RetrogeneDB ID: retro_lper_4

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 1:14480298..14481327(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR01G16440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR01G31380
• Aliases: None
• Description: None

Sequence

>retro_lper_4
ATGGATGGCATGCCGCCGCCGCCGCACCACCACCATCCCGCAGCATCAGGACCGGCCATGCCGTACGCCGACGCGGACCG
CACCCTGCGCGCGCTGGCCGGCGCCGCGGAGGGCTTCGGCCGCGGCACGATCGGCGGGCTCCACGGCCCGATCTACCGCG
TCACGTCCCTCGACGACGACGGCCACGGCACCCTCCGCCACGCCTGCCGCGCGCACGGCCCGCTCTGGATCGTCTTCGAC
GTCTCCGGCACAATCCACCTCGCCACCTACCTCCGCGTCGCCTCCCACAAGACCATCGACGGCAGGGGGCAGCGCGTCCG
CCTCGTCGGGAAGGGGATCCAGCTCAAGGACTGCCACCACGTGATCGTCTGCAACCTCGAGATCGAGGGCGGGCGCGGGC
ACGACGTGGACGCCGTGCAGATCAAGCCCAACTCCACCAACATCTGGATCGACCGGTGCAGCCTCGCGGACTGCGACGAC
GGGCTGATCGACATCACGAGGAGCAGCACCGACATCACCGTCTCGCGCTGCAGGTTCTCGCGGCACGACAAGACGATGCT
GGTGGGGGCCGACCCGTGCCACGTCGGCGACCGCTGCATCCGCGTCACGATCCACCACTGCTTCTTCGACGGCACGAGGC
AGCGGCACCCGCGGCTCAGGTTCGGGAGGGCGCACCTGTACAACAACTACACGAGGGGGTGGGGGATCTACGCCGTGTGC
GCGGGCGTCGAGGCGCAGGTGGCGTCGCAGTGCAACGTGTACGAGGCCGGCCCGGAGAAGAAGACGGTGTTCAGGTACAT
GCCGGAGAAGGCGGCGGATCGCGGCGAGGCGGCGGCCGGGTGGATCAGGTCGGAGGGGGACGCCTTCCTCAACGGCGCGA
GGCCGTGCCTTGTGGATGGAGGGGAGGCGGTGTTCAGGCCGGAGGAGTACTACGAGAGGTGGACCATGGAGGCCGTGTCG
CCGGCGCTCAAGGAGGTTGTCATGCTCTGCGCCGGTTGGCAGCCTGTGCCCAGACCACCCGGCGAGTGA

Alignment

ORF - retro_lper_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.55 %
• Parental protein coverage: 78.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEAAPLMPYATADSSLRAMAGLAEGFGRHAIGGLHGDVYHVTTLDDDGDGSLREGCGRREPVWIVFDVSG
          A...P.MPYA.AD..LRA.AG.AEGFGR..IGGLHG..Y.VT.LDDDG.G.LR..C....P.WIVFDVSG
Retrocopy AASGPAMPYADADRTLRALAGAAEGFGRGTIGGLHGPIYRVTSLDDDGHGTLRHACRAHGPLWIVFDVSG

Parental  TIHLSTPIRVSSYTTIDGRGQRVTLSGKGLQLRECEHVIVCNVEVEGGRGHDADAVQIKPGSRHVWIDRC
          TIHL.T..RV.S..TIDGRGQRV.L.GKG.QL..C.HVIVCN.E.EGGRGHD.DAVQIKP.S...WIDRC
Retrocopy TIHLATYLRVASHKTIDGRGQRVRLVGKGIQLKDCHHVIVCNLEIEGGRGHDVDAVQIKPNSTNIWIDRC

Parental  GLRDCADGLLDVTRGSTDVTVSRCRFSAHDKAVLIGSSSGHVEDRRIRVTIHHCLFDGTRQRHPRVRFGR
          .L.DC.DGL.D.TR.STD.TVSRCRFS.HDK..L.G....HV.DR.IRVTIHHC.FDGTRQRHPR.RFGR
Retrocopy SLADCDDGLIDITRSSTDITVSRCRFSRHDKTMLVGADPCHVGDRCIRVTIHHCFFDGTRQRHPRLRFGR

Parental  VHLYNNYTRGWGIYAVCASVESQIVSQCNIYEAG-EKRRVFMYMEEQAADRDQSSTGLIRSEGDLFLNGA
          .HLYNNYTRGWGIYAVCA.VE.Q..SQCN.YEAG.EK..VF.YM.E.AADR.....G.IRSEGD.FLNGA
Retrocopy AHLYNNYTRGWGIYAVCAGVEAQVASQCNVYEAGPEKKTVFRYMPEKAADRGEAAAGWIRSEGDAFLNGA

Parental  EECTAQDSE
          ..C.....E
Retrocopy RPCLVDGGE

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_4 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004758	1 retrocopy	retro_oind_37,
Leersia perrieri	LPERR01G31380	1 retrocopy	retro_lper_4 ,
Oryza meridionalis	OMERI01G33590	1 retrocopy	retro_omer_1,
Oryza nivara	ONIVA01G41460	1 retrocopy	retro_oniv_25,
Oryza punctata	OPUNC01G35260	1 retrocopy	retro_opun_9,
Oryza glaberrima	ORGLA01G0303100	1 retrocopy	retro_ogla_4,
Oryza sativa japonica	OS01G0837100	1 retrocopy	retro_osat_37,