RetrogeneDB ID: retro_bdis_9

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:72427920..72430293(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G75570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G74922
• Aliases: None
• Description: None

Sequence

>retro_bdis_9
ATGTCGGGCACGTCGTCGGCTTCGAAGAAGGCTGCGAACCGGCTGGTGGTGGAGGAGGCCCCCGAGGACGACAACTCCAT
GTGCAGCCTCCACCCTGCCACCATGGAGCGTCTCTCGTTATTCAAAGGCGACGTCGTCCTGCTCAAGGGGAAGCGCCGCC
GCAGCACCATCTGCATCGCCATCCCCGACGACGACTGCGAGGAGCACAAGCTCAGGATCAACAAGGCGGTCCGCTCCAAC
CTCAGGGCACGCATCGCCGACGTGGTGTCGATCCACGAGTGCCGTGACGCCAAGTACGGGAAGCGCGTGCACATCCTCCC
CATTGACGACACCGTGGAGGGCATCACGGGGAACCTCTTCGACGCGTACCTCAAGCCCTACTTCTTGGACGCCTACCGCC
CCGTCCGCAAGGGCGACCTCTTCCTCGTCCGCGGCGGCATGCGGAGCGTCGAGTTTAAGGTCGTCGAGGTCGACGCCGAT
GCCGCTGTCGAGTACTGCATCGTGGCGGCCGACACGGAGATCTTTTGTGATGGCGAGCCGTTGAAGAGGGAGGACGAGGA
GAGGCTCGACGACGTGGGCTATGACGATGTCGGCGGCATGCGTAAGCAGATGACGCAGATCAGGGAGCTCGTCGAGCTAC
CGCTCAGGCATCCGCAGCTCTTCAAGTCCATCGGTGTCGAGCCTCCCAAGGGGATCCTTCTTTACGGCCCTCCCGGCTCC
GGTAAGACGCTCATCGCCCGTGCCGTGGCCAACGAGACTGGAGCCTTCTTTTTCCTCATCAACGGGCCCGAGATCATGTC
CAAGTTGGCCGGGGAGAGCGAGAGCAACCTGAGGAAGGCGTTCGAGGAGGCCGAGAAGAACGCGCCGTCCATCATCTTCA
TTGACGAGATCGACTCCATCGCTCCCAACAGAGAGAAGACTCACGGCGAGGTCGAGAGGCGTATTGTGTCGCAGCTGCTG
ACGCTCATGGACGGCATGAAGTCTCGCGCGCACGTCATCGTCATGGGCGCCACGAACCGCCCCAACAGCATCGACCCTGC
TCTCCGCCGCTTCGGCAGGTTCGACCGGGAGATCGACATCGGCGTGCCGGACGAGGTTGGCCGCCTCGAAGTGCTTCGTA
TCCACACTAAAAACATGAAGCTCGACGCGGACGTCAACTTGGAAGTGGTCGCCAAGGACACGCACGGCTACGTTGGCGCC
GACCTTGCAGCGCTCTGCACGGAGGCGGCGTTGCAGTGCATCAGAGAGAAGATGGACATTATCGACTTGGAGGATGACAC
CATCGATGCCGAGATCTTGAACTCCATGGCCGTCACCAACGACCACCTAAAGACGGCTCTGGTCGGCACCAACCCTTCGG
CGCTCCGCGAGACCGTGGTGGAGGTGCCCAACGTGAGCTGGAGCGACATCGGCGGGTTGGACGGCGTGAAGAGGGAGCTA
CAGGAGACGGTGCAGTACCCGGTGGAGCACCCGGAGATGTTCGAGAAGTTCGGCATGTCGCCTTCCAAGGGCGTCCTCTT
CTACGGGCCGCCGGGCTGCGGCAAGACGCTGCTGGCCAAGGCCATCGCCAACGAGTGCCAGGCAAACTTCATCAGCATCA
AGGGGCCCGAGCTGCTCACCATGTGGTTCGGCGAGAGCGAGGCCAACGTGCGCGAGATCTTCGACAAGGCCAGGCAGTCG
GCGCCCTGCGTGCTCTTCTTCGACGAGCTCGATTCGATCGCCATGCAACGCGGCGGCAGCGTGGGTGACGCCGGCGGCGC
GGCTGACCGTGTGCTGAACCAGCTGCTGACGGAGATGGATGGCATGAACGCGAAGAAGACGGTCTTCATCATCGGAGCCA
CCAACAGGCCGGACATCATCGACTCGGCGCTGCTCCGTCCGGGCCGCCTCGACCAGCTCATCTACATCCCATTGCCGGAC
GAGGCCTCACGGCACCAGATCTTCAAGGCATGCCTCAGGAAGTCTCCGCTGGCCAAGAACGTCGACCTCGGCGCGCTTGC
GAGGTTCACCAAGGGCTTTAGCGGTGCCGACATCACGGAGATTTGCCAGAGGGCGTGCAAGTACGCGATTAGGGAAGACA
TCGAGAAGGATATCGAGAGGGAGAGGCTGGGGAAGGAAGCCATGGAGGTGGACGACTCCGGAGAGGTGGCTGAGATCAAG
GCGGCGCACTTCGAGGAGTCGATGAAGTACGCCAGGAGGAGCGTCAGTGATCGCGACATCACCAAGTATCGGGCCTTCGC
GCAGACGCTGCAGCAGTCCAGGGGCTTTGGCACCGAGTTCCGCTTCCCTGAGCAGTCCAAACCGGCAGAAGCTTCAGCTG
CCACGGCCAACGCCTACGCTGCAGCTGACGAAGAAGATGACCTTTACAACTGA

Alignment

ORF - retro_bdis_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.41 %
• Parental protein coverage: 96.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKSPNRLVVDEATNDDNSVVALHPDTMERLQLFRGDTVLLKGKKRKDTICIVLADETCEEPKVRMNKTVR
          KK..NRLVV.EA..DDNS...LHP.TMERL.LF.GD.VLLKGK.R..TICI...D..CEE.K.R.NK.VR
Retrocopy KKAANRLVVEEAPEDDNSMCSLHPATMERLSLFKGDVVLLKGKRRRSTICIAIPDDDCEEHKLRINKAVR

Parental  KNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTVEGITGNLFDAFLKPYFLEAYRPLRKGDLFLVRGGMR
          .NLR.R..DVVS.H.C.D.KYGKRVHILPIDDTVEGITGNLFDA.LKPYFL.AYRP.RKGDLFLVRGGMR
Retrocopy SNLRARIADVVSIHECRDAKYGKRVHILPIDDTVEGITGNLFDAYLKPYFLDAYRPVRKGDLFLVRGGMR

Parental  SVEFKVIETDP---AEYCIVAPDTEIFCDGEPIKREDEERLDEVGYDDVGGVRKQMAQIRELVELPLRHP
          SVEFKV.E.D.....EYCIVA.DTEIFCDGEP.KREDEERLD.VGYDDVGG.RKQM.QIRELVELPLRHP
Retrocopy SVEFKVVEVDADAAVEYCIVAADTEIFCDGEPLKREDEERLDDVGYDDVGGMRKQMTQIRELVELPLRHP

Parental  QLFKSIGVKPPKGILLFGPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNA
          QLFKSIGV.PPKGILL.GPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNA
Retrocopy QLFKSIGVEPPKGILLYGPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNA

Parental  PAIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREI
          P.IIFIDEIDSIAP.REKT.GEVERRIVSQLLTLMDG.KSRAHVIVMGATNRPNSIDPALRRFGRFDREI
Retrocopy PSIIFIDEIDSIAPNREKTHGEVERRIVSQLLTLMDGMKSRAHVIVMGATNRPNSIDPALRRFGRFDREI

Parental  DIGVPDEVGRLEVLRIHTKNMKLAEDVELEHISKDTHGYVGADLAALCTEAALQCIREKMDIIDLEDETI
          DIGVPDEVGRLEVLRIHTKNMKL..DV.LE...KDTHGYVGADLAALCTEAALQCIREKMDIIDLED.TI
Retrocopy DIGVPDEVGRLEVLRIHTKNMKLDADVNLEVVAKDTHGYVGADLAALCTEAALQCIREKMDIIDLEDDTI

Parental  DAEILNSMAVTNDHFKTALTTSNPSALRETVVEVPNVSWEDIGGLENVKRELQETVQYPVEHPEKFEKFG
          DAEILNSMAVTNDH.KTAL...NPSALRETVVEVPNVSW.DIGGL..VKRELQETVQYPVEHPE.FEKFG
Retrocopy DAEILNSMAVTNDHLKTALVGTNPSALRETVVEVPNVSWSDIGGLDGVKRELQETVQYPVEHPEMFEKFG

Parental  MSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVREIFDKARGSAPCVLFFD
          MSPSKGVLFYGPPGCGKTLLAKAIANECQANFIS.KGPELLTMWFGESEANVREIFDKAR.SAPCVLFFD
Retrocopy MSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQSAPCVLFFD

Parental  ELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDPALLRPGRLDQLIYIPL
          ELDSIA.QRG.SVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIID.ALLRPGRLDQLIYIPL
Retrocopy ELDSIAMQRGGSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIIDSALLRPGRLDQLIYIPL

Parental  PDVESRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADITEICQRACKYAIRENIEKDIEMERRRKDNP
          PD..SR.QIFKACLRKSP.AK.VDL.ALA..T.GFSGADITEICQRACKYAIRE.IEKDIE.ER..K...
Retrocopy PDEASRHQIFKACLRKSPLAKNVDLGALARFTKGFSGADITEICQRACKYAIREDIEKDIERERLGK---

Parental  EAMEEDEADEIAEIRAAHFEESMKYARRSVSDADIRKYQAFAQTLQQSRGFGSEFRFPDQ--PAAGAAAA
          EAME.D...E.AEI.AAHFEESMKYARRSVSD.DI.KY.AFAQTLQQSRGFG.EFRFP.Q..PA...AA.
Retrocopy EAMEVDDSGEVAEIKAAHFEESMKYARRSVSDRDITKYRAFAQTLQQSRGFGTEFRFPEQSKPAEASAAT

Parental  ADPFASAAAAAEDDDLYS
          A...A...AA.E.DDLY.
Retrocopy ANAYA---AADEEDDLYN

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_9 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9 ,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g020910	1 retrocopy	retro_sbic_10,