RetrogeneDB ID: retro_pper_48

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_6:28473613..28474669(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa007906mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa007588mg
• Aliases: None
• Description: None

Sequence

>retro_pper_48
ATGTCTAACACAAGCATCAACAATAATGAGGTTGACATCGTGATTGCGGCAATCAACTCCGACCTGGAGCCATTCATGAA
TGAATGGAGACCAGTATTCTCCCAGTTCCACCTGATTATTGTCAAAGACCCTGATATGAATGGGGAGCTCCACATTCCGG
AAGGGTTTAATGTGGATGTCTTTACTAAGTCTGACATAGACCGAGTGGTGGGCTCTTCCACTTCCATTCTCTTCTCTGGT
TACTCGTGCAGGTACTTTGGTTATCTAGTATCTCGGAAAAAATATATTATCTCAATTGATGATGATTGCATTCCCGCTAG
GGACACAAATGGTGATTTAGTAGATGTAGTGGCACAGCATATTGCCAATCTTCAAGCTCCAGCTACCCCTTTCTTTTTTA
ACACACTCTATGATCCTTATCGGAAAGGGGCAGATTTTGTTCGTGGTTACCCATTTAGTCTGAGGAGTGGGGTTACATGT
GCGCTATCATGTGGACTGTGGCTTAATCTGGCAGACTATGATGCACCAACACAGGCCCTCAAGCCAGAGCAGAGGAATTC
TCGATATGTGGATGCTGTAATGACTGTTCCAGTGAGGTCCTTAATGCCTGTAAGTGGTATCAACATTGCTTTCAATCGTG
AGGTTGTGGGGCCAGCTTTGTTCCCGGCTTTGAGGTTGGCAGGGGAAGGAAAGTTGAGGTGGGAGACAGTGGAAGATATA
TGGTCTGGAATGTGTGTTAAGGTTATATGTGATCACCTGGGACTTGGTGTAAAAAGTGGGATACCTTATGTATGGAGAAG
GGAAAGAGGTGATGCCATTGAAAGCTTGAAGAAAGAGTGGGAAGGGGTGAAGCTGATGGAGGAAGTGGTTCCTTTCTTTC
AGTCGGTTAGGTTACCCCAAACAGCTGTTACAGCCGAAGACTGTGTTGTCGAAATGGCAAAGTCGGTGAAGGAGCAGTTG
GGAAAGGTAGATCCTATGTTTGCTCGTGCTGCTGATGCCATGGGGGATTGGGTGAAGCTCTGGAAGTCAGTGGGATCCAG
CTCACCTGGAGTTTAA

Alignment

ORF - retro_pper_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.3 %
• Parental protein coverage: 93.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPLLKDELDIVIPTIRN--LDFLEMWRPFFEQYHLIIVQDGDPSKVIKVPEGFDYELYNRNDINRILGPK
          T.....E.DIVI..I......F...WRP.F.Q.HLIIV.D.D.......PEGF........DI.R..G..
Retrocopy TSINNNEVDIVIAAINSDLEPFMNEWRPVFSQFHLIIVKDPDMNGELHIPEGFNVDVFTKSDIDRVVGSS

Parental  ASCISFKDSACRCFGYMVSKKKYIFTIDDDCFVAKDPSGKDINALEQHIKNLLTPSTPFFFNTLYDPYRE
          .S.I.F....CR.FGY.VS.KKYI..IDDDC..A.D..G.......QHI.NL..P.TPFFFNTLYDPYR.
Retrocopy TS-ILFSGYSCRYFGYLVSRKKYIISIDDDCIPARDTNGDLVDVVAQHIANLQAPATPFFFNTLYDPYRK

Parental  GADFVRGYPFSLREGIPTAVSHGLWLNIPDYDAPTQLVKPLERNTRFVDAVLTIPKGTLFPMCGMNLAFN
          GADFVRGYPFSLR.G...A.S.GLWLN..DYDAPTQ..KP..RN.R.VDAV.T.P...L.P..G.N.AFN
Retrocopy GADFVRGYPFSLRSGVTCALSCGLWLNLADYDAPTQALKPEQRNSRYVDAVMTVPVRSLMPVSGINIAFN

Parental  RELIGPAMYFGLMGDGQPIGRY---DDMWAGWCMKVICDHLGLGVKTGLPYIWHSKASNPFVNLKKEYKG
          RE..GPA....L...G....R.....D.W.G.C.KVICDHLGLGVK.G.PY.W..........LKKE..G
Retrocopy REVVGPALFPALRLAGEGKLRWETVEDIWSGMCVKVICDHLGLGVKSGIPYVWRRERGDAIESLKKEWEG

Parental  IYWQEELIPFFQSATLPKDCTTVQSCYIELSKQVKAKLGKVDDYFLKLADAMVTWVEAWDELNPS
          ....EE..PFFQS..LP....T...C..E..K.VK..LGKVD..F...ADAM..WV..W.....S
Retrocopy VKLMEEVVPFFQSVRLPQTAVTAEDCVVEMAKSVKEQLGKVDPMFARAADAMGDWVKLWKSVGSS

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_48 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
Musa acuminata	GSMUA_Achr8G28120_001	1 retrocopy	retro_macu_52,
Medicago truncatula	MTR_2g461970	1 retrocopy	retro_mtru_4,
Prunus persica	PRUPE_ppa007588mg	1 retrocopy	retro_pper_48 ,
Setaria italica	Si030277m.g	1 retrocopy	retro_sita_19,