RetrogeneDB ID: retro_lper_26

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 8:5466970..5467840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR08G06310
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR04G20020
• Aliases: None
• Description: None

Sequence

>retro_lper_26
ATGGCCGTGGACCTCATGGGCTTCAGCCCCCGCGGCGCCTGCCCTCCTCCTCTCCCCTCCTCCTCCTCCGACGACGACGC
CAGGGAGCAGCTCGCGTTCCAGGAAGCCGCCGCCGCCGGCCTCCGCAGCCTCGAGCTCCTCGTCTCCTCCCTTTCCGGCT
CCGCCGCCGATCTCCACCGTCTCCCTTCCCCGCCGCTCGGGGAGATCACCGACCAGGCCGTCTTCCGCTTCCGCAAGGTC
ATCTCCATCCTCGACCGCACCGGCCACGCCCGCTTCCGCCGCGCCCCTACCGCCGCATCCTCGCCGCCGTCGCCGTCATC
TCCGCCTCCTCCTCCTCCCCCTCCGGCGACGCCGCATCCGAAGACCCTGAACCTCGATTTCACCAAAGCGGCGGCGGCAA
CAGCGTCGGCGTCGTTAATCTCGTCGGTAACAGCCGGCGGAGGCGGCGGAGGGGAAGGAAGCGTATCAAAGGGGAAAAGC
CTCATCTCCACAGGAAAACCCCCACTCGCCGGCGGCGCCAAGCGCAAGCCGCCGCCGCCGACGACGGCGTGCGAGGGACA
CGTGGCGGGGCACGGGGGATGCCACTGCGCGGCGGGGAAGAAGAGGAAGCAGCATCATCATCGAGGGGCTCGGAGGACGG
TGAGGGTGGCGGCGGCGAGCGAGCGGGTGGCGGATATTCCGGCGGACGAGTACTCGTGGAGGAAGTACGGGCAGAAGCCG
ATCAAGGGCTCGCCATACCCGCGCGGCTACTACCGCTGCAGCTCCGTCAAGGGCTGCCCCGCAAGGAAGCATGTCGAGCG
CGCCGCCGACGACCCCGCCGTCCTCCTCGTCACCTACGACGGCGACCACCGCCACTCGCCGCCGGCCTAA

Alignment

ORF - retro_lper_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APPPPPAPVVAAVAPLAIGPTSSSQPQSLTLDFTKPNLMAMSAATSVTSTSFFSSVTAGEGSVSKGRSLL
          AP.....P......P....P.....P..L.LDFTK....A..A..S..S.........GEGSVSKG.SL.
Retrocopy APTAASSPPSPSSPPPPPPPPATPHPKTLNLDFTKA--AAATASASLISSVTAGGGGGGEGSVSKGKSLI

Parental  SSGKPPLSGH-KRK--PCAGGHSEATANGSRCHCS--KRRKNR----VKRTIRVPAISSKIADIPPDEYS
          S.GKPPL.G..KRK..P.........A....CHC...K.RK........RT.RV.A.S...ADIP.DEYS
Retrocopy STGKPPLAGGAKRKPPPPTTACEGHVAGHGGCHCAAGKKRKQHHHRGARRTVRVAAASERVADIPADEYS

Parental  WRKYGQKPIKGSPYPRGYYKCSTVRGCPARKHVERATDDPAMLVVTYEGEHRHTP
          WRKYGQKPIKGSPYPRGYY.CS.V.GCPARKHVERA.DDPA.L.VTY.G.HRH.P
Retrocopy WRKYGQKPIKGSPYPRGYYRCSSVKGCPARKHVERAADDPAVLLVTYDGDHRHSP

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_26 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
Leersia perrieri	LPERR04G20020	1 retrocopy	retro_lper_26 ,
Oryza punctata	OPUNC04G21880	1 retrocopy	retro_opun_5,
Oryza rufipogon	ORUFI04G26070	1 retrocopy	retro_oruf_29,
Oryza sativa japonica	OS04G0605100	1 retrocopy	retro_osat_10,