RetrogeneDB ID: retro_bdis_45

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:58274239..58275706(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G59160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G10560
• Aliases: None
• Description: None

Sequence

>retro_bdis_45
ATGGTCTCCGGCGCCGGCGAGCCGCCGGCGGCGCAGTCGAAGAAGGTGTGCGTGGTGGGCGGCGGGCTGGCGGGGCTGGC
GGCGGCGCGCGAGCTGCGGCGGGAGGGCCACGCCGTGACGGTGCTGGAGCAGAGCCACGACGTCGGCGGCCAGTGGCTCT
ACGACCCTCGCGCCTCCGCCGCCGACGCCGATAACGGGCCGCCAGTGCACAGCAGCGTCTACGCGTCGCTCCGGCTCGTC
GGCCCGCGGGAGATCGTGGGCTTCTCCGACTTCCAGTTCCGGCCCGTCCACGGCCGCGACGCGCGCCGCTTCCCGGGCCA
CCGCGAGGTCCACCGCTTCATTAAAGACTTCGTGGCCCAGTTCGGGCTCGCCGACGCCATCAAGCTCGACACCACGGTCA
CCCGCGTCGCCAGAGCCGCGTCTTCTTCTCCGACACCGGCGGAGAGCCAATGGGTTGTCACCTCCGTTCACGGCGGCGGC
GCCATGGATGACGAGGTGTTTGATGCTGTCGTGGTGGCCACGGGACACTTCACGAAGCCGAGGTTTCCGCGCATTGAAGG
CATGGAGGAGTGGGGTCTTCTCCGGCGCCGGCAGGGGCACAGCCACTGGTACCGGACGCCGAAGCCGTACCGCGGCGAGG
CGGTGGTCGTGGTCGGCTGCGGGGACAGCGGCAAGGACATCGCGCTCGACCTCCTCCGCGGCGGCGCCATGGCGGTGCAC
GTCTCCGCCGCCAGCCTCGACGGATCCATGTCGCCGGCCATGGCCAAGCTCCAGGCCAAGCACCACAACCTGCATCTCCA
TCCGCGGCTCGAGCGGCTTCAAGCCGCCGACGGCCGCGCCGTCTTCGCCGACGGGTCCAGCATCTTCGTCGACGCCGTGC
TCTACTGCACCGGCTACGCCTACTCGTTCCCCTTCCTCGACCTCGACGCTGCGGCGATCTCCGTCGACGAGGAAGACGAC
GGCGTGGGCACGCCGGTGCTGTTCGAGGGCGTGTTCCCGCCGTCGGCGTCCGTGGCGCCGTCGCTGTCCTTCGTCGGCAT
CCCGAGGACGGTCCTCGTGCCGCGGTCATTCGAGGCGCAGGCGAGATGGGTGGCGCAGATGCTCTCCGGACGCCGCAAGC
TGCCGCCGGAGGAGGAGATGTTGAGGAGGGCTTTGGAGTCGCAGGAGCGCCGCCGCCGACATCGAGCCGGGTTGGAGCCT
GTGGAGATCTTTGAGGATGGAGAGGAGTACTACCGGGACTTCCCGCCGGTGGAGAGCTGGAGGAAGGAGCTGGTCATGTC
CTCCATTGCTAGAAGGAGCCAGGACTTGGAGAGCTTCCGCGACCTCCCCGAAGAAGACGAATGCGAGACCGCCCCGAAGG
GCACCGGTGGCGACGACTTGGCGGCAGCTCAGGATCGACAAGGTCATCAAATTGTGGATGCTCAAGTTGCTCTGCCGGCC
ATGGACAAGCTCCTTCTGAACGTATAA

Alignment

ORF - retro_bdis_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.44 %
• Parental protein coverage: 62.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHSSMYASVRLISPRETTGFTDFPFATMDGRDNRRFPGHREVYLYLKDFCDAFGLMDAVRLN---TKVLR
          VHSS.YAS.RL..PRE..GF.DF.F....GRD.RRFPGHREV....KDF...FGL.DA..L....T.V.R
Retrocopy VHSSVYASLRLVGPREIVGFSDFQFRPVHGRDARRFPGHREVHRFIKDFVAQFGLADAIKLDTTVTRVAR

Parental  VAM---TPSRRQWTVRSVGLTDADDKKEEVFDAVVVATGHYSQPRFPTIQGMEKW---RGRQMHGHSYRE
          .A....TP...QW.V.SV....A.D...EVFDAVVVATGH...PRFP.I.GME.W...R.RQ.H.H.YR.
Retrocopy AASSSPTPAESQWVVTSVHGGGAMD--DEVFDAVVVATGHFTKPRFPRIEGMEEWGLLRRRQGHSHWYRT

Parental  AEPFRGQVVVVVGTGESGKDITMEL-RDVAKEVHIVARSME-DVTPGLSKVLAKYSTNLHLKLNLERL-C
          ..P.RG..VVVVG.G.SGKDI...L.R..A..VH..A.S......P...K..AK...NLHL...LERL..
Retrocopy PKPYRGEAVVVVGCGDSGKDIALDLLRGGAMAVHVSAASLDGSMSPAMAKLQAKHH-NLHLHPRLERLQA

Parental  EEGRVVFGDGSVVVADAVIYCTGYNYSFPFLDT-AGAVTID--DNRVGP--LFEHVFPPS--LAPSLSFV
          ..GR.VF.DGS....DAV.YCTGY.YSFPFLD..A.A...D..D..VG...LFE.VFPPS...APSLSFV
Retrocopy ADGRAVFADGSSIFVDAVLYCTGYAYSFPFLDLDAAAISVDEEDDGVGTPVLFEGVFPPSASVAPSLSFV

Parental  GIPRKVFAPRFFETQGRWVAQVLSGKRTLPTEEEMLRSVEEFYRAR
          GIPR.V..PR.FE.Q.RWVAQ.LSG.R.LP.EEEMLR...E....R
Retrocopy GIPRTVLVPRSFEAQARWVAQMLSGRRKLPPEEEMLRRALESQERR

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_45 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	BRADI3G10560	1 retrocopy	retro_bdis_45 ,