RetrogeneDB ID: retro_pper_4

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_1:30224844..30225462(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa016793mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa011207mg
• Aliases: None
• Description: None

Sequence

>retro_pper_4
ATGATCCAGGACGACAACGACGTTTTGGAGCCGCCGATCAATTTCTCGACGGTGGACGAGGGCATTTTCAGATCGGGCTT
CCCTCAGCCGCCCAATTTCCCATTCCTCAAAACCCTTCAACTCCGATCCATCATATATCTGTGCCCCGAGCCCTACCCGG
AGGAGAATCTGGAGTTTCTTCGGTCTCAAAACATCCAGCTGTTCCAATTCGGAATCGAGGGGAAGAAGAAGGCTTCTTCT
TCGGCTGCATCGTCGATCCCCAAGCAGACGATCTTGGAGGCTCTGAAGGTGTTGATCGACGTGAGGAACCATCCGGTGTT
GATCCACTGCAAACGTGGCAAGCATCGGACGGGTTGTCTCGTGGGTGTGCTGAGGAAATTTCAGAATTGGTGCTTGGCTT
CGGTGTTTGAGGAGTACCAGAGATTCGCGGGCGCGAAATCTAGGACGACCGATTTGAGATTTATTGAGACGTTTGACGTG
GTGGGGCTGAGGGACTGCCTGTACGGCATCATCCACCATTACTATCGACTAGCCTACTACGCTTCCAAGAAGAGGCGCTT
GTTATTGTACACACAAGCACAACAAGACATGCAAACCTATCGACATTATAAACCCTAA

Alignment

ORF - retro_pper_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 88.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNNDHDDVLEPPTNFSMVEDGIFRSGFPQPSNFPFLQSLNLRSIIYLCPEPYPEENLEFLRSQNIQLLQF
          M..D..DVLEPP.NFS.V..GIFRSGFPQP.NFPFL..L.LRSIIYLCPEPYPEENLEFLRSQNIQL.QF
Retrocopy MIQDDNDVLEPPINFSTVDEGIFRSGFPQPPNFPFLKTLQLRSIIYLCPEPYPEENLEFLRSQNIQLFQF

Parental  GIEGK----TEPSVSILKDTILEALKVLIDVRNHPVLIHCKRGKHRTGCLVGCLRKFQNWCLSSVFEEYQ
          GIEGK.........SI.K.TILEALKVLIDVRNHPVLIHCKRGKHRTGCLVG.LRKFQNWCL.SVFEEYQ
Retrocopy GIEGKKKASSSAASSIPKQTILEALKVLIDVRNHPVLIHCKRGKHRTGCLVGVLRKFQNWCLASVFEEYQ

Parental  RFAGVKSRATDLRFLEGFDTLLLRQCLYSIIYQYQG---YGSNKRRLLYREDNLQKPQTMK
          RFAG.KSR.TDLRF.E.FD...LR.CLY.II..Y.....Y.S.KRRLL......Q..QT..
Retrocopy RFAGAKSRTTDLRFIETFDVVGLRDCLYGIIHHYYRLAYYASKKRRLLLYTQAQQDMQTYR

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_4 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Prunus persica	PRUPE_ppa011207mg	1 retrocopy	retro_pper_4 ,