RetrogeneDB ID: retro_slyc_30

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:10339681..10340404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc03g044670.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc11g020060.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_30
ATGAACTCTGATGTTCACTCCCGTGCAAAGAGGATGAAGCTCATAATGCAATTTGGAGTTGGGTTAGAAGGTGTTGACAT
TACTGCTGCCACAAATCATTGCATTAAGGTCGCCAAAATTTCGGGTGGTGCAACTGGAAATGCTGCTTCATATGCTGAAA
TGGCCATATATCTCATCTTGGGCCTCCTGCGTAAGCAACATCAAATGAAAATTTCCGTGGAGCAGAAAAAGCTAGGGGAG
CCAACTGGTGTCAACCTGCATGGGAAAACGGTATTTATCCTGGGGTTTGGAAATATCGGGATACATTTAGCAAAGCGTCT
ACGCCCATTTGACGTGAAAATACTTGCTACAAAACGAAGTTGGGGCCGGCCTGCACAGGACTCGAGCAAATCCGAGGCAC
CGTCTGTTGAGAATGGTGGCTACGCTGACCTAGTTGACGAGAGGGGAAACCATGCTGATATCTTGAAGTTTGCAAGCAAA
GCTGATATTGTTGTATGTTGCTTAGCTATGAACAATGAAACTATTGGCATCGTGAACAACGATTTTATATCTGTCATGAG
AAAGGGTGTCGTTCTGATTAATATAGCTCAAAGGGAGGAGGATTGTCCAAGCCTTATAAAGATTCCACCCATCTGTCATT
CTTTTAACACTCCACCTCACGCCCAGTGCTTAGCATCTAGTGCGTGGGCAATTTTTAATTTTGGGGACCCCAACATCGGG
TGA

Alignment

ORF - retro_slyc_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.43 %
• Parental protein coverage: 70.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNSDVLSRAKRMKLIMQFGVGLEGVDITAATKHGIKVAKIPGGATGNAASCAEMAIYLILGLLRKQHQMK
          MNSDV.SRAKRMKLIMQFGVGLEGVDITAAT.H.IKVAKI.GGATGNAAS.AEMAIYLILGLLRKQHQMK
Retrocopy MNSDVHSRAKRMKLIMQFGVGLEGVDITAATNHCIKVAKISGGATGNAASYAEMAIYLILGLLRKQHQMK

Parental  ISVEQKKLGEPTGVNLQGKTVFILGFGNIGIHLAKRLRPFDVKILATKRSWGRPAQDSSKSEAPSVENGG
          ISVEQKKLGEPTGVNL.GKTVFILGFGNIGIHLAKRLRPFDVKILATKRSWGRPAQDSSKSEAPSVENGG
Retrocopy ISVEQKKLGEPTGVNLHGKTVFILGFGNIGIHLAKRLRPFDVKILATKRSWGRPAQDSSKSEAPSVENGG

Parental  YADLVDERGNHADILKFASKADIVVCCLAMNNETIGIVNNDFISVMRKGAILINIAR
          YADLVDERGNHADILKFASKADIVVCCLAMNNETIGIVNNDFISVMRKG..LINIA.
Retrocopy YADLVDERGNHADILKFASKADIVVCCLAMNNETIGIVNNDFISVMRKGVVLINIAQ

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_30 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	Solyc11g020060.1	1 retrocopy	retro_slyc_30 ,