RetrogeneDB ID: retro_bdis_25

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:33602393..33603449(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G31440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G77460
• Aliases: None
• Description: None

Sequence

>retro_bdis_25
ATGGATCGATCGGTTGAAGGGGCAGCGGCGCAGTACTACTCCTCGGCGATGGGCCCGCTGGCGGGCCAGCTTGGCGAGTG
GCTGTGCCGGGCCGTGCAGCCCCCGGCACCGACGCCGTGCGGTTCCCCCGGCGGGCCGCCCGTCACGGCCCGGCGCGTCC
GGCTGCGGGACGGGCGCCACCTGGCCTACGAGGAGACCGGTGTGCCCCTGCACCGCGCGCGCTTCCGTGTCGTCTTCTCC
CACGGCTTCACCGGCTCCCGCCTCGACTCCCTCCGCGCCTCGCCGGAGGTGGCCGAGGAGCTAGGCGTCTACATGGTGGG
CTTCGACCGGGCCGGCTACGGCGAGAGCGACCCCAACCCGGCCCGCACCGTCGAGAGCGCGGCCCTGGACGTGGCCGACC
TCGCCGACGCGCTGGGCCTCGGCGACAAGTTCCACCTCGTGGGCTTCTCCCTGGGCTGCCACGCCGTCTGGGGCGCGCTC
CGCTACATCCCGCACCGCCTCGCCGGCGCCGCCATGCTGGCCCCCGTCGTCAACTACTGGTGGCCGGGGTTCCCGCCGGA
GCTCGCGGCCCAGGAGTACGGCAAGCAGGCCCGAGGTGACCAGTGGGCGCTCCGCGTGTCGCACCACGCCCCGGGCCTCC
TCCACTGGTGGATGGAGCAGAGCTGGCTGCCATTGCCGACCTCCACCGTGGCCTCCAACACGACGCACCTCCCCAACAAG
CGCGACGCCGAGGTCCGCCGGACGCTCGCCGCCGACGGGACGCTGAGGGCCAAGAGGGAGATGGCCACGCAGCAGGGGAT
CATGGAGTCTTACTACAGGGACATGGCGGTCATGTTCGGGAAGTGGGAGTTCGACCCCATGGCGCTGCCGGAGCCGGAGT
GCGAGGTGCACCTGTGGCAGGGCGACGAGGACGGGCTCGTGCCCGTTGTGCTGCAGCGCCATGTCGCCGGGAGCCTCCGG
TGGGTCAAGTACCACGAGCTCCCCGGCACCGGACACTTCCTCTCCGCCGTTCCCGGGCTCGGCGACACCGTTCTCCGGAC
ACTCTTCAGTAATTGA

Alignment

ORF - retro_bdis_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.45 %
• Parental protein coverage: 95.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAGSSSSSPMGPLMGALGRWIYRAVKPPPPPRICGAPGGPPVTAPRVTLRDGRHLAYAESGVRKEDARF
          G.A....SS.MGPL.G.LG.W..RAV.PP.P...CG.PGGPPVTA.RV.LRDGRHLAY.E.GV....ARF
Retrocopy GAAAQYYSSAMGPLAGQLGEWLCRAVQPPAPTP-CGSPGGPPVTARRVRLRDGRHLAYEETGVPLHRARF

Parental  KVVFSHGFSGSRLDTLRASPEVAEELGVYMVGFDRAGYGESDPNPNRSVKSAALDVEELADALGLGSKFY
          .VVFSHGF.GSRLD.LRASPEVAEELGVYMVGFDRAGYGESDPNP.R.V.SAALDV..LADALGLG.KF.
Retrocopy RVVFSHGFTGSRLDSLRASPEVAEELGVYMVGFDRAGYGESDPNPARTVESAALDVADLADALGLGDKFH

Parental  VIGISLGCHAVWGALKYIPDRIAGAAMMAPVVNYWWPGFPADLAAEVYNKQEVGDQWALRVSHHAPGILH
          ..G.SLGCHAVWGAL.YIP.R.AGAAM.APVVNYWWPGFP..LAA..Y.KQ..GDQWALRVSHHAPG.LH
Retrocopy LVGFSLGCHAVWGALRYIPHRLAGAAMLAPVVNYWWPGFPPELAAQEYGKQARGDQWALRVSHHAPGLLH

Parental  WWMEQSW--LPTSTVIAGTTPLPNKRDAEIRSNMKADGTFQKKMELATQQGIHESYYRDMMVMFGKWEFD
          WWMEQSW..LPTSTV...TT.LPNKRDAE.R....ADGT...K.E.ATQQGI.ESYYRDM.VMFGKWEFD
Retrocopy WWMEQSWLPLPTSTVASNTTHLPNKRDAEVRRTLAADGTLRAKREMATQQGIMESYYRDMAVMFGKWEFD

Parental  PMSLPKPPCPVHIWQGDEDGLVPVVLQRHLASQLSWVNYHELPGVGHFMSPVPGLGDTVLRTLF
          PM.LP.P.C.VH.WQGDEDGLVPVVLQRH.A..L.WV.YHELPG.GHF.S.VPGLGDTVLRTLF
Retrocopy PMALPEPECEVHLWQGDEDGLVPVVLQRHVAGSLRWVKYHELPGTGHFLSAVPGLGDTVLRTLF

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_25 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	BRADI1G77460	1 retrocopy	retro_bdis_25 ,