RetrogeneDB ID: retro_pper_22

Retrocopy location

• Organism: Peach (Prunus persica)
• Coordinates: scaffold_7:14719797..14720487(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PRUPE_ppa010963mg
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PRUPE_ppa012586mg
• Aliases: None
• Description: None

Sequence

>retro_pper_22
ATGGCAGCCTCTCTCACCATCTCCAGGCTCCTCGCAGCCCCCAAATCCCTCTCTCTCTCCACCACCGCACCTAAATCTTC
TCTTTTCTCACCTAAATCCTTCTCTTCAAAGCTCTCCTACACCCCTCTCCCTCTCAAACACTACCCCCACCCAAAACCCC
TCCTCCGCTTCTCCACCACCGCCAAACCCACCATCTCCGCCACCATCGCCGTCGGCGACAAGCTCCCAGAAGCCACCCTC
TCATACCTCGACGCCGCGGGCGACGTTCAGACCGTCACTCTCTCCGAGCTCACCAAGTCCAAGAAAGCCGTCCTCTTCGC
CGTCCCCGGCGCCTTCACCCCCACCTGCTCTCTGAAGCACGTCCCCGGGTTCGTGGAGAAGTCCGCCGAGCTCAAGGCCA
AGGGGGTCGACACCATTGCCTGCATTGCGGTCAACGACGCCTTTGTGATCAAGGCCTGGAAGGAGAGCCTCAAGATCGGG
GATGAGGTGCTGCTGTTGTCTGATGGAAATGGGGATTTCACCAGGGCCATTGGGGCTGAGCTCGATTTGAGCGATAAGCC
TGTGGGGCTGGGCGTGAGGTCCAGAAGGTACTCGCTTTTGGCTGAAGATGGAGTTGTGAAGGTCTTGAATTTGGAGGAAG
GCGGTGCCTTCACTTCCAGTGGAGCTGAGGACATTCTCAAAGTGCTGTGA

Alignment

ORF - retro_pper_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.67 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APIAVGDVIPDGTLSHFDEEDKVQAVNIHSLAAGKKVILFGVPGAFTPTCSLKHVPGFIEKADELKSKGV
          A.IAVGD..P..TLS..D....VQ.V....L...KK..LF.VPGAFTPTCSLKHVPGF.EK..ELK.KGV
Retrocopy ATIAVGDKLPEATLSYLDAAGDVQTVTLSELTKSKKAVLFAVPGAFTPTCSLKHVPGFVEKSAELKAKGV

Parental  DKILCLSVNDPFVMKAWAKSFPENKHVLFLADGSAKYTHDLGLELDLSEK--GLGTRSRRFALLVDDLKV
          D.I.C..VND.FV.KAW..S......VL.L.DG....T...G.ELDLS.K..GLG.RSRR..LL..D..V
Retrocopy DTIACIAVNDAFVIKAWKESLKIGDEVLLLSDGNGDFTRAIGAELDLSDKPVGLGVRSRRYSLLAEDGVV

Parental  KAANIESGGEFTVSSADDILKAL
          K..N.E.GG.FT.S.A.DILK.L
Retrocopy KVLNLEEGGAFTSSGAEDILKVL

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_22 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22 ,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,