RetrogeneDB ID: retro_bdis_43

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:45389159..45390764(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G46870
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G61420
• Aliases: None
• Description: None

Sequence

>retro_bdis_43
ATGGCGGTAGCGGCGTTGGGGCTGGTCGTGGTGGCTGTGGCGGCGGTGTTGGCGACATGGCTGTGGGCGGCGGCGTTTCA
CCTGGTGTGGCGGCCCTACGCCGTCGGCAAGGCGTTCCGGCGGCAGGGGATCCGCGGGCCGGCGTACCGCTTCTTCGTGG
GCAACAACGAGGAGACCAAGGCGATGCGTGTGGCGACAGCCGGCGACGTCCTGGACCGGGCCTCCCACGACATCGTGCCA
CGCGTGCTGCCGCAGTACAAGGCCTGGATGTCCTCCTACGGCAAGGTGTTCCTGTCCTGGACCGGGTTCACGCCGTCGCT
GTGCGTGGGCGACCACGACATGGCGAAGCAGATCCTGTCGAACCGGGCCGGGCTGTTCGGCAAGTCCGACCCGGGCCCCA
ACATCATGGCGCTGCTGGGCAAAGGGCTCGTGTTCACCGACGGCGAAGACTGGGCGCGCCACCGCCGCGTCGTGCACCCG
GCCTTCGCCATGGACAAGCTCAAGTCGATGGCGAGGACCATGGAGGACTGCGCCGGGGAGGTGGTGCGCGCGTGGGAGGC
GAGGGCTGAGGTCGTTGCCGGTGGCGGCGTGGGTGTGGCCACGGTGGAAGTCGGGCAGCAGTTCGTGGAGCTGACTGCCG
ACGTGATCTCGCACACGGCGTTCGGGAGCAGCTACAAGGAAGGGAAGGAGGTGTTTCTGGCGCAGCGGGAGCTGCAGGGG
ATTGCTTTCGCCACCATTAACAATGTTCGTGTCCGGGGCCTCGGGAACCTCCCCACCAAGATGAATGTCCGGCGGTGGCA
GCTGGAGCGCAAGGTCCGCGGCACGCTCATGGCGATCATCGACGGCCGGCTGGCTGCCGCCGCCAAGGAAGGCGCCACGG
GCTACGGCAGCGACCTCCTCGGCCTCATGCTCGAGGCCAACACCAACGCCTCCTCCGGTACTCACAAGGGAGGAGCTGCC
ATGATGAGCATGGACGAGATCATCGACGAGTGCAAGACCTTCTTCTTCGCGGGCCACGACACCACCTCGCACCTCCTCAC
CTGGGCCGTCTTCCTCCTCGGCACGCACCGGGACTGGCAGTCCAAGCTCCGCGACGAAGTCCTCAAAGAGTGCTCCACGG
GGACGCCGCTCCACGGGGACGCGCTCAACAAGCTGAAGCTCACAACGATGGTGCTCTACGAGACGCTGCGGCTGTACGGG
GCCGTGATCATGATGGCGCGGACGGCGACGGCGGACACGGAGCTCGTTGGCGGGGCGATGAGCGTGAAGGTTCCTAAAGG
AACGATGACGATGATCCCGATCGCGATCATGCACCGGGACGAGGCCGTGTGGGGAGCGGACGCCGGGGAGTTTAACCCGC
TCCGGTTCAAGGACGGCGTCGGGAAGGCGGCCAAGCACCCGAGCGCGATGCTGGCGTTCTCGTTCGGCCCCAGGGCGTGC
ATCGGGCAGGATTTTGCGATGCTGGAAGCCAAGGCCACGCTCGCTGTTATCCTTCGTAAGTTCGAGTTCGAGGTCGCGCC
CGAGTACGTGCACGCGCCGGCTGAGTTCCTCACGCTGCAGCCCAAGACCGGCCTCCCCGTCCGGCTCAGGCTCTTGGATC
GCTAG

Alignment

ORF - retro_bdis_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.37 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPVVLVVLAALLALATSRLWSYAVVRLAWRPRAMARRFREQGVHGPSYRFLTGSNEDVRRMKAEADGV
          MA......V..A..A.....LW..A...L.WRP.A....FR.QG..GP.YRF..G.NE....M.....G.
Retrocopy MAVAALGLVVVAVAAVLATWLWA-AAFHLVWRPYAVGKAFRRQGIRGPAYRFFVGNNEETKAMRVATAGD

Parental  ELDLRDHDYLPRIVPHLVKWKHQYGSPYVYWFGPQPRICIFDYELVKQVLANKYGHFIKNDTHPTILAMI
          .LD...HD..PR..P....W...YG.....W.G..P..C..D....KQ.L.N..G.F.K.D..P.I.A..
Retrocopy VLDRASHDIVPRVLPQYKAWMSSYGKVFLSWTGFTPSLCVGDHDMAKQILSNRAGLFGKSDPGPNIMALL

Parental  GKGLVLVDGSDWVRHRRVVNPAFAMDKLKMMTGTMVSCAECLIKKWEDQATYSKSREIEVEFSKESQE--
          GKGLV..DG.DW.RHRRVV.PAFAMDKLK.M..TM..CA......WE..A.........V......Q...
Retrocopy GKGLVFTDGEDWARHRRVVHPAFAMDKLKSMARTMEDCAGEVVRAWEARAEVVAGGGVGVATVEVGQQFV

Parental  -LTADVISCTAFGSSFMEGKEVFHAQKQLQAITVATMLNVQIPGFKYLPTKQNRCKWMLENKLKNTLSRI
          .LTADVIS.TAFGSS..EGKEVF.AQ..LQ.I..AT..NV...G...LPTK.N...W.LE.K...TL..I
Retrocopy ELTADVISHTAFGSSYKEGKEVFLAQRELQGIAFATINNVRVRGLGNLPTKMNVRRWQLERKVRGTLMAI

Parental  IQCRV--ASKE--SGFGNDLLGVMLEACFTKEQGGKK-GEQILSVDEIIDECKTFFFAGHETTSHLLTWT
          I..R...A.KE...G.G.DLLG.MLEA......G..K.G....S.DEIIDECKTFFFAGH.TTSHLLTW.
Retrocopy IDGRLAAAAKEGATGYGSDLLGLMLEANTNASSGTHKGGAAMMSMDEIIDECKTFFFAGHDTTSHLLTWA

Parental  MFLLSVYPEWQERLREEVLRECGKGNP-NADMLSKLKEMTMVLLETLRLYSPIIFMLRKPISDMKL--GN
          .FLL.....WQ..LR.EVL.EC..G.P...D.L.KLK..TMVL.ETLRLY...I.M.R....D..L..G.
Retrocopy VFLLGTHRDWQSKLRDEVLKECSTGTPLHGDALNKLKLTTMVLYETLRLYGAVIMMARTATADTELVGGA

Parental  LNLPKGSAIVIPIP--MLHRDKEVWGDRANEFDPMRFENGITKAAKIPHALLGFSIGPRSCIGQNFAMLE
          ............IP....HRD..VWG..A.EF.P.RF..G..KAAK.P.A.L.FS.GPR.CIGQ.FAMLE
Retrocopy MSVKVPKGTMTMIPIAIMHRDEAVWGADAGEFNPLRFKDGVGKAAKHPSAMLAFSFGPRACIGQDFAMLE

Parental  AKSVLAMILQKFSFTLSPKYVHAPADLLTLQPKSGLPIILSPLD
          AK..LA.IL.KF.F...P.YVHAPA..LTLQPK.GLP..L..LD
Retrocopy AKATLAVILRKFEFEVAPEYVHAPAEFLTLQPKTGLPVRLRLLD

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_43 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	BRADI1G61420	1 retrocopy	retro_bdis_43 ,