RetrogeneDB ID: retro_lper_15

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 7:17200516..17200972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR07G16880
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR08G01520
• Aliases: None
• Description: None

Sequence

>retro_lper_15
ATGGGTCGCATGCACAGCAGCGGGAAGGGCATGTCCAGCTCGGTGCTCCCCTACAAGCGGGAGGCCCCGGCCTGGGTCAA
GTCCTCCGTGTCGGAGGTGGAGGAGGCGATCGTGCGCGCCGCCAAGAAGGGCCAGCTGCCGTCGCAGATCGGGGCGATGC
TCCGCGACGCCCACGCCATCCCGCTCTCCCGCGGCCTCACCGGCGGCAAGGTCCTCCGCGTGCTCAAGTCCCGTGGCCTC
GCGCCCGAGGTGCCCGAGGACCTCTACTTCCTCATCAAGAAGGCGGTGGCGATGAGGAGGCACCTGGAGAGGAACAGGAA
GGACAAGGACACCAAGTTCCGCCTCATCCTCGTCGAGAGCAGGGTTCATCGCCTCACCCGCTACTACCGCCTCGCCAAGA
AGATCCCCGCCTCCTGGAAGTATGACTCCGTCACCGCGAGCACCCTCGTCGCCTGA

Alignment

ORF - retro_lper_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHSRGKGISSSALPYKRTPPSWVKTAASDVEDMIMKAAKKGQMPSQIGVVLRDQHGIPLVKSVTGSK
          MGRMHS.GKG.SSS.LPYKR..P.WVK...S.VE..I..AAKKGQ.PSQIG..LRD.H.IPL....TG.K
Retrocopy MGRMHSSGKGMSSSVLPYKREAPAWVKSSVSEVEEAIVRAAKKGQLPSQIGAMLRDAHAIPLSRGLTGGK

Parental  ILRILKAHGLAPEIPEDLYFLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWK
          .LR.LK..GLAPE.PEDLYFLIKKAVA.R.HLERNRKDKD.KFRLILVESR.HRL.RYY...KK.P..WK
Retrocopy VLRVLKSRGLAPEVPEDLYFLIKKAVAMRRHLERNRKDKDTKFRLILVESRVHRLTRYYRLAKKIPASWK

Parental  YESTTASTLVA
          Y.S.TASTLVA
Retrocopy YDSVTASTLVA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Leersia perrieri was not studied using RNA-Seq expression data.

ChIP-Seq

Leersia perrieri was not studied using ChIP-Seq data.

EST

Leersia perrieri was not studied using EST data.

TSS

Leersia perrieri was not studied using FANTOM5 data.

Lab

retro_lper_15 was not experimentally validated.

Homology

Retrocopy orthology:

Leersia perrieri 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027748	1 retrocopy	retro_oind_48,
Leersia perrieri	LPERR08G01520	1 retrocopy	retro_lper_15 ,
Oryza sativa japonica	OS08G0117300	1 retrocopy	retro_osat_33,
Sorghum bicolor	Sb07g001620	1 retrocopy	retro_sbic_47,