RetrogeneDB ID: retro_lper_2

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 7:22380684..22381299(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR07G24000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR03G12390
• Aliases: None
• Description: None

Sequence

>retro_lper_2
ATGGCGATGGTCGCCTCCCCCAACACCGGCAAGCTGGCACTGCCGCCTCCACCGCTCAATCCCACCACCACCACCCACAA
GGCGGCGGCGCCGTACAACCCCTACAGCGGCGGCGGCCGAAGACGGGCGTCGCCGTCGCAGCACGGCGGCGTCGACGGCG
ACATGCAGGGAGTGGACGGGATCGTCCTGGTGCTACGCGCGGCGGCGGCGGCGCTGGCCTTCGTGGCGGTGGCGCTGGTG
GCGTCGTGCCGGCACGGCGACTGGATGGAGTTCACGCGGTACCAGGAGTACAGGTACCTCCTCGCCGTCTCCGTCGTCGC
CTCCGTCTACTCCGCTCTCCAGGCCATGCGAGGGTTTCTCCGGATGCGCGCCGCCGGCAACGGCGCCTGCGCCGCCACCT
TCCTTGATTTCGCCGGAGATCAGGCGGTGGGGTACTTGCTGATAACGGCGTCGTCGGCTGCTCTTCCGATCACCATCCGG
ATGAGATCGGCGGTGGTCAATACCTTCACGGATGCCATCACGGCGTCCATCAGCTTGGCCTTCGTCTCCTTCGCCGCCCT
CTCCTTCTCAGCCATGCTCACCGGCTTCAGGCTCTCCGCCGCCTACAGCTATTGA

Alignment

ORF - retro_lper_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 69.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKSPLALHAAAAAFAFVALVLAASNQHGNWMQFDRYQEYKYLLAIAALAFAYSLAQAVRHAFRMRRGVD
          .D...L.L.AAAAA.AFVA..L.AS..HG.WM.F.RYQEY.YLLA....A..YS..QA.R...RMR....
Retrocopy VDGIVLVLRAAAAALAFVAVALVASCRHGDWMEFTRYQEYRYLLAVSVVASVYSALQAMRGFLRMRAAGN

Parental  PVPAASGRILDFVSDQVVAYLLMSALSAATPITNRMRSAVINSFTNTTAAAISMTFLAFVALALSAMVSG
          ...AA....LDF..DQ.V.YLL..A.SAA.PIT.RMRSAV.N.FT....A.IS..F..F.AL..SAM..G
Retrocopy GACAAT--FLDFAGDQAVGYLLITASSAALPITIRMRSAVVNTFTDAITASISLAFVSFAALSFSAMLTG

Parental  YKLS
          ..LS
Retrocopy FRLS

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_2 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
Zea mays	GRMZM2G007475	1 retrocopy	retro_zmay_8,
Leersia perrieri	LPERR03G12390	1 retrocopy	retro_lper_2 ,
Sorghum bicolor	Sb01g038100	1 retrocopy	retro_sbic_28,