DEN..A.K..Y.EKLKE.E..CNP...A......G..GG.D.A..
Retrocopy EAGQGMDGGDKERVREAAREASEWIDENPEADKDEYVEKLKELEDLCNPVFAAADSHKSG--GGHDEA--

Parental  VDDEEHDEL
          .....HDEL
Retrocopy -EEDDHDEL

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_30 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30 ,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,