RetrogeneDB ID: retro_pper_11

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_1:46502418..46503750(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa005789mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa005966mg
• Aliases: None
• Description: None

Sequence

>retro_pper_11
ATGGACTTGAAGATAACCCCTTTCTTTTTCTTCTTCTTCTTTGCTCTTTTAATCTCTGTCACCAAAGCCCTAGACCCTTG
TGCCTCCCAATCCGACGGCTCACATGACCTCTCCATCATTCCCACCTACAGCAAATGCTCTCCCTTCAGCCCACCCAAGG
CAGACTCTTGGGTCACCACAGTACTCAACATGGCCTCCAAAGACCCTGCAAGGATAAATTACTTGTCAACCCTAGTGGCC
CAAAAGACCACTTCGGCTCCAATCGCTTCGGGCCAGCAGGTCCTCAACATTGCCAACTACGTGGTCCGGCTCAAGCTCGG
TACCCCGGGCCAGCTCATGTTCATGGTTCTCGACACTAGCAATGACATCGCTTGGGCCCCATGTTCCGGGTGCACCGGGT
GCTCCGCTACCACCTTCTTGACTAACTCTTCGACCACTTACAGGTCGTTGGATTGCTCTGTGCATGAGTGTGCCCAGGCC
CGGGGTCTCTCGTGCCCGGCCACTGGGTCTACTGGAGCCAATGGTTGCTTCTTTAATCAATCGTACGGTGGAGATTCATC
ATTTTCTGCCACCCTTGTACAAGATGCTTTGATATTAGGCAATGATGTTCTTCCAAAATTCTCTTTTGGATGCATCAATT
CCATCTCGGGTGGGTCTGTCCCGTCCCAAGGGTTATTGGGCTTGGGTCGTGGATCCATGTCTCTACTCTCACAATCTGGG
TCACTCTACTCGGGCGTGTTTTCATATTGTTTACCAAGTTTCAAATCCTACTACTTTTCAGGATCACTTAAACTTGGCCC
AGCAGGCCAACCCAAATCAATCCGAACCACCCCACTTCTAAGAAACCCGCACCGGCCCTCATTGTATTACGTCAACCTCA
CTGGAATCACTGTGGGCCGGGTTCCCGTACCCATTGCCCCGGAGCTCCTAGCATTCAACCCGAACACAGGAGCTGGAACC
ATAATAGACTCGGGTACGGTCATAACTCGATTCGTGCAACCCGTTTACACCGCACTGCGGGACGAATTTAGAAAACAAGT
GAAGGGTACATTTTCATCATTGGGGGCCTTCGACACCTGTTTTGCTGCAACCAATGAAGCTGTGGCCCCAACCATCACGT
TCCAATTCACAGGCTTGAAGTTGACATTGCCATTGGAGAACAGCTTGATTCACAGCAGCTCAGGGTCAGTAGCTTGCTTG
GCAATGGCTGCTGCGCCTAATAATGTGAACTCAGTACTGAACGTGATAGCCAACTTGCAGCAGCAGAACCTCAGGATTTT
GTTTGATGTTGCCAACTCTGTTGTGGGCATAGCCCGTGAGAATTGTAATTAA

Alignment

ORF - retro_pper_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.21 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVAFSLCLLFFSIAQGLSNNPQCSEAKDQGSNLQVFHVYSPCSPFRPTKPMSWEESVLQMQAKDQARLQF
          F..F....L..S....L.....C....D....L.....YS.CSPF.P.K..SW...VL.M..KD.AR...
Retrocopy FFFFFFFALLISVTKALD---PCASQSDGSHDLSIIPTYSKCSPFSPPKADSWVTTVLNMASKDPARINY

Parental  LSSLVARKSV-VPIASGRQIIQSPTYIVRAKIGTPPQTLLMAVDTSNDAAWVPCNGCVGCGSNVFNSAKS
          LS.LVA.K....PIASG.Q......Y.VR.K.GTP.Q...M..DTSND.AW.PC.GC.GC....F....S
Retrocopy LSTLVAQKTTSAPIASGQQVLNIANYVVRLKLGTPGQLMFMVLDTSNDIAWAPCSGCTGCSATTFLTNSS

Parental  TTYKTLGCQTAQCKQVPNPTC--LGST----CSFNTSYGS-STLAANLSQETFTLATDAVPGYTFGCLQK
          TTY..L.C....C.Q.....C...GST....C.FN.SYG..S...A.L.Q....L..D..P...FGC...
Retrocopy TTYRSLDCSVHECAQARGLSCPATGSTGANGCFFNQSYGGDSSFSATLVQDALILGNDVLPKFSFGCINS

Parental  TTGSSVPPQGLLGLGRGPLSLLSQTQNLYQSTFSYCLPSFKSLNFSGSLRLGPVGQPIRIKYTPLLKNPR
          ..G.SVP.QGLLGLGRG..SLLSQ...LY...FSYCLPSFKS..FSGSL.LGP.GQP..I..TPLL.NP.
Retrocopy ISGGSVPSQGLLGLGRGSMSLLSQSGSLYSGVFSYCLPSFKSYYFSGSLKLGPAGQPKSIRTTPLLRNPH

Parental  RSSLYYVNLNAIRVGRRIVDIPPAALAFNPTTGAGTIIDSGTVFTRLVEPAYVAVRNEFRRRVGKYPFQT
          R.SLYYVNL..I.VGR..V.I.P..LAFNP.TGAGTIIDSGTV.TR.V.P.Y.A.R.EFR..V.K..F..
Retrocopy RPSLYYVNLTGITVGRVPVPIAPELLAFNPNTGAGTIIDSGTVITRFVQPVYTALRDEFRKQV-KGTFSS

Parental  LGGFDTCYSV--PFVVPTITFMFSGMNVTLPEDNIVIHSTAGSITCLAMAAAPDNVNSVLNVIANMQQQN
          LG.FDTC.......V.PTITF.F.G...TLP..N..IHS..GS..CLAMAAAP.NVNSVLNVIAN.QQQN
Retrocopy LGAFDTCFAATNEAVAPTITFQFTGLKLTLPLENSLIHSSSGSVACLAMAAAPNNVNSVLNVIANLQQQN

Parental  HRVLIDVPNSRLGVARERC
          .R.L.DV.NS..G.ARE.C
Retrocopy LRILFDVANSVVGIARENC

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_11 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
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10,
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11 ,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,