RetrogeneDB ID: retro_lper_24

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 5:20627332..20628199(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR05G23700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR01G16570
• Aliases: None
• Description: None

Sequence

>retro_lper_24
ATGGAGGGGGGATCATACGACCGTGAGTTCTGGCAGTTCAGCGACCAGCTGCGTGTGCACAACTTCTCCAGCCTCTCCAT
CGCCGATTCCATCTGGTCCCCTGCACCTGCTGCTGCTCCCCTCGACAACAGCAACAAGCTCGCCTTCAGCAACGCCACCA
CCAACGCGGCCGACCGCTACAACAACATCATCAACAACAAGAGCAGCAGCAGCTACCTATTCCCCTCCCAACAGCTGCTC
AACAACGCCACCGCCAAGACCTACTTCGACAAGTCCGTCGGCAGGCCAGCCAAGAACAACAACAACAACACCGTCTTCGT
CAACGACGGCAAGAAGAAGGGCATCGACGGCGGCAGGAACAACAACAGCAACAAGAACAACAACAAGAACGAGAACAAGA
GCATCAGCAACAGGTTCAAGAGCCTGCCGGCGTCGGAGTCGCTGCCCAAGGAGGAGGCGATCGGAGGATACATATTCGTG
TGCAACAACGAGACGATGGAGGAGAACCTAAAGAGGCAGCTCTTCGGCCTGCCGTCCAGGTACAGGGACTCGGTCAGGGC
AATCAGGCCCGGACTGCCGCTCTTCCTCTACAACTACTCCACGCACCAGCTGCACGGCATCTTCGAGGCAGCCAGCTTCG
GTGGATCAAACATCGATCCGGCCGCGTGGGAGGACAGCAAGTGCCCCGGCGAGTCGAGGTTCCCGGCGCAGGTGAGGGTG
GCCACGCGCAAGATTTGTGACCCGCTCGAGGAGGACGCCTTCAGGCCGGTGCTGCACCACTATGATGGGCCAAAGTTCAG
GCTGGAGCTCAGCGTCGCCGAGGCCGTCTCCCTTCTTGACATCTTCGCCGAGAAGCTCTTCGCTTGA

Alignment

ORF - retro_lper_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.44 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGGEVKSYFNKSVGRAANNNNNSNSGGYYGKKGG-EGGKKKQGGKNEGGNGGGAQAASDKRFKTLPASEA
          N....K.YF.KSVGR.A.NNNN.......GKK.G..GG......KN...N..........RFK.LPASE.
Retrocopy NNATAKTYFDKSVGRPAKNNNNNTVFVNDGKKKGIDGGRNNNSNKNNNKN---ENKSISNRFKSLPASES

Parental  LPRDEAIGGYIFVCNNDTMEENLKRQLFGLPSRYRDSVRAIRPGLPLFLYNYSTHQLHGIFEAASFGGSN
          LP..EAIGGYIFVCNN.TMEENLKRQLFGLPSRYRDSVRAIRPGLPLFLYNYSTHQLHGIFEAASFGGSN
Retrocopy LPKEEAIGGYIFVCNNETMEENLKRQLFGLPSRYRDSVRAIRPGLPLFLYNYSTHQLHGIFEAASFGGSN

Parental  IDPTAWEDKKCPGESRFPAQVKVATRKIYDPLEEDAFRPILHHYDGPKFRLELSVAEALSLLDIFADK
          IDP.AWED.KCPGESRFPAQV.VATRKI.DPLEEDAFRP.LHHYDGPKFRLELSVAEA.SLLDIFA.K
Retrocopy IDPAAWEDSKCPGESRFPAQVRVATRKICDPLEEDAFRPVLHHYDGPKFRLELSVAEAVSLLDIFAEK

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_24 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR01G16570	1 retrocopy	retro_lper_24 ,
Oryza sativa japonica	OS01G0550300	1 retrocopy	retro_osat_23,