RetrogeneDB ID: retro_slyc_62

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 11:33442042..33442442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g028500.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_62
ATAAGCTTAGGGAACAAGCTAAGGAAAATAAGAAGGCTAGGACTGGGAACTATGACTATTCTCAGCAGAAATCAGGTGGT
GGAAATCGCTCACAGGGTCAGAAGAATTTTTGGCTTCAGCCCCTTCATTAGCTAGTGTTCCATCCTCCAAGAACATATAT
GACCAGAAGGGTAGAGCACCAGACTCTAAATCTCAGGGAAGTGTTTCAGGCACCAAGACTTACCCCACTTGCCTTAAGTG
TGGTAAGAACCATCCGGGCGAGTGTCTTGCAGGAAAATATGGAGGTTTTAGGTGGGGTCAGTCTGGTCACAGGTTGAGGG
ATTGTTCTTCTAGACAAGGTCAAGGAGGTGGTAATTGTAGTGCTCAGTCTACAACTTTAGTAGCACCAGCAAGGCGCCTA

Alignment

ORF - retro_slyc_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.48 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSPGNRLRRIRRLGIGTMTILSR-IRVGRNLLKSQEKFLAPTPSSASFPSSKSRYDQKGRAPGSKSQGSV
          .S.GN.LR.IRRLG.GTMTILSR.IR....L..S.E.FLA..PS.AS.PSSK..YDQKGRAP.SKSQGSV
Retrocopy ISLGNKLRKIRRLGLGTMTILSR>IRWWKSLTGSEE-FLASAPSLASVPSSKNIYDQKGRAPDSKSQGSV

Parental  SCTKTYLTYPKCGKNHPAVPTSCLTQQGNSSGTGGGQHQNKLYTLQSCKDEEGSLDVVTEDLPKVVPKRE
          S.TKTY.T..KCGKNHP.....CL...G...G...GQ....L....S.....G...........V.P.R.
Retrocopy SGTKTYPTCLKCGKNHPG---ECLA--GKYGGFRWGQSGHRLRDCSS-RQGQGGGNCSAQSTTLVAPARR

Parental  I
          .
Retrocopy L

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_62 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	Solyc04g028500.1	1 retrocopy	retro_slyc_62 ,