RetrogeneDB ID: retro_bdis_1

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:6156457..6157222(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G07810
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G07830
• Aliases: None
• Description: None

Sequence

>retro_bdis_1
ATGGCGAAGCTTGCTCTCGGGCACCTCCGCGAGGCAGCCGAGCCCGGCTGCGCCCGCGCCGTGCTCGCCGAGGCCGTGCT
CACCTTCCTCTTCGTCTTCTCCGGCGTCGCCTCCGCCATGGCCGCCGGGAAGCTGGGCGGCGGCGCGGACACGATCATGG
GCCTGACGGCGGTGGCTTCGGCCCACGCGATGGCGGTGGCCGTGATGGTCTCGGCGGGCCTCCACGTCTCCGGCGGCCAC
ATCAACCCGGCCGTCACGCTGGGCCTGGCGGCCGGCGGCCACATCACGCTCTTCCGCTCCGCCCTCTACGTGCCTGCCCA
GCTGCTCGGCTCCTCCCTCGCCTGCCTCCTCCTCTCCTTCCTCTCCGGCTCCGGCGCCGGCGCTCCACCAATCCCCGTGC
ACGCGCTGGCCGCCGGCGTGGGCGCCGCGCAGGGGCTGCTGTGGGAGGCCACGCTCACCTTCTCGCTCCTCTTCGCCGTC
TACGCCACCGTCGTCGACCCGGCCCGCACCGTGGGGAACCTCGGCCCGCTCCTCGTGGGCCTCGTCGTCGGCGCCAACGC
GCTGGCTGGTGGGCCGTTCTCTGGCGCGTCCATGAACCCGGCGCGCTCGTTTGGGCCTGCGCTGGTGACGGGAGAGTGGG
CTGGGCACTGGGTCTACTGGGTCGGCCCGATGATCGGTGGGCTGCTTGCTGGGCTTGTTTACGACGGGGTGTTCATGGTC
CGGCCAGGCCATCAGCAGCTTCCAACAGACGACGCGGAGTTCTGA

Alignment

ORF - retro_bdis_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.6 %
• Parental protein coverage: 97.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTKLVLGHGREASDPGCLRAVLGELVLTFLFVFVGVGSTITAGSAAAAGADPSAALIAVALAHALVVAVF
          ..KL.LGH.REA..PGC.RAVL.E.VLTFLFVF.GV.S...AG.....GAD....L.AVA.AHA..VAV.
Retrocopy MAKLALGHLREAAEPGCARAVLAEAVLTFLFVFSGVASAMAAGKLGG-GADTIMGLTAVASAHAMAVAVM

Parental  ATAGFHISGAHMNPAVTLSLAVGGHITLLRSSFFVVAQMLGSSCACLLLRALT----GGLVTPVHALAAG
          ..AG.H.SG.H.NPAVTL.LA.GGHITL.RS...V.AQ.LGSS.ACLLL..L.....G....PVHALAAG
Retrocopy VSAGLHVSGGHINPAVTLGLAAGGHITLFRSALYVPAQLLGSSLACLLLSFLSGSGAGAPPIPVHALAAG

Parental  VGPIQGVVAEVVFTFTLLFTIYAAILDPRSSAPGFGPLLTGLLVGANTIAGGALTGASMNPARSFGPALA
          VG..QG...E...TF.LLF..YA...DP.......GPLL.GL.VGAN..AGG...GASMNPARSFGPAL.
Retrocopy VGAAQGLLWEATLTFSLLFAVYATVVDPARTVGNLGPLLVGLVVGANALAGGPFSGASMNPARSFGPALV

Parental  SGDWANHWVYWVGPLAGGPLAVAVYEFVFTVPPTHQQLPT
          .G.WA.HWVYWVGP..GG.LA..VY..VF.V.P.HQQLPT
Retrocopy TGEWAGHWVYWVGPMIGGLLAGLVYDGVFMVRPGHQQLPT

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_1 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	BRADI2G07830	1 retrocopy	retro_bdis_1 ,