RetrogeneDB ID: retro_bdis_21

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:32887243..32887714(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G37080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G06560
• Aliases: None
• Description: None

Sequence

>retro_bdis_21
ATGCCGACGGGTAGGCTGAGCGGTAACATCTCGCAGGACTGGGAGCCGGTGGTGCTGCGGCGGACGAAGCCTAAGGCGGC
CGACCTCAAGTCCACCAAGGCGGTGAACCAGGCGCTGCGTTCTGGCGCACCGGTGGAGACGGTGCGAAAGGCGGCGGCCG
GGACGAACAAGAAGGCCTCCGCCACTGCCGCGGCGACCCCCACGCGGAAGCTCGACGAGATGACGGAGCCGGCGGCGCTG
GATCGCGTGGCGGGCGAGGTGCGGGCCGCGATCCAGAAGGCGCGCGTGGCCAAAGGGTGGAGCCAGGCGGAGCTGGCCAA
GCGCATCAACGAGCGCGCCCAGGTGGTGCAGGAGTACGAGAGCGGCAAGGCGGCGCCCGTTCAGGCCGTGCTCGCCAAGA
TGGAGCGCGCCCTGGAGGTCAAGCTCCGCGGCAAAGCCGTCGGCGCGCCGGTGGCCGCTGGAGCGAAGTGA

Alignment

ORF - retro_bdis_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.9 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPITQDWEPVVVRKKLPNAAAKKDEKAVNAARRAGADIDIVKKHNAGTNK-AAHSGTSLNTKKLDDDTEN
          G.I.QDWEPVV.R...P.AA..K..KAVN.A.R.GA....V.K..AGTNK.A........T.KLD..TE.
Retrocopy GNISQDWEPVVLRRTKPKAADLKSTKAVNQALRSGAPVETVRKAAAGTNKKASATAAATPTRKLDEMTEP

Parental  LAHERVPSDLKKSIMQARMDKKLTQAQLAQVINEKPQVIQEYESGKAIPNQQIIAKLERALGTKLRGK
          .A..RV.......I..AR..K...QA.LA..INE..QV.QEYESGKA.P.Q...AK.ERAL..KLRGK
Retrocopy AALDRVAGEVRAAIQKARVAKGWSQAELAKRINERAQVVQEYESGKAAPVQAVLAKMERALEVKLRGK

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_21 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI2G06560	1 retrocopy	retro_bdis_21 ,
Medicago truncatula	MTR_2g084220	1 retrocopy	retro_mtru_80,
Populus trichocarpa	POPTR_0001s40090	1 retrocopy	retro_ptri_9,
Physcomitrella patens	PP1S96_94V6	1 retrocopy	retro_ppat_19,
Prunus persica	PRUPE_ppa013074mg	1 retrocopy	retro_pper_2,
Arabidopsis lyrata	scaffold_503053.1	1 retrocopy	retro_alyr_11,
Solanum lycopersicum	Solyc10g007350.2	1 retrocopy	retro_slyc_40,
Theobroma cacao	TCM_001730	1 retrocopy	retro_tcac_24,
Triticum aestivum	Traes_3AS_719D37CCA	1 retrocopy	retro_taes_74,
Vitis vinifera	VIT_12s0028g02020	1 retrocopy	retro_vvin_6,