RetrogeneDB ID: retro_pper_6

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_4:4414358..4416152(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa018024mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa003107mg
• Aliases: None
• Description: None

Sequence

>retro_pper_6
ATGGTGACTGGCATTGAAGCTGCTGGTGGTGGACAGGGCAATGGGATCAGGAAAAGAAGTTGCTTTTGCAGCAAGGAAGA
TTTTTTGCCAGAGGAGTCATTCAAGAGCTGGGGAAACTATGTTCATGCACTGGCCAACACAAAAACAAGGCTCACAGACC
GTATCCTGGCACGGTCCATGGACCACCAGGAGCTCGAACAAATGCGTGCACGGAGCAACAATCAGATGAAGAAAACCCTC
AATTGGTGGGACCTCATTTGGTTCGGCATTGGAGCAGTCATGGGGGCAGGAATTTTCGTGCTAACTGGTCAGGCGGCTAG
GAACGATGCTGGCCCTGCAGTAGTAATCTCTTATTTCATATCAGGTGTTTCTGCACTATTATCAGTGCTGTGCTACACTG
AGTTCTCAGTGGAACTCCCTGTGGCTGGAGGCTCATTTTCCTATCTTAGAGTAGAACTTGGTGATTTTGTGGCCTATATT
GCTGCTGGAAACATCCTTTTTGAGTATGTAGTAGCAGGTGCTAGTGTGGCAAGGTCATGGACCTCATACTTTGCTACATT
GTGCAATCACAATCCCAACGATTTTCGAATCAACGTGCCAGCCCTTGCCGACAACTTCAACCATTTAGACCCGATCGCCG
TCGTTATCTCCATTGTGGTTTGCATCGGTGCAGCCTTGAGCATGAAGGCCTCGTCTAGATTCAATTCGGTTACAACTATC
GTCCATCTGGTGGTTTTGGTTTTCATCTTCATTACCGGCATGACCAAGGCCAACCCTGCTAATTTCACCACAAACTTTTT
ACCATTTGGCTTCCGCGGTGTCTTGAAAGCTTCAGCGGTTCTCTTCTTTGCTTATGTAGGATTTGATGGTGTGGCAACCT
TGGGGGAGGAGATTAAAAACCCTGGTAGAGATATCCCGATTGGGCTGATTGGCTCAATGTTGGTTACCATAACAACTTAT
TGCGTCCTTTCAGCTACGTTGTGCCTGATGCAGCCATACAGCCAAATTGATGCTGATGCCTCATTCACCATGGCCTTTCA
AGCTGCAGGTATGAATTGGGCAAAGTACATTGTTGCTTTGGGAGCAATTAAAGGCATGACAACAGTCCTGCTAGCCAACC
TCATCGCTCAAGCTCGGTATTTCACTCACATTGGGCGCACCCACATGGCACCAGCAATCCTGGCATCCATCCACCCAAAA
ACTGGCACGCCTGTGAATGCCACGGTCATTATGACTGTTGCAAACTGCCTTGTTGCCCTCTTCACAAGCCTTGATGTCCT
GGCAAACCTTCTTTCTATATCAACCCTGTTCATCTTTTCCCTTGTTTCCTTAGCACTGATCGTACGACGATACTACGTTA
CTGGTGAAACATCAACTTCTGACAGAAACAAGCTCATTATATTCTTGACATTAATCGTAGGATCATCAATTGCTACTGCT
GTTTATTGGGTGCTTAGCCAGGGTTGGATTGGCTACGTCGTGACAGGCGTAATTTGGTTTGCTGCCACTTTAGGCTTGCA
ATTGACCCTCAAACAAGCAAAGAAACCTAAACTGTGGGGGGTGCCATTGGTTCCTTGGTTGCCATCAGCTAGCATTGCAT
TCAATGTTTTCATCTTGGGTTCTATTGATGTACCTTCATTCATAAGATTCGCAATTTGGACGTTGGTTTTGCTCGTCTAC
TATATATTCGTCGCACTGCATGCTTCATATGATGCAGCAAGGGAGACTGATAGAGTAGAAGCTCAAGCTAGTCAAGCTAG
TCAAGCAACCAACATGGAGGCTGGGACTAGCTAA

Alignment

ORF - retro_pper_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.32 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VASGTEASGGGD-EGLRRRGCTYRKYDFLPEESFQTWGNYVKALSQTPGRFKDRVLTRSLDSTELVEMKA
          ...G.EA.GGG...G.R.R.C...K.DFLPEESF..WGNYV.AL..T..R..DR.L.RS.D..EL..M.A
Retrocopy MVTGIEAAGGGQGNGIRKRSCFCSKEDFLPEESFKSWGNYVHALANTKTRLTDRILARSMDHQELEQMRA

Parental  QSHNEMKKTLNWWDLIWFGIGAVIGAGIFVLTGLEAKKHAGPAVVLSYVVSGVSALLSVFCYTEFAVEIP
          .S.N.MKKTLNWWDLIWFGIGAV.GAGIFVLTG..A...AGPAVV.SY..SGVSALLSV.CYTEF.VE.P
Retrocopy RSNNQMKKTLNWWDLIWFGIGAVMGAGIFVLTGQAARNDAGPAVVISYFISGVSALLSVLCYTEFSVELP

Parental  VAGGSFAYLRVELGDFTAFIAAGNILLEYVIGGAAVARSWTSYFATLCNHNSNDFRIVAPGLGENYKYLD
          VAGGSF.YLRVELGDF.A.IAAGNIL.EYV..GA.VARSWTSYFATLCNHN.NDFRI..P.L..N...LD
Retrocopy VAGGSFSYLRVELGDFVAYIAAGNILFEYVVAGASVARSWTSYFATLCNHNPNDFRINVPALADNFNHLD

Parental  PIAVVVIIGICFLAVLSTKGSSRLNYIASIVHVIVILFIIIAGLTKADTKNYE-KFAPFGPRGVFQASAV
          PIAVV..I..C..A.LS.K.SSR.N....IVH..V..FI.I.G.TKA...N....F.PFG.RGV..ASAV
Retrocopy PIAVVISIVVCIGAALSMKASSRFNSVTTIVHLVVLVFIFITGMTKANPANFTTNFLPFGFRGVLKASAV

Parental  LFFAYVGFDAVSTMAEETKNPGKDIPIGLVGSMVITTFVYCLLAVTLCLMQPYGSIDEQAPFSVAFEAVG
          LFFAYVGFD.V.T..EE.KNPG.DIPIGL.GSM..T...YC.L..TLCLMQPY..ID..A.F..AF.A.G
Retrocopy LFFAYVGFDGVATLGEEIKNPGRDIPIGLIGSMLVTITTYCVLSATLCLMQPYSQIDADASFTMAFQAAG

Parental  MGWAKYVVAAGALKGMTSVLLVGAVGQARYLTHIARTHMVPPWFAQVDGKTGTPVNATVTMLSATAFIAF
          M.WAKY.VA.GA.KGMT.VLL.....QARY.THI.RTHM.P...A....KTGTPVNATV.M..A....A.
Retrocopy MNWAKYIVALGAIKGMTTVLLANLIAQARYFTHIGRTHMAPAILASIHPKTGTPVNATVIMTVANCLVAL

Parental  FSSLDVLASLLSISTLFIFSLVAIALLVRRYYVSGVTTQATRNKFIACLVLIVGSSIATSVYWSKTDKWT
          F.SLDVLA.LLSISTLFIFSLV..AL.VRRYYV.G.T....RNK.I..L.LIVGSSIAT.VYW.....W.
Retrocopy FTSLDVLANLLSISTLFIFSLVSLALIVRRYYVTGETSTSDRNKLIIFLTLIVGSSIATAVYWVLSQGWI

Parental  AYVVTAPLWFLGTLGIWILVPQARSPKLWGVPLVPWLPSLSVAINIFLLGSIDRDSFIRFAAWTLIILVY
          .YVVT...WF..TLG......QA..PKLWGVPLVPWLPS.S.A.N.F.LGSID..SFIRFA.WTL..LVY
Retrocopy GYVVTGVIWFAATLGLQLTLKQAKKPKLWGVPLVPWLPSASIAFNVFILGSIDVPSFIRFAIWTLVLLVY

Parental  YFFFGLHASYDTAKDSLAKRLEAAARDSGLDGKSGSN
          Y.F..LHASYD.A.........A...........G..
Retrocopy YIFVALHASYDAARETDRVEAQASQASQATNMEAGTS

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_6 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR12G15690	1 retrocopy	retro_lper_7,
Prunus persica	PRUPE_ppa003107mg	1 retrocopy	retro_pper_6 ,