RetrogeneDB ID: retro_slyc_76

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:51877117..51877371(+)
• Located in intron of: Solyc04g054170.2

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g097870.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_76
ATGGCAGACAAGATAGTGACTATTAGAACTAGGAAGTTCATGACCAATAGATTATTTGCAAGGAAACAATTCATTATTGA
TGTCTTACATCCTGGAAGAGTCAATGTTTTTAACGCTGATTTGAAAGAAAATTGGCAAGGATGTATGAAGTGAAAGATTT
AAATGCCATCTATGTGAAGTTCAGAACCCACTTTCGAAGAGGCAAATCTTCTGGCTTTGATTTGATCTATGACTGTTGAG
AATGCAGAGAAAAA

Alignment

ORF - retro_slyc_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 64.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADKAVTIRTRKFMTNRLLARKQFIIDVLHPGRANVSKAELKE-KLARMYEVKDANAIFVFKFRTHFGGG
          MADK.VTIRTRKFMTNRL.ARKQFIIDVLHPGR.NV..A.LKE.KLARMYEVKD.NAI.V.KFRTHF..G
Retrocopy MADKIVTIRTRKFMTNRLFARKQFIIDVLHPGRVNVFNADLKE<KLARMYEVKDLNAIYV-KFRTHFRRG

Parental  KSTGFGLIYDSVENAKK
          KS.GF.LIYD..E...K
Retrocopy KSSGFDLIYDC*ECREK

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_76 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	Solyc01g097870.2	1 retrocopy	retro_slyc_76 ,