RetrogeneDB ID: retro_lper_29

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 6:20748505..20749318(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR06G23420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR03G02450
• Aliases: None
• Description: None

Sequence

>retro_lper_29
ATGGAGACGCTGCCGGGATTCAGGTTCCACCCGACGGAGGAGGAGCTACTGGAGTTCTACCTGAAGCAGGTGGTCCACGG
CAAGAAGCTCAAATTCGACATCATCCCCACCGTCCATCTCTACCGCCATGACCCTCGCGAGCTCCCCTCCCTCGCCCGCA
TCGGCGAGCGCGAGTGGTACTTCTTCGTCCCCCGCGACGGCGCCGGCGCACGGAAGAACGGATCCTCCGCCGGCGGCCGG
CCGAGCCGCACGACGGAGCACGGGTTCTGGAAGGCGACCGGGTCGGACCGAGCCGTCCGTTGCGCCGCCGACCCGAAGAA
GCTGATCGGGCTCAAGAAGACGCTCGTCTACTACGAGGGGCGCGCGCCACGTGGCACCAAGACCGACTGGGTCATGAACG
AGTATCGCCTCCCCGACGCCGCCGGCGAGGATCATCGTCCTCATCAGGAGGACGTGGTGCTGTGCAAGGTGTACCGGAAG
GCGGTTTCGCTCAAGGAGCTGGAGCAGAGGGTGGCCATGGAGGAGCTCGCGCGCTGCACGTCGGCGTCCCAGAACGCAGG
CTCGCCGGTGGACTCCTCGTCGATCTGCTCGTCGGCGGAGTACGGCGTGATGATGAAGAAGGAAGCGGTGGTACAGGTGG
ATGAGGCGGCGGCGCATGAGCTGGTCCGGCCGGCGATGATGAGGCTGCCGGAGTTGGAGGTGGCGAAGATCAGTGGGCTG
GAGTGGATGCAAGAACCGTTCTTGACGCAGCTTAGGAGCCCATGGATGGAGAGCTGGTCGCCTTACTACGCCAGCAGCGT
CCTCAACTTCTAA

Alignment

ORF - retro_lper_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.34 %
• Parental protein coverage: 63.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDLPGFRFHPTEEELLDFYLARVVLGKKLQFDIIGTLNIYRHDPWDLPGMAKIGEREWYFFVPRD----R
          ..LPGFRFHPTEEELL.FYL..VV.GKKL.FDII.T...YRHDP..LP..A.IGEREWYFFVPRD....R
Retrocopy ETLPGFRFHPTEEELLEFYLKQVVHGKKLKFDIIPTVHLYRHDPRELPSLARIGEREWYFFVPRDGAGAR

Parental  KAGN--GGRPNRTTERGFWKATGSDRAIRSSGDPKRVIGLKKTLVFYQGRAPRGTKTDWVMNEYRLPDFA
          K.G...GGRP.RTTE.GFWKATGSDRA.R...DPK..IGLKKTLV.Y.GRAPRGTKTDWVMNEYRLPD.A
Retrocopy KNGSSAGGRPSRTTEHGFWKATGSDRAVRCAADPKKLIGLKKTLVYYEGRAPRGTKTDWVMNEYRLPD-A

Parental  AGRAAPPFPKEDMVLCKIYRKATPLKELEQRASAMEEMQRRSSHGDHTNIASIVHDASASTGDDY
          AG....P...ED.VLCK.YRKA..LKELEQR..AMEE..R..S.....N..S.V...S......Y
Retrocopy AGEDHRPH-QEDVVLCKVYRKAVSLKELEQRV-AMEELARCTSASQ--NAGSPVDSSSICSSAEY

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_29 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR03G02450	1 retrocopy	retro_lper_29 ,
Oryza meridionalis	OMERI03G02480	1 retrocopy	retro_omer_9,
Oryza punctata	OPUNC03G02420	1 retrocopy	retro_opun_1,