RetrogeneDB ID: retro_lper_17

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 8:145034..145736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR08G00200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR04G16060
• Aliases: None
• Description: None

Sequence

>retro_lper_17
ATGGCGAAGGGGGATGGCGGCGTGGGCGCGTGGACGGTGGTGGCTCACGTGCTGGCGGTGGCGGCGACGGCGCTGGTGCT
GATATGGTGCATCCACTTCCGCGGCGGCCTTGCCCTGCGCTCCCACAACAAGCAGCTCATCTTCAACATCCACCCCGTGC
TGATGCTGATCGGCCCCATCGTGCTGGGCGCCGAGGCAATCCTCTCCTACCGCTCCCTCATCAAGATTAGCAGCAGCAGG
GAGGTTCGGAAGAAGGCGCACCTGGCGCTGCACGGCGTGGCGCTGGCGGTGGGCGCGGTGGGCATCTACGCGGTGTTCAA
GTACCACGCCGAGGCTGACATCCCGGACCTCTACTCGCTCCACTCCTGGATCGGCATCGCCACCATCTCCCTCTACGCCC
TCAACTGGCTCGCCGCCTTCCTCACCTTCTTCTTCCCCAAAGCCTCCCCCGACACCAGGCGCTCCGTCGTCCCATGGCAC
GCGCTCCTGGGCCTCCTCATCTTCGGCCTCGCCATCGCCACCGCGCTGCTCGGCTTCCTCGAGAAGCTCACCTTCCTGCA
GGCCCCGCCCATGCACCTCGTCTCCAGGTACGGCGCCGAGGCCCTGCTCGTCAATTTCACGGCGCTGATTGTCCTCTTTC
TCGGCGGCGCCGTCTTGCTCGCCACCGCCAACATCGACTCCACTAGGTACACTGCCATGTAA

Alignment

ORF - retro_lper_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 91.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGLGVKAAPFTYVAHALAVVAAVMVLVWCISFRGGLAFEADNKNLIFNVHPVLMLIGFIILGSEAIMI
          MA.G.G...A..T.VAH.LAV.A...VL.WCI.FRGGLA....NK.LIFN.HPVLMLIG.I.LG.EAI..
Retrocopy MAKGDGGVGA-WTVVAHVLAVAATALVLIWCIHFRGGLALRSHNKQLIFNIHPVLMLIGPIVLGAEAILS

Parental  YKIFPKLN--HDTTKLIHLILHAIAIVLGAVGIYCAFKFHNESGIANLYSLHSWLGIGTISLYGIQWIFG
          Y....K........K..HL.LH..A...GAVGIY..FK.H.E..I..LYSLHSW.GI.TISLY...W...
Retrocopy YRSLIKISSSREVRKKAHLALHGVALAVGAVGIYAVFKYHAEADIPDLYSLHSWIGIATISLYALNWLAA

Parental  FVAFFYPGAAPHVRRGALPWHVLFGLFVYVLTLATAELGLLEKLTFLQSAGL---DKYGAEAFLVNFTGL
          F..FF.P.A.P..RR...PWH.L.GL....L..ATA.LG.LEKLTFLQ.........YGAEA.LVNFT.L
Retrocopy FLTFFFPKASPDTRRSVVPWHALLGLLIFGLAIATALLGFLEKLTFLQAPPMHLVSRYGAEALLVNFTAL

Parental  VVALFGAAVVVA
          .V...G.AV..A
Retrocopy IVLFLGGAVLLA

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_17 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17 ,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,