RetrogeneDB ID: retro_pper_14

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_5:15694866..15696420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa016144mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa004404mg
• Aliases: None
• Description: None

Sequence

>retro_pper_14
ATGCAATCTCAAGTACCCTTTTCTACAACGGATCTCGTTCTATTGCCCATCTCAACAATTCTCATCTTCCTAGCTTGCAA
ACTCCACAACCGTCTAAGATTTAAGCTTCCTCCAGGACCCTACCCATGGCCTATCATTGGGAACCTTCACAACCTGGGAG
CCGTTAGATCTCGGTGTTTTTTTGAGTTGTCACAAGTTTATGGTCCAATCGTATCGGTGTGGTTGGGCTCAAGTTTGCAC
ATAGTAGTTTCAAACCCTGAATTGGCAAAGCAAGTGCTCAAAGACAATGATGAGCAGTTAGCACATAGGCACAGGACTTG
GTCTAGTTCTAGGATCACAAAAAATGGTAAGGACCTTATATGGGCAGATTATGGTCCTCACTACATAAAGCTTCGGAAGA
TTTGTATGCTTGAACTTTTATCTCCTAAGAATCTTGAGACTTTTAGACACGTTAGAGAAGATGAAGTTAGAGCCATGATA
GAGTCCATTTTCAAAGATTGTAGCAAGTCTCAAGATTATAGAAAATGTTTAGTGGTCAGAAAATACTTGAGATCAGTGGC
ATTCAACATTATCACAATGCTATTGTTTGGAAAGCGGTTTGAGAATGAAGTGGGTGAGCTAAACCAGCAAGGGTTGGAAA
TTGTGGCAATTCTGGCTAATGAAAGAAAGCTTGGTGCATATCTACCTATTTTTGAAGAGAATTGGTGGCTCAGATGGGTT
TTGTGGTTTCAAAGTACTGCAATTTCCAGACATTTGGCAAGGAAAGAGAAATTCACACAAGCAATCAAGGAGGAGCATAT
GCTTGAGAGTAAGTCTAACGGCGTTGGTGGTGTCAAGCAGCATTTTTTGGGTGCATTGCTTGGTGATCAAGAAAAATACG
AACTCACTGAGGATAGTGTTGAAGGACTACTTTGGGATATGATCACTGCAGGCACGGACACAATTGCTATCTCAGCTGAA
TGGGCCTTGGCGCAGTTGATCAAGAACCCGAGGGTGCAACGAAAGTCCCAAGAGGAGCTTGATCGCGTAATTGGGCTGGA
CCGCACGATGACAGAATCCGATATTTCAAGCCTTCCTTACCTAAAATGTGTAGCCAAGGAGGCACTGAGGCTGCACCCTC
CAACCCCACTAATGCTACCTCACAAGGCCAATGCCAGAGTCAAGATTGGTGGGTATGATATCCCTAAGGGAACCACTGTT
CATGTAAATGTTTGGGCCATAGGGCGTGATCCGAAAGCGTGGCCCAACCCGGTTGATTTTCGACCCGAAAGGTTCATTGA
AGAAGACATTGATGCAAAGCGTCATAATTTTCAGCTTCTACCATTTGGTGCAGGAAGGCGTGTGTGCCCAGCAGCACAAC
TAGGCACCAATTTGGTCACCTACATGCTGGGGCAACTTTTGCATAGCTTTTGTTGGACATTGCCTGAAGGGATCCAGCCC
AAGGATATTGACACGTCAGAGGGCCCAGGATTGGTAAGCTATATGCAGACCCCTCTACAAGGGGTCCCAAATTTGAGATT
GCCACCACACTTGTACAAGCAGTCCCAAGATTGA

Alignment

ORF - retro_pper_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.95 %
• Parental protein coverage: 97.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPISSIIILIFLAYKLYQRLRFKLPPGPRPWPIVGNLYDIKPVRFRCYAEWAEAYGPIISVWTGSTLNVI
          LPIS.I..LIFLA.KL..RLRFKLPPGP.PWPI.GNL.....VR.RC..E....YGPI.SVW.GS.L...
Retrocopy LPISTI--LIFLACKLHNRLRFKLPPGPYPWPIIGNLHNLGAVRSRCFFELSQVYGPIVSVWLGSSLHIV

Parental  VSSSELAREVLKEHDQKLADRHRSRSAAKFSKDGQDLIWADYGPHYVKVRKVCTLELFSPKRIEALRPIR
          VS..ELA..VLK..D..LA.RHR..S.....K.G.DLIWADYGPHY.K.RK.C.LEL.SPK..E..R..R
Retrocopy VSNPELAKQVLKDNDEQLAHRHRTWSSSRITKNGKDLIWADYGPHYIKLRKICMLELLSPKNLETFRHVR

Parental  EDEVTAMVESIFKHCTNPENNGKSLLVKKYLGAVAFNNITRLAFGKRFVNSEDVIDEQGLEFKAIVANGL
          EDEV.AM.ESIFK.C.......K.L.V.KYL..VAFN.IT.L.FGKRF.N.......QGLE..AI.AN..
Retrocopy EDEVRAMIESIFKDCSKSQDYRKCLVVRKYLRSVAFNIITMLLFGKRFENEVGELNQQGLEIVAILANER

Parental  KLGASLAMAEHIPWLRWMFPLEEEAFAKHGARRDRLTRAIMEEHT--QARNKSGGAKQHFVDALLTLQDK
          KLGA.L...E...WLRW.......A...H.AR....T.AI.EEH......N..GG.KQHF..ALL..Q.K
Retrocopy KLGAYLPIFEENWWLRWVLWFQSTAISRHLARKEKFTQAIKEEHMLESKSNGVGGVKQHFLGALLGDQEK

Parental  YDLSEDTIIGLLWDMITAGMDTTAITVEWTMAELIKNPRVQQKAQEELDRVIGFERVMTETDFSNLPYLQ
          Y.L.ED...GLLWDMITAG.DT.AI..EW..A.LIKNPRVQ.K.QEELDRVIG..R.MTE.D.S.LPYL.
Retrocopy YELTEDSVEGLLWDMITAGTDTIAISAEWALAQLIKNPRVQRKSQEELDRVIGLDRTMTESDISSLPYLK

Parental  CVAKEGMRLHPPTPLMLPHRANANVQIGGYDIPKGSNVHVNVWAVARDPEVWKNPYEFRPERFLEEDVDM
          CVAKE..RLHPPTPLMLPH.ANA.V.IGGYDIPKG..VHVNVWA..RDP..W.NP..FRPERF.EED.D.
Retrocopy CVAKEALRLHPPTPLMLPHKANARVKIGGYDIPKGTTVHVNVWAIGRDPKAWPNPVDFRPERFIEEDIDA

Parental  KGHDFRLLPFGAGRRVCPGAQLGINLVTSMLGHLLHHFSWTPAEGAKPEEIDMSENPGLVTYMRTPLQAV
          K.H.F.LLPFGAGRRVCP.AQLG.NLVT.MLG.LLH.F.WT..EG..P..ID.SE.PGLV.YM.TPLQ.V
Retrocopy KRHNFQLLPFGAGRRVCPAAQLGTNLVTYMLGQLLHSFCWTLPEGIQPKDIDTSEGPGLVSYMQTPLQGV

Parental  PTPRLPSHLYKR
          P..RLP.HLYK.
Retrocopy PNLRLPPHLYKQ

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_14 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_ppa004404mg	1 retrocopy	retro_pper_14 ,