RetrogeneDB ID: retro_pper_47

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_3:16514497..16515220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa010686mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa010591mg
• Aliases: None
• Description: None

Sequence

>retro_pper_47
ATGGGGGTGATCAAGGCAGCTCTAGGAGATGCAGTTCTGACTTCCCTGTGGGTTTTCAGCGCACCAAGTATGGGGGTTTT
CACAGTCATCATCGCCTCGTTTCTCGGCATTCAAGCTAGTTCTTTGCTAGGCCTCTTCATCACCACCATAGTTGCCACAA
TTCTGGTCCTAGCTTTCAGCTTGATAGGCAAGGTTTTGGGTGATGCCAGCTTCAACCCCTCCACCACTGCAAGTTTCTAC
GCTGCAGGCCTCACCCCCGGCACATCTCTCTTCTCCATGGCCGTCCGGTTCCCGGCTCAGGCAGCCGGTGGAGTAGGAGG
TGCCAAGGCAATTCTGCAGGTGATGCCAAAGCAGTACAAGCATATGCTTAAAGGGCCTTTTTTGAAAGTGGATTTGTACA
CCGGTGTCATAGCTGAGGGGCTGTTGACTTTTGTTCTCTGCTTTTCTCTGCTTGTGATTATTCTCAGAGGTCCTAGAAAT
CCAATACTGCAGATATGGCTGCTTTCAATTGCTACTGTGGGATTGGTTGTTGCAGGTGGTGGGTACACAGGGCCTTCCAT
GAACCCAGCAAATGCTTTTGCCTGGGCTTATGTGAATAATTGGCACAACACTTGGGAGCTGTTCTTGGTTTATTGGATTG
GCCCCTTCATAGGAGCAACTTTGGCTGCTTCGGTTTTCAAGACTTTGCTTCCCCCACCAATAGCAAAGGAAAAGAAAGCC
TAA

Alignment

ORF - retro_pper_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.09 %
• Parental protein coverage: 97.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAIKAAVGDTMLTFLWISCASMLGLATSFIANAVGVQDLPWPPLFITTALVFVLVFVFTFLGDALGGAS
          MG.IKAA.GD..LT.LW...A...G..T..IA...G.Q......LFITT.....LV..F...G..LG.AS
Retrocopy MGVIKAALGDAVLTSLWVFSAPSMGVFTVIIASFLGIQASSLLGLFITTIVATILVLAFSLIGKVLGDAS

Parental  FNPTGTASFYAAGLGADT-LLSMALRFPAQAFGAVGGVLAINEVMPHQYKHMLGGPSLKVDVHTGAIVEG
          FNP..TASFYAAGL...T.L.SMA.RFPAQA.G.VGG..AI..VMP.QYKHML.GP.LKVD..TG.I.EG
Retrocopy FNPSTTASFYAAGLTPGTSLFSMAVRFPAQAAGGVGGAKAILQVMPKQYKHMLKGPFLKVDLYTGVIAEG

Parental  VLTFVISFLVLIIILKGPRSPVLKMLLLSVVTVTLVVSGSVYTGPSMNPANAFGWAYLNNWHNTWEQFYV
          .LTFV..F..L.IIL.GPR.P.L...LLS..TV.LVV.G..YTGPSMNPANAF.WAY.NNWHNTWE.F.V
Retrocopy LLTFVLCFSLLVIILRGPRNPILQIWLLSIATVGLVVAGGGYTGPSMNPANAFAWAYVNNWHNTWELFLV

Parental  YWICPFIGAILAGWIFRAVFPPLLAKGKK
          YWI.PFIGA.LA...F....PP..AK.KK
Retrocopy YWIGPFIGATLAASVFKTLLPPPIAKEKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Prunus persica was not studied using RNA-Seq expression data.

ChIP-Seq

Prunus persica was not studied using ChIP-Seq data.

EST

Prunus persica was not studied using EST data.

TSS

Prunus persica was not studied using FANTOM5 data.

Lab

retro_pper_47 was not experimentally validated.

Homology

Retrocopy orthology:

Prunus persica 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
Medicago truncatula	MTR_7g085070	1 retrocopy	retro_mtru_16,
Populus trichocarpa	POPTR_0013s05030	1 retrocopy	retro_ptri_8,
Prunus persica	PRUPE_ppa010591mg	1 retrocopy	retro_pper_47 ,
Theobroma cacao	TCM_026035	1 retrocopy	retro_tcac_30,