RetrogeneDB ID: retro_pper_3

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_2:13317899..13319240(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa021368mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa006608mg
• Aliases: None
• Description: None

Sequence

>retro_pper_3
ATGCTTACCTTGAATCTAAGTTGTCCTGCTTCCACTGTCACTTTCCCCCAATCCGGACATCAACACCCCATTAATGCCTC
CTCTTCACTTCTCAATCCGAATCTTCTCAACCGAATCCAAATCCAGAGAACCCTACACACCTCATTTCCTCTGCTCCACA
AACCCACCTCTCCCAAACTTGAAGCATCCACCAAAGTCTCAAGCTTTAGCAGAATTTATGGCCACCCAATTGGAATTTCT
TCAAAACCCATATCTCAGGTCCAAGATTGGGGCTCAAAGATCAGTCAATTGAACAAAACCTGTGGATTCCCATCTGGGTT
TTCTTCCAAACCCAGATTCCAAATCCCCAAAGCTGCATCTGAGGCCAATCCAGAACGAGGAGAAAGTGAAGCTGCAGTTT
CAAAGCCCAAGGCCACAACCGCCCAGCTTGCACTTATTTTTGGGCTCTGGTACTTCCAGAACATTGTCTTTAACATTTAC
AACAAGAAGATATTAAATATTTTCCCATTTCCATGGCTTCTTGCTTCTTTTCAGCTCTTTGCTGGGTCTGTTTGGATGTT
GGCTCTCTGGTCTTTGAAGCTCCAACCATGCCCCAAAATATCAAAACCATTCATAGTTGCACTCCTTGGACCTGCATTGT
TCCACACAATAGGCCACATCTCAGCATGTGTCTCATTCTCTAAGGTGGCTGTTTCTTTCACCCATGTAATCAAATCTTCA
GAGCCTGTTTTCTCGGTTGTCTTTTCGTCGTTCGTAGGCGATTCGTACCCTTTACAGGTCTGGCTTTCAATCCTCCCTAT
TGTCTTGGGTTGTTCTCTAGCTGCAATTACTGAGGTGTCATTCAATTTCCAAGGCCTGTGGGGTGCGTTGATTAGCAATG
TTGGGTTTGTGTTGAGAAATATTTACTCAAAACGCAGTTTACAGAACTTCAAGGAGGTAGATGGGTTGAATTTGTATGGT
TGGATCACCATACTTTCACTCCTCTATCTGTTTCCTGTTGCTATTTTTGTTGAAGGGTCTCAATGGGTTCAAGGGTATCA
CAGAGCTATTGCAACTGTAGGAAAACCATCCACATTTTATATATGGGTGTTGTTATCTGGAGTGTTTTACCATCTCTATA
ACCAGTCGTCTTATCAGGCTCTTGATGAAATTAGCCCCTTGACATTTTCAGTTGGAAACACAATGAAGAGAGTGGTGGTA
ATTGTATCTACTGTGTTGGTGTTCAGAAATCCAGTTAGACCTCTTAATGCACTTGGATCCGCCCTTGCGATATTTGGGAC
TTTCCTGTATTCACAGGCAACAGCATCTAAAAAGCAAAAGGGCGGTGAAAAGAAGAATTGA

Alignment

ORF - retro_pper_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.92 %
• Parental protein coverage: 80.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADKSRPLKVNIELPDQQAASQRFKIGIYFATWWALNVVFNIYNKKVLNVFPYPWLTSTLSLATGSLMMLI
          A....P.....E................F..W...N.VFNIYNKK.LN.FP.PWL.....L..GS..ML.
Retrocopy ASEANPERGESEAAVSKPKATTAQLALIFGLWYFQNIVFNIYNKKILNIFPFPWLLASFQLFAGSVWMLA

Parental  SWATRIAEAPKTDLDFWKTLFPVAVAHTIGHVAATVSMAKVAVSFTHIIKSSEPAFSVLVSRFLLGESFP
          .W.......PK....F...L...A..HTIGH..A.VS..KVAVSFTH.IKSSEP.FSV..S.F..G.S.P
Retrocopy LWSLKLQPCPKISKPFIVALLGPALFHTIGHISACVSFSKVAVSFTHVIKSSEPVFSVVFSSF-VGDSYP

Parental  LSVYLSLFPIIGGCALAAITELNFNMIGFMGAMISNLAFVFRNIFSKKGMKG-KSVSGMNYYACLSMLSL
          L.V.LS..PI..GC.LAAITE..FN..G..GA.ISN..FV.RNI.SK......K.V.G.N.Y.....LSL
Retrocopy LQVWLSILPIVLGCSLAAITEVSFNFQGLWGALISNVGFVLRNIYSKRSLQNFKEVDGLNLYGWITILSL

Parental  LILIPFAIAVEGPKVWAAGWNTALAQIG--PNFVWWVAAQSIFYHLYNQVSYMSLDQISPLTFSIGNTMK
          L.L.P.AI.VEG...W..G...A.A..G....F..WV.....FYHLYNQ.SY..LD.ISPLTFS.GNTMK
Retrocopy LYLFPVAIFVEGSQ-WVQGYHRAIATVGKPSTFYIWVLLSGVFYHLYNQSSYQALDEISPLTFSVGNTMK

Parental  RISVIVSSIIIFHTPVQPVNALGAAIAILGTFLYSQRKTTSKNNKG
          R..VIVS....F..PV.P.NALG.A.AI.GTFLYSQ..T.SK..KG
Retrocopy RVVVIVSTVLVFRNPVRPLNALGSALAIFGTFLYSQ-ATASKKQKG

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_3 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_2g022700	1 retrocopy	retro_mtru_13,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Prunus persica	PRUPE_ppa006608mg	1 retrocopy	retro_pper_3 ,