RetrogeneDB ID: retro_bdis_17

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:20698106..20699492(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G21550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G04491
• Aliases: None
• Description: None

Sequence

>retro_bdis_17
ATGGGCAGGCTGCAGCTGCTGCTCTCCTTCCTCCTGGTTACCGCCGCAAACTGCCGCGGCAGCCGGGCGGCGAGGAACAG
CATAACGCACGTGAAGGGCTTCGACGGCGCGCTCCCCTTCTACCTGGAGACAGGGTACGTGGAAGTGGACTCCACCCACG
GCGCGGAGCTCTTCTACTACTTCATCCAGTCAGAGCGCAGCCCGAGCACGGACCCGCTGATCCTCTGGATCACGGGCGGG
CCGGGCTGCTCCGCGCTGTCGGGCCTGCTCTTCGAGATCGGCCCGCTCAAGTTCGACGTCGCCGGCTACACGGGGGAAGG
CTTCCCGCGGCTCCTCTACTTTGAGGACTCATGGACCAAAGTGAGCAACGTCATCTTCCTCGACGCCCCCGTGGGCACGG
GCTTCTCCTACGCCCGCGAGGAGCAAGGCCTCAACGTCAGCCTGACTGGCACGGGCGGCCAGCTCCGTGTGTTCCTTGAG
AAATGGCTGGACCAGCACCCGGAGTTCAAGTCCAACCCGCTGTACATCGGCGGGGACTCCTACTCCGGGTACACGGTGCC
CGTCACGGCTCTCGACATCGCCGACCACCCGGAGAGCGGGCTGAATCTTAAAGGGTACCTGGTCGGCAACGCGGCCACGG
AGGACAGGTATGACACGGGCGGCAAGGTGCCGTTCATGCACGGGATGGGGCTGATCTCCGACGAGATGTACGCGGCGGCG
CAGGGCAGCTGCGCCGGGGACTTCGTCACCACGCCACGGAACACGCAGTGCGCCAACGCGCTGCAGGCCATCAACCTGGC
CACTTTCGCCGTCAACCCCGTCCACATCCTCGAGCCCATGTGCGGCTTCGCGCTCCGGTCCCCCGCCGACACGGTCTTCC
CGAGGAGGACGGCGGCGAGGCTTCTGGTCCAGGAGAACGACATGTTGGGGTTGCCGGTGGAGTGCCGGGACAACGGGTAC
AGGTTGTCTTATACCTGGGCGGACGACCCGGAGGTGAGGGAGACGCTGGGGATCAAGGAAGGGACGATCGGGGCGTGGAG
CCGGTGCACGACGCTGAGCCACTTCCGGCACGACCTGGCGAGCACGGTGCCGCACCACAGGGAGCTTACAACGCGCGGGT
ACAGGGCGCTGGTGTACAACGGCGACCACGACATGGACATGACGTTCGTGGGCACGCAGCAGTGGATCCGGGCGCTCGGG
TACGGCGTGGTGGCGCCATGGCGGCCCTGGTACGCCAACCGGCAGGTGGCCGGGTTCGCCACGGAGTACGAACACAACCT
CACCTTCGCCACCGTCAAGGGAGGCGGCCACACCGCGCCCGAGTACAGGCCCAAGGAGTGCCTCGCCATGCTCGACAGAT
GGACCTCGCCTGCCGGCAGGCTCTGA

Alignment

ORF - retro_bdis_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.7 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITHLPGFNGPLPFQLQTGYVEVDGINGVRLFYYFIRSERKPEEDPVILWLTGGPGCSALSGLVYEIGPLS
          ITH..GF.G.LPF.L.TGYVEVD...G..LFYYFI.SER.P..DP.ILW.TGGPGCSALSGL..EIGPL.
Retrocopy ITHVKGFDGALPFYLETGYVEVDSTHGAELFYYFIQSERSPSTDPLILWITGGPGCSALSGLLFEIGPLK

Parental  FDSHAYV-DGIPKLLYRADSWTKVSNIIFLDSPVGTGFSYSKTDQGCKSGDTTAVNQIVIFLKKWFDEHP
          FD...Y...G.P.LLY..DSWTKVSN.IFLD.PVGTGFSY....QG.....T....Q...FL.KW.D.HP
Retrocopy FDVAGYTGEGFPRLLYFEDSWTKVSNVIFLDAPVGTGFSYAREEQGLNVSLTGTGGQLRVFLEKWLDQHP

Parental  EFMSNPLYIAGDSYSGLLVPAITLELAKGIEDASGPLLNLKGYLVGNPVTDNNFDDPAKIPFAHGMGLIS
          EF.SNPLYI.GDSYSG..VP...L..A...E......LNLKGYLVGN..T....D...K.PF.HGMGLIS
Retrocopy EFKSNPLYIGGDSYSGYTVPVTALDIADHPESG----LNLKGYLVGNAATEDRYDTGGKVPFMHGMGLIS

Parental  DEIYQVYKESC-GVQENSHQRDKCTNSLDVIDKCVKDICTNHILEPLCSFA
          DE.Y.....SC.G..........C.N.L..I..........HILEP.C.FA
Retrocopy DEMYAAAQGSCAGDFVTTPRNTQCANALQAINLATFAVNPVHILEPMCGFA

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_17 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	BRADI4G04491	1 retrocopy	retro_bdis_17 ,