RetrogeneDB ID: retro_bdis_57

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:36320681..36322178(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G39400
• Aliases: None
• Description: None

Sequence

>retro_bdis_57
GACAAGTCCGGCGCGAGGTACTAGAGAGAAAGCTGGGACGCGCTGCGGAGGAGCATAACCGGGCTGGTGAACAAGGCCAC
GGCAGCCAACATCCGGCACGTGCTTCCCGAGCTGCTCGCCGAGAACCTCGTCTGCGGGCGCGGTCTGCTGTGCCGCGCGC
TCATCAAGTCGCAGGCAGCCTGCCCGGCCTTCACCGACGTGTTTGCGGCGCTCGCTGCCGTTGTCAACTCGAAGCTGCCC
AGCGTCGGCCGCCTCCTCCTGGTCCGCCTCGCGATCCGCATCAGGCACTCCTTGCACAGCAACGACAAGCCCCAGCTGGT
GGCCGCGGCGAGGTTCGTCGCCCACCTCGTGAACCAGGGCGTGGCGCACGAGCTGCTGGCCCTGGAGATCCTCGAGACGC
TGCTCGCCAGGCCCACGGACGGCAGCGTGGAGGTGGCCGTGGGGGTTGTCAGGGAGTGCGGCGCCACTCTGCGCGACGCG
TGCCCCCGTTTGCTCGACGCCGTGTTCGACGCCCTCATGAGCATCCTCCGCGACGGCAACATGGTCGACAGGCGCCGCAC
CGAGTTCATGATCGAGGGACTGTTGGCCGTCCGGAAGGCCCAGTTCCGGGCGCACCCTTCCGTCCGGCCGGAGCTAGACC
TTGTCGAGACGGAGGACCAACTGACGCACCAAGTTGAGATCTCCAGCCGAGGTCTCGACCCCGAGAGCCACCTCGATGTG
TTCAGCTTCAGCGCCACGTTCCTTCAGGACGAGGCTGCCTACGAGGACCTCAAAAGAAGCATGCTTGGTCTTGGAGGCGA
CCTTTCTTCTTCTGAAGATGAAGATGACGCACAAGTCTGCAGCAGCGACGAGCGAGACATGGAGGAGGAGGTGATGATCA
AGGACGAGACCGCGACCGATCTGGTCGGCCTCCAGAGGACGATATACCTGACGATAATGTCAGCCGTCGGCTTCGAGGAA
GCCGGGCACAAGCTGATGTCGGTCGTGAGGCCCGGCCAGGAGTCCGAGCTGTGCGCCATGCTCATCGAGTGCTGCCGCCA
GGAGAGGACATACACCCGCTACTACGGCCTGCTCGCGCAGAGGCTCTGCGGCGTCCACCACAGGGCGTACCAGGCCGGCT
TCGAGGCCTGCTTCTCGCGGCTCTACGCGAACACGCACCGGATGGGCACCGACGAGCTGCGAGGCAGCGCCAGGCTCTAC
GCGCACCTGCTGGCCACGGACGCCGTCTCGTGGCGCCGCGTGCTGGCCGGCTGCGTCAGGCTGACGGAGGAGGACACCAC
GTCTTCCTCGCACATATTCATCAAGTTGCTCTTCCAGGAGCTGTCGGAGCAGCTCGGGGTACCGCTGCTCAGCCGGAGGT
TGAACGACCAAGACCCCGCGGTCCGGGATGCCCTTTTCCCCGCTGACTCTGTCCGGAATACTCGATTCGCCGTCAACTTC
TTCACGGCGATTGGTCTGGCAGGTGTCACACAATCAGCCAGGGACTGTCTGGTTAAC

Alignment

ORF - retro_bdis_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.35 %
• Parental protein coverage: 64.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKSSPEYQRLTWDALKKSINGLVNKVNATNIKNLVPELLAENLVRGRGLFCQSCIKSQMASPGFTDVFAA
          DKS...Y.R..WDAL..SI.GLVNK..A.NI....PELLAENLV.GRGL.C...IKSQ.A.P.FTDVFAA
Retrocopy DKSGARY*RESWDALRRSITGLVNKATAANIRHVLPELLAENLVCGRGLLCRALIKSQAACPAFTDVFAA

Parental  LVAVVNTKFPEIGRLLLVRVMLQLKRAYKRNDKPQLLAATKFVAHLVNQVVVHEVVALELLTVLLADPTD
          L.AVVN.K.P..GRLLLVR...........NDKPQL.AA..FVAHLVNQ.V.HE..ALE.L..LLA.PTD
Retrocopy LAAVVNSKLPSVGRLLLVRLAIRIRHSLHSNDKPQLVAAARFVAHLVNQGVAHELLALEILETLLARPTD

Parental  DSVEVAVGFVKECGAILQDLTPQGLHAMFERFRGILHEGEI--DKRVQFLIEGLFAIRKAKFQGFPAIRP
          .SVEVAVG.V.ECGA.L.D..P..L.A.F.....IL..G......R..F.IEGL.A.RKA.F...P..RP
Retrocopy GSVEVAVGVVRECGATLRDACPRLLDAVFDALMSILRDGNMVDRRRTEFMIEGLLAVRKAQFRAHPSVRP

Parental  ELDLVEQEDQCTHDISLETE-LDPETNLNVFRLNPNFAEDEKAYENLKKSILGDEMDEDEEGSDDASDDE
          ELDLVE.EDQ.TH........LDPE..L.VF.....F..DE.AYE.LK.S.LG.....D...S.D..DD.
Retrocopy ELDLVETEDQLTHQVEISSRGLDPESHLDVFSFSATFLQDEAAYEDLKRSMLG--LGGDLSSSED-EDDA

Parental  DEEESDDEEDEEQMEIRDKTETNLINLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELNIMLLECCS
          ....SD....EE...I.D.T.T.L..L.RTIYLTIMS.V.FEEAGHKL......PGQE.EL..ML.ECC.
Retrocopy QVCSSDERDMEEEVMIKDETATDLVGLQRTIYLTIMSAVGFEEAGHKLMSV-VRPGQESELCAMLIECCR

Parental  QERTYLRYYGLLGQRFCMI-NKVFQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTDALPW-HVLA
          QERTY.RYYGLL.QR.C.......Q..FE.CF...Y...HR..T..LR..A...AHLL.TDA..W..VLA
Retrocopy QERTYTRYYGLLAQRLCGVHHRAYQAGFEACFSRLYANTHRMGTDELRGSARLYAHLLATDAVSWRRVLA

Parental  -YIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLNDPNMQDSFESVFPRDHPKNTRFSINFFTSIG
          ...RLTEEDTTSSS.IFIK.LFQELSE.LG..LL..RLND..........FP.D...NTRF..NFFT.IG
Retrocopy GCVRLTEEDTTSSSHIFIKLLFQELSEQLGVPLLSRRLNDQDPAVR-DALFPADSVRNTRFAVNFFTAIG

Parental  LGGITESLREYLKN
          L.G.T.S.R..L.N
Retrocopy LAGVTQSARDCLVN

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_57 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G39400	1 retrocopy	retro_bdis_57 ,
Medicago truncatula	MTR_3g434840	1 retrocopy	retro_mtru_18,
Sorghum bicolor	Sb03g029810	1 retrocopy	retro_sbic_32,
Arabidopsis lyrata	scaffold_202963.1	1 retrocopy	retro_alyr_10,
Solanum lycopersicum	Solyc04g079920.2	1 retrocopy	retro_slyc_47,