RetrogeneDB ID: retro_slyc_16

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 6:39799586..39800618(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc06g063040.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g010950.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_16
ATGGCAGAAGAAGTGAGCAACAAACAGGTCATTCTGAAACACTTTGTCACCAGTGACCTTAAGGAATCAGACATGGAATT
CAAAAATACCACCATCAAATTGAATGTTCCAGAAGGTTGTAATGCTATGGTTTTGAGGAATCTTTTCTTGTCATGTGACC
CTTACATGCGGTTACGCATGAAGAAATTTGAGGGTAGCTATATTGAGTCCTTCACTCCTGGCTCTCCTATCACAGGATAT
GGAGTGGCTAAAGTTTTGGAGTCTGGTGATTCGAACTTCCAGAAAGGTGACTTAGTTTTGGGAAGGACTGGATGGGAGGA
GTATAGTATTGTAACAGCTACTCCGACTCTGTTTAAAATTCATGACAAGGATGTGCCTCTTTCCTACTATACAGGAATCC
TCGGTATGCCTGGTCTCACAGCTTATGCTGGTTTTTACGAGGTTTGCTCCCCTAAGAAGGGAGAAACCGTCTTTGTTTCA
GCTGCTTCTGGAGCAGTTGGTCAGCTTGTTGGGCAATTTGCAAAGATGTTGGGTTGCTATGTTGTCGGTAGTGCTGGAAG
TAAAGAAAAGGTTGATCGGTTGAAGAGCACGTTTGGTTTTGATGAAGCTTTTAACTACAAAGAGGAGCAGGATTTAGACG
CGGCTCTGAAGAAGTACCTCCCTGATGGAATCGACATCTACTTTGAGAACGTTGGAGGGAAGATGCTTGATGCAGTTCTT
CTGAATATGAAAATCCATGGTCGTATTGCTGTGTGTGGGATGATCTCACAATACAACCTTGAGCAGACTGAAGGAGTGCA
CAACTTGTTCTGTCTCATCTCGAAACGAATCCGCATGGAAGGATTTCTTGTTCATGATTACTATCATCTTTACCCTAAGT
ATTTGGACATGATCATTCCGCAAATCAAGGCTGGTAAGGTTGTGTATGTGGAAGACATAGCTGAAGGCCTCGAAAGTGCT
CCCAGTGCTCTTGTTGGTCTCTTCTCTGGTCGCAATATTGGAAAGCAAGTTGTGATGGTTTCGCGTGAATGA

Alignment

ORF - retro_slyc_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEMIMNNKQIILKHYVEGYPKESDLEFKNNNIKLNVPEGSNVVVLKNLYLSCDPYMRSRMSKLEGSYV
          MAEE....NKQ.ILKH.V....KESD.EFKN..IKLNVPEG.N..VL.NL.LSCDPYMR.RM.K.EGSY.
Retrocopy MAEEV--SNKQVILKHFVTSDLKESDMEFKNTTIKLNVPEGCNAMVLRNLFLSCDPYMRLRMKKFEGSYI

Parental  QSFTPGSPITGCGVAKVLKSGDSNFQEGDLVWGMIGWEEYSIVNATQSALFKIHDKNVPLSYYTGILGMP
          .SFTPGSPITG.GVAKVL.SGDSNFQ.GDLV.G..GWEEYSIV.AT...LFKIHDK.VPLSYYTGILGMP
Retrocopy ESFTPGSPITGYGVAKVLESGDSNFQKGDLVLGRTGWEEYSIVTATPT-LFKIHDKDVPLSYYTGILGMP

Parental  GMTAYVGFYEICSPKKGETVYVSAASGAVGQLVGQFAKTLGCYVVGSAGTKEKVDLLKNKLGFDEAFNYK
          G.TAY.GFYE.CSPKKGETV.VSAASGAVGQLVGQFAK.LGCYVVGSAG.KEKVD.LK...GFDEAFNYK
Retrocopy GLTAYAGFYEVCSPKKGETVFVSAASGAVGQLVGQFAKMLGCYVVGSAGSKEKVDRLKSTFGFDEAFNYK

Parental  EEKDLVADLKRYFPNGIDIYFENVGGKMLDAVLMNMKLHGRIAVCGMISQYNLEKTEGVHNLFCLITKRI
          EE.DL.A.LK.Y.P.GIDIYFENVGGKMLDAVL.NMK.HGRIAVCGMISQYNLE.TEGVHNLFCLI.KRI
Retrocopy EEQDLDAALKKYLPDGIDIYFENVGGKMLDAVLLNMKIHGRIAVCGMISQYNLEQTEGVHNLFCLISKRI

Parental  RMEGFLVSDHYHLYPKYLEMIIPQIKAGNVVYVEDIAEGLENAPKALVGLFYGRNVGKQLVMVSRE
          RMEGFLV.D.YHLYPKYL.MIIPQIKAG.VVYVEDIAEGLE.AP.ALVGLF.GRN.GKQ.VMVSRE
Retrocopy RMEGFLVHDYYHLYPKYLDMIIPQIKAGKVVYVEDIAEGLESAPSALVGLFSGRNIGKQVVMVSRE

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_16 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc12g010950.1	1 retrocopy	retro_slyc_16 ,