RetrogeneDB ID: retro_slyc_10

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:41735109..41735862(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g072570.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g006120.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_10
ATGGCAACTGATTCAAAAAAAACTGATCGTGAGGAACAAGAATATGCAAAGTGTGTTTGGATGAGTCTTCAACACGAAGA
ACTAACCGAACTTGAAGATGCTGCAGCTCAAATCCAAGACGGTGAAAAAGATGAAGGGAAACTGACACAACTCGCTGAAA
AAATCATACAACATTTTCAAGAGCACTCTGACAACCGTCTCCGTCTAGCCCGAAAAGACGTGTCCCCATTCTTCGCACCG
GTCACGTGCTCACCTTTGGAGAATTCGGTCTTATGGATCGCTGGCTGTAGACCTTCTTCTTTCATTAGACTCATTTATGC
TCTCTGTGGATTCGAACCCGACGTCCAAGGAACTGATCCGTGCCTTGAAGGGATAGTAACCGAGGATCTTCGCGAACTAT
CTGAGAAACAGCTGAGGATGATTAACGAGTTGCAAGGCAAGACGATTCGAGAGGAGAGGAGGATTTCAACGAAATTTGCT
AGCTTACAAGAGGACACGGTGGATCAACCGCTTGCGGGGAAGATGAAGAAAGAGGGACATGGTTGTGAGAAAGCGGATGA
AGCTTTAGATGAACATAGTGGACACATGGCGGATGTAATTGAAGAAGCTGATCGACTGAGAATGAAGACGCTGAAGGAAA
TAGTGAACATACTTGAACCGGTTCAGGCGGTGGAATACTTAGCAGCAGCTAAGAAAATGAGGTTTTGTGTGCAACAATGG
GGAGAGAAGAGGGATCAGCAGCATAAGGAGTAG

Alignment

ORF - retro_slyc_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.3 %
• Parental protein coverage: 97.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNNFQGYANGRSRLARVDVSPFFAPTWCTPLENSVLWIGGCRPSTFIRLIYALCGIEIQ-SHTARYLQG
          ....FQ.....R.RLAR.DVSPFFAP..C.PLENSVLWI.GCRPS.FIRLIYALCG.E.....T...L.G
Retrocopy IIQHFQEHSDNRLRLARKDVSPFFAPVTCSPLENSVLWIAGCRPSSFIRLIYALCGFEPDVQGTDPCLEG

Parental  MKIGEFGHLSGEQITMIDKLQRQIILEERRFSSRLASLQEDVVDQPFA--MAARIYDTERDENEIEPLNK
          ........LS..Q..MI..LQ...I.EERR.S...ASLQED.VDQP.A..M.......E...........
Retrocopy IVTEDLRELSEKQLRMINELQGKTIREERRISTKFASLQEDTVDQPLAGKMKKEGHGCEKADEALDEHSG

Parental  HGEDMSNLLEEVDELRMKTLKEILGILTPIQGVEYLAATKRIRLCLQQWGKKREQEH
          H...M....EE.D.LRMKTLKEI..IL.P.Q.VEYLAA.K..R.C.QQWG.KR.Q.H
Retrocopy H---MADVIEEADRLRMKTLKEIVNILEPVQAVEYLAAAKKMRFCVQQWGEKRDQQH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Solanum lycopersicum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum lycopersicum was not studied using ChIP-Seq data.

EST

Solanum lycopersicum was not studied using EST data.

TSS

Solanum lycopersicum was not studied using FANTOM5 data.

Lab

retro_slyc_10 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum lycopersicum 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
Solanum lycopersicum	Solyc03g006120.2	1 retrocopy	retro_slyc_10 ,