RetrogeneDB ID: retro_bdis_28

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:74103579..74105673(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G78010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G13740
• Aliases: None
• Description: None

Sequence

>retro_bdis_28
ATGGACGTCCCGGGCGGCGGGCACCAGATGGACGGCTACTTCTCAGGCCGGACCAAGATCCGGTCCCGCTCCATCCGCAT
CGCGGCCGCCGGGGTCATCAACCGCTCCGAACGCCTCAAGAACATCGGCCGGGTCTTCCAGGAAGACCTCAAGAACATCT
CCCTCAAGATCTACGACCCGCAGGACGCGTTCCTGATGCGGATGAACCGGCTGTTCCTCTTCGCCTGCATCGTCTCCGTC
GCCGTCGACCCGCTCTTCTTCTACCTCCCCGTCGTCAACGAGAACCAGAACAACACCTGCATCGGCTTCGACCGCGCCCT
GGCCACCTTCGCCACCGCCGTCCGCACCGCCGTCGACGCCTTCTACCTGGCCCGGATCGCGCTGCAGTTCCGCACCGCCT
TCATCGCCCCTTCCTCCCGCGTCTTCGGCCGCGGCGAGCTCGTCGTCGACTCCGCCGCCATCGCGCGCCGCTACGTGCGC
CGCTTCTTCGTCTTCGACCTCCTCTCCGTGCTGCCCTTGCCGCAGCTCCAGATCATCAAGTTCTTGCTGCGGCACAAGGG
GCAGGACCTGCTGCCCATCAAGACGGCGCTCTTCTTCATCGTGCTCGTCCAGTACGTGCCGCGGCTCGTCAGGATCTACC
CGATCACCTCCGAGCTGAAGCGGACCACGGGGGTCTTCGCCGAGACGGCTTTCGCCGGCGCCGCGTTCTACCTGCTGCTG
TACATGCTGGCGTCGCACATGGTGGGCGCGTTTTGGTACTTGCTGGCCATCGAGCGGCTGGACGACTGCTGGAGGGAGAA
GTGCACGGGGCTCAAGTTCCACCAGTGCAAGACTTACATGTACTGTGGTGGCGGGATACTGGGCCAGCCCGGGTTCGTCG
AGTGGAGGACCATGATCCGGCAGGTGCTGGCCCAGGAATGCGCGCCGATCGACGGCGGCGGCACCGGGTTCAACTACGGG
TTGTACACCACTGCCATCACCTCTGGGGTCACGTACACGCCTAACCTCTTTGCCAGGATCCTCTTCTGCCTCTGGTGGGG
GCTCCAGAACCTCAGCACCGTTGGGCAGGGGCTTGACCAGACGACGCACTACAAAGGGGAAGCGTTGTTTGCCATCCTGC
TGGCGCTCTTCGGGCTCATCCTCATGGCGCTGCTCATCGGCAACATGCAGACGTACCTCCAGTCGATGACGCTGCGGATG
GAGGAGATGCGGCTCAAGCGCCGCGACTCGGAACAATGGATGCACCACCGCCTGCTCCCCGACGACCTCCGCGACAGGGT
CTGGCGCCACAACCAGTACAAGTGGCTCGAGACGCGTGGCGTCGACGAGGACGGGCTCGTCAGCTGCCTGCCCAAGGACA
TCCGGAGAGACGTGAAGCGCCACCTCTGCCTCCGCCTCGTGCGCCGCGTGCCGCTGTTCGCGAACATGGACGAGCGACTC
CTCGACGCCATCTGCGAGCGGCTCAAGCCCAGCCTATGCACGGAGGCGACATACGTGGTGCGCGAAGGGGACCCGGTCGA
CGAGATGTTGTTCATCATCCGTGGCCGGCTCGAGAGCTCGACCACCGACGGCGGCCGGACCGGGTTCTTCAACAGGGGTT
TGTTGAAAGAAGGGGACTTCTGTGGGGAAGAGCTGCTGACGTGGGCGCTGGACCCCAAGGCGTCGGCGAACCTGCCGCTG
TCGACGCGCACCGTGAAGGCGATATCCGAGGTGGAAGGCTTCGCGCTGCACGCCGACGAGCTCAAGTTCGTGGCCGGGCA
GTTCAGGCGGCTGCACAGCAAGCAGCTGCAGCAGACCTTCAGGTTCTACTCGCAGCAGTGGCGCACCTGGGCGTCCTGCT
TCATCCAGGCGGCGTGGCGGAGGTTCCAGAAAAGGAGGGCGGTGGAGCAGCGGCGGAGGGAGGAGGACGAGATGTACATG
GCGGCGGAGGAGGTGGCGGCGTCGTCGAGCAGCCAGATGAAGACCACGTTCCTGGTGTCCAGGTTCGCCAAGAAGGCCAT
GCGCGGCGTGCAGCGCCAGCGGTCGCTCAAGGCCGAGAGCCTCATCATACTGCCCAAGCCGCCCGAGCCAGACTTCGGCA
AAATGGACTACTGA

Alignment

ORF - retro_bdis_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.56 %
• Parental protein coverage: 82.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFQEDLKNTSRKIFDPQDRMLVRLNRSFLISCILSIAIDPLFFYTPRITDSMHGINICIGIDRELAVFTA
          VFQEDLKN.S.KI.DPQD..L.R.NR.FL..CI.S.A.DPLFFY.P.........N.CIG.DR.LA.F..
Retrocopy VFQEDLKNISLKIYDPQDAFLMRMNRLFLFACIVSVAVDPLFFYLPVVNENQN--NTCIGFDRALATFAT

Parental  VFRSVVDLFFVARIVLQFRTAFIAPSSRVFGRGELVIDTMEIAKRYFRRFFIADVLSIVPLPQLVVWLFT
          ..R..VD.F..ARI.LQFRTAFIAPSSRVFGRGELV.D...IA.RY.RRFF..D.LS..PLPQL....F.
Retrocopy AVRTAVDAFYLARIALQFRTAFIAPSSRVFGRGELVVDSAAIARRYVRRFFVFDLLSVLPLPQLQIIKFL

Parental  KRVRGTAVLATKDNLVLVILLQYVPRLARIYPLSTELKRTSGVFAETALAGAAYYLLWYMLASHIVGAFW
          .R..G...L..K..L....L.QYVPRL.RIYP...ELKRT.GVFAETA.AGAA.YLL.YMLASH.VGAFW
Retrocopy LRHKGQDLLPIKTALFFIVLVQYVPRLVRIYPITSELKRTTGVFAETAFAGAAFYLLLYMLASHMVGAFW

Parental  YMLSIERLSDCWRNACD--EFLGCNRIYMYCGRNLEEKEDPGFQEWITITRQVINETCEPQKDGEMPFNY
          Y.L.IERL.DCWR..C....F..C...YMYCG........PGF.EW.T..RQV....C.P...G...FNY
Retrocopy YLLAIERLDDCWREKCTGLKFHQC-KTYMYCGGGILGQ--PGFVEWRTMIRQVLAQECAPIDGGGTGFNY

Parental  GIYSSAVQSNVIGSLDVTSKILFCLWWGLANLSTLGQGL-KTTIYTGEALFSITLATFGLILMAMLIGNI
          G.Y..A..S.V.........ILFCLWWGL.NLST.GQGL..TT.Y.GEALF.I.LA.FGLILMA.LIGN.
Retrocopy GLYTTAITSGVTYTPNLFARILFCLWWGLQNLSTVGQGLDQTTHYKGEALFAILLALFGLILMALLIGNM

Parental  QTYLQSLTVRLEEMRVKRRDSEQWMHHRLLPQELRERVRRYDQYKWINTRGVDEEVLIQNLPKDLRRDIK
          QTYLQS.T.R.EEMR.KRRDSEQWMHHRLLP..LR.RV.R..QYKW..TRGVDE..L...LPKD.RRD.K
Retrocopy QTYLQSMTLRMEEMRLKRRDSEQWMHHRLLPDDLRDRVWRHNQYKWLETRGVDEDGLVSCLPKDIRRDVK

Parental  RHLCLGLVRRVPLFANMDERLLDAICERLKPSLYTEKTHIIREGDPVDQMLFIIRGLLESITTDGGRSGF
          RHLCL.LVRRVPLFANMDERLLDAICERLKPSL.TE.T...REGDPVD.MLFIIRG.LES.TTDGGR.GF
Retrocopy RHLCLRLVRRVPLFANMDERLLDAICERLKPSLCTEATYVVREGDPVDEMLFIIRGRLESSTTDGGRTGF

Parental  YNRSLLQEGAFCGEELLTWALDPKSGVSLPSSTRTVMALSEVESFALHAEELKFVAGQFRRMHSKQVQHT
          .NR.LL.EG.FCGEELLTWALDPK....LP.STRTV.A.SEVE.FALHA.ELKFVAGQFRR.HSKQ.Q.T
Retrocopy FNRGLLKEGDFCGEELLTWALDPKASANLPLSTRTVKAISEVEGFALHADELKFVAGQFRRLHSKQLQQT

Parental  FRFYSQQWRTWAATYIQAAWRRHLKRKAAELRRREEEE
          FRFYSQQWRTWA...IQAAWRR..KR.A.E.RRREE.E
Retrocopy FRFYSQQWRTWASCFIQAAWRRFQKRRAVEQRRREEDE

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_28 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G13740	1 retrocopy	retro_bdis_28 ,