RetrogeneDB ID: retro_bdis_5

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:39446726..39447923(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G37140
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G00910
• Aliases: None
• Description: None

Sequence

>retro_bdis_5
ATGGCATCAGCTATTACCATTAGTTCAGTTAGTGCTCAGGCTGCTCTGATCTCAAAGCCAAGAAATCATGGCATCACTAG
CTACAGTGGCTTAAAGGCATCATCGTCGTCGATTAGCTTCGAAACAGGATCGTCATTCCTCGGCAAGAATGCATCCCTTC
GGGCATCTGTTACCCCAAGGATCGTGCCAAAGGCCAAATCTGGAGCTCAGATATCACCTGAGGCATCTTACAAAGTGGCG
GTACTTGGTGCTGCTGGTGGCATTGGTCAACCATTGGGCCTGTTAATTAAGATGTCTCCTCTGGTCTCAGAACTGCGCCT
GTATGATATTGCAAACGTCAAGGGAGTTGCTGCTGATCTCAGCCATTGCAACACACCTTCTCAGGTTCTGGACTTTACTG
GCCCGGGAGAATTAGCCGACTGCTTGAAAGGTGCGGATGTTGTTGTCATTCCTGCCGGGGTCCCAAGGAAGCCAGGCATG
ACTCGTGATGACCTTTTTAACATCAATGCGGGCATTGTCAAGTCACTTATTGAGGCTGTTGCAGACAATTGCCCAGAGGC
CTTCATCCATATTATCAGCAACCCAGTCAACTCCACAGTGCCAATTGCTGCTGAGATTCTGAAACAGAAGGGTGTCTACA
ATCCCAAGAAGCTTTTCGGAGTTTCCACCCTGGATGTTGTCCGAGCTAACACATTTGTTGCTCAGAAGAAGAACCTTAAG
CTCATTGATGTTGATGTTCCAGTTGTGGGTGGTCATGCTGGGATTACAATCCTACCGTTGTTGTCAAAGACTAGGCCATC
TGTCACCTTCACGGAAGAGGAAACTGAGGAGCTGACAAAGAGGATACAGAATGCGGGGACAGAGGTGGTGGAGGCGAAAG
CTGGTGCTGGATCTGCTACCCTGTCCATGGCTTATGCTGCTGCCAGATTTGTCGAGTCATCACTCCGTGCACTGGCTGGT
GATCCAGATGTTTATGAGTGCACGTATGTTCAGTCTGAGTTAACCGAGCTGCCATTTTTCGCATCCAGAGTGAAGCTTGG
AAAGAACGGCGTTGAGTCCATCATTTCCTCCGACCTGGAGGGAGTGACCGAGTACGAGGCCAAGGCTCTCGAAGCTTTGA
AGCCTGAGCTGAAGGGCAGCATCGAGAAGGGCATTGAGTTTGTGCACAAACAGCAGGGAGCTACTGCATCCGTTTGA

Alignment

ORF - retro_bdis_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 86.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FKVAVLGASGGIGQPLSLLMKMNPLVSVLHLYDVVNMPGVTADISHMNTGAVVRGFLGQPQLENALTGMD
          .KVAVLGA.GGIGQPL.LL.KM.PLVS.L.LYD..N..GV.AD.SH.NT...V..F.G...L...L.G.D
Retrocopy YKVAVLGAAGGIGQPLGLLIKMSPLVSELRLYDIANVKGVAADLSHCNTPSQVLDFTGPGELADCLKGAD

Parental  LVIIPAGIPRKPGMTRDDLFNINAGIVRTLCEGIAKCCPNAIVNVISNPVNSTVPIAAEVFKKAGTYDPK
          .V.IPAG.PRKPGMTRDDLFNINAGIV..L.E..A..CP.A....ISNPVNSTVPIAAE..K..G.Y.PK
Retrocopy VVVIPAGVPRKPGMTRDDLFNINAGIVKSLIEAVADNCPEAFIHIISNPVNSTVPIAAEILKQKGVYNPK

Parental  RLLGVTTLDVVRANTFVGEVLGLDPRDVNVPVVGGHAGITILPLLSQVNPSCSFTSEEISYLTSRIQNGG
          .L.GV.TLDVVRANTFV.....L...DV.VPVVGGHAGITILPLLS...PS..FT.EE...LT.RIQN.G
Retrocopy KLFGVSTLDVVRANTFVAQKKNLKLIDVDVPVVGGHAGITILPLLSKTRPSVTFTEEETEELTKRIQNAG

Parental  TEVVEAKAGAGSATLSMAYAAAKFADACLRGLHGDAGIVECSYVASQVTELPFFASKVRLGRCGVEEIL-
          TEVVEAKAGAGSATLSMAYAAA.F....LR.L.GD....EC.YV.S..TELPFFAS.V.LG..GVE.I..
Retrocopy TEVVEAKAGAGSATLSMAYAAARFVESSLRALAGDPDVYECTYVQSELTELPFFASRVKLGKNGVESIIS

Parental  -PLGPLNEFERAGLEKAKKELSESIQKGVSFINK
          ..L....E.E...LE..K.EL..SI.KG..F..K
Retrocopy SDLEGVTEYEAKALEALKPELKGSIEKGIEFVHK

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_5 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G09660	1 retrocopy	retro_atha_10,
Brassica rapa	Bra009397	1 retrocopy	retro_brap_19,
Brachypodium distachyon	BRADI4G00910	1 retrocopy	retro_bdis_5 ,
Prunus persica	PRUPE_ppa007722mg	1 retrocopy	retro_pper_5,