RetrogeneDB ID: retro_pper_41

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_5:9696043..9697129(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa007625mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa009115mg
• Aliases: None
• Description: None

Sequence

>retro_pper_41
ATGGTGGAGGCACAGACATGGACGACGCGTCGTATGAGCAACCCCCGGCTGCAGGACACGACGTCGTCGCCGGACCAGGT
CGTGGACATCCCAGCCACGCCCACTGGCGACGTCCGCAACGGCACAAGCTACGGGTTCTCCTCCGCCGTTGGATCGCTGC
TCTCCCCGACGCTGTCGACGGCGGCGATCATCGCCTCCTGGTACCTCTCCAACATCGGCGTCCTCCTCCTGAACAAGTAC
CTCCTCAGCTTCTACGGCTTCCGCTACCCCATCTTCCTCACCATGCTCCACATGATCTCCTGCGCCGCCTACAGCTACAT
CGCCATCCACCTCCTCGAGCTCGTGCCACGTCAGCACATCCTCTCCCGCCGCCAGTTCTTCAAGATACTCGCCCTCAGCG
CCATCTTCTGCTTCTCCGTCGTCTGCGGCAACACCTCCCTCCGCTACCTCCCGGTCTCCTTCAACCAAGCCATCGGCGCA
ACGACGCCGTTCTTCACCGCCATCTTCGCCTTCATCATCACCTGTAAGAAAGAGTCCGCCGAGGTCTACGGCGCCCTCCT
CCCCGTCGTCTTCGGGATCGTGGTCGCCAGCAACAGCGAGCCGCTCTTCCACCTCTTCGGCTTTTTAGTCTGTGTGGGGT
CCACTGCCGGACGAGCTTTGAAATCCGTCGTTCAGGGGATCCTGCTCACCTCCGAAGCTGAGAAGCTCCACTCGATGAAC
TTGCTTCTGTACATGGCTCCAATGGCTGCCTGCATTCTGCTGCCCTTCACTCTGTACATCGAGGGCAACGTGGCGGCGGC
GACGGTGGAGAAGGCCCGGACCGACCCGTTCATTGTTTTCTTGCTGGTCGGGAATGCCACGGTGGCTTACTTGGTCAACT
TGACCAACTTCTTGGTGACCAAGCACACCAGCGCATTGACCCTGCAGGTGCTTGGCAACGCCAAAGCGGCGGTGGCGGCC
GTCGTTTCGGTGTTGATATTCCGGAACCCAGTCACGGTCATGGGTATGACCGGGTTCGCGGTGACCATCATGGGGGTGGT
GCTTTACAGCGAGGCGAAGAAAAGGTCCAAAGTTACAACTCATTGA

Alignment

ORF - retro_pper_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFTIGLVTAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLLSYIAIAWMKMVPMQTIRSRVQFL
          L.T......WY.SNIGVLLLNKYLLS.YGF.YPIFLTM.HM..C...SYIAI.....VP.Q.I.SR.QF.
Retrocopy LSTAAIIASWYLSNIGVLLLNKYLLSFYGFRYPIFLTMLHMISCAAYSYIAIHLLELVPRQHILSRRQFF

Parental  KITALSLVFCVSVVFGNISLRYLPVSFNQAIGATTPFFTAVFAYFMTLKREAWLTYLTLVPVVTGVIIAS
          KI.ALS..FC.SVV.GN.SLRYLPVSFNQAIGATTPFFTA.FA...T.K.E....Y..L.PVV.G...AS
Retrocopy KILALSAIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAIFAFIITCKKESAEVYGALLPVVFGIVVAS

Parental  GGEPSFHLFGFLICVAATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVFLLPATLIMEENVVGI
          ..EP.FHLFGFL.CV..TA.RALKSV.QGILL.SE.EKL.SMNLLLYMAP.A...LLP.TL..E.NV...
Retrocopy NSEPLFHLFGFLVCVGSTAGRALKSVVQGILLTSEAEKLHSMNLLLYMAPMAACILLPFTLYIEGNVAAA

Parental  TLALARDDVKIIWYLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVSILIFRNPVSVTGMM
          T...AR.D..I...L..N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.VVS.LIFRNPV.V.GM.
Retrocopy TVEKARTDPFIVFLLVGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVSVLIFRNPVTVMGMT

Parental  GYSLTVFGVILYSEAKKRSK
          G...T..GV.LYSEAKKRSK
Retrocopy GFAVTIMGVVLYSEAKKRSK

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_41 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41 ,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,
Vitis vinifera	VIT_13s0019g03270	1 retrocopy	retro_vvin_10,