RetrogeneDB ID: retro_bdis_52

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:10896446..10897410(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI5G03800
• Aliases: None
• Description: None

Sequence

>retro_bdis_52
GAGTCACACTCGGTGGTTCAGTGCACGCCGGACATGCAGGTTCAGCGCGCTCATCTTGAGGGGCACGGAGTCATCTCCTG
GCTTGATGACGCACGGCGTGGTGCGGACAAGGAGGCCATCGCCGACGCCATTGCTTCGCACTTCGGGATTCGCCGTTCCG
ACATGCGTGCGGCGAACCACCGCGATGGCTTCTTCCTCACCTTCGAGCATCGTCACCACCAGGAGACCGTGGAGGCCGCG
TGCTCCTTCACTGCCAGCTTCGGGGTCATCAACCTGCGACCGTGGCGTGCCAGCGCCCACGCCTACCACGTCGCCTTGCG
CCACCACATCCACATCTCGCTGGAAAACGTGCCCCTTGAGGCATGGAACGAGGTCACCGTGCGCTCCATCATCGGTGACG
CTTGTGAGCTGCACTACTTCGACTCGCGCTCCCTGCGTCACGAGGACGCGGTCATCCTCGGCTGTTGGGCGTGGACGACG
AACCCGTCCAAGATCCCTCTGGTGCACTGGCTGACGCTCACTGATGCGCCAAAATCCTCCACTACGCCGGCGACCGAGCG
TCCTGGGCTTCAGCACCGCATCCTCGTGCACCTGGGGATCCACGAGGACCACACGAAGACGAAGGTGGAAACGAACGAGT
TTGATTGGACTTATGGCGAGATTGACGGCCAGGGCTCGCGACGCCAACGCCCATGCTCTCCAGCATGTTCTGGGCGTTCC
AACCGCAGGCATGACGATGACGACGACGACCAGCGCCGTGGACGCATGGACGACCGGAACTCCGGCTGGCGCGCCTTCTT
CCGCGGCCGCTCACGTGCGCCGCGGGATGATGGCCGGGGTGGCCACGATGGTCGCCGCGCCCGTGATGATGACCAAGACC
GGCAGCGTGGCCGTGACGGCCGGCGCATTCAGGAGGACCGCCGTCGCTGCCGTGGGGACCGCTCGCCCTCCGTCTTGCGC
CCTC

Alignment

ORF - retro_bdis_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.02 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRHKISSAFNASPVQRAHLEGHGVIAWLDDARCGVDKEAIADTIASHFGIRRSDMRAANHRDSFFLTFEH
          ..H..........VQRAHLEGHGVI.WLDDAR.G.DKEAIAD.IASHFGIRRSDMRAANHRD.FFLTFEH
Retrocopy ESHSVVQCTPDMQVQRAHLEGHGVISWLDDARRGADKEAIADAIASHFGIRRSDMRAANHRDGFFLTFEH

Parental  RHHRETVVAVCSFTASFGVINLRPWRASAHADHVALRHNVHISLENVPLEAWNEVTVRSIIGDACELHYF
          RHH.ETV.A.CSFTASFGVINLRPWRASAHA.HVALRH..HISLENVPLEAWNEVTVRSIIGDACELHYF
Retrocopy RHHQETVEAACSFTASFGVINLRPWRASAHAYHVALRHHIHISLENVPLEAWNEVTVRSIIGDACELHYF

Parental  DSRSLRHEDAVILGCWVWTTNPSKIPLVHWLTLTDAPRSSTTPATERPGLQHRILVHLGIHEDHTKTKVE
          DSRSLRHEDAVILGCW.WTTNPSKIPLVHWLTLTDAP.SSTTPATERPGLQHRILVHLGIHEDHTKTKVE
Retrocopy DSRSLRHEDAVILGCWAWTTNPSKIPLVHWLTLTDAPKSSTTPATERPGLQHRILVHLGIHEDHTKTKVE

Parental  TNEFDWTYGEIDGQGSRRQRPRSPARSGCSNRRHDD-ATTTSAVDAWTTGTPAGAPSSAAAHVRRGMMAG
          TNEFDWTYGEIDGQGSRRQRP.SPA.SG.SNRRHDD..TTTSAVDAWTTGTPAGAPSSAAAHVRRGMMAG
Retrocopy TNEFDWTYGEIDGQGSRRQRPCSPACSGRSNRRHDD>TTTTSAVDAWTTGTPAGAPSSAAAHVRRGMMAG

Parental  VATMVAAPVMMTKTGSVAVTAGAVEMPAASRSAEVAPACDAL
          VATMVAAPVMMTKTGSVAVTAGA....A........P...AL
Retrocopy VATMVAAPVMMTKTGSVAVTAGAFRRTAVAAVGTARPPSCAL

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_52 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI5G03800	2 retrocopies	retro_bdis_52 , retro_bdis_55,