RetrogeneDB ID: retro_slyc_14

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:55297506..55298586(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g094750.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g067100.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_14
ATGGAGTCCAACTGCAAATCCACTAGGCTTACGCCTAAGAAATGCTCCAAGAATACCAAAAATTTGAACCCAAATGTCGA
AAATAGTCCGGGGTTTTCAAAATCTTGTAAATCACCAATGATGGCCAAATCGGCGATGAAAACCCAAAAGTCAGTTTCCA
GAAACCCTAATACTAGTCAATTGGCTTCGCCTTCACCCAAAAACAAAATTCGTCAGAGGAAGTTTGTTATTGCCAAGAAG
AAGAAGTCTAATAGAGATGAAGTGAGCGCTTCAATGGTTTGTAAGTGTAATAAGGTTGGTGATGAGAAAAAGAAGTGTCT
TTGTGTTGCTTACGAGACTCTCAGGGCTTCTCAAGAAGAGTTCTTCAAGAATCGTAGTGGAAATGAACAGGAGGAGGACA
ATGAAGTAGAGAAGTTGGATCGCGATGACAAGTCCTTGATTTCAAACGTTCAGAGTATTACTGGGTGTATGGGTGATTTG
CCAGTCAGGAACAACCAGGAGGTAACAGTTCCTGTTTCAATTTCTGAGGGTGAATTAGTTGAATTGGCGGAAACGTCAAA
GGAAGGGGTGGGTTCGGGTGGAATGAATGTTGTTGGGACTATAAAGAGGGGGAGGGAGAGGTTGTTGGAAGAAGCAAGAC
AAAGTGTACCTGACTCTAGTTCTGGGAAAGTGTTAAATCTTGTCAAGGCTTTTGAGAAGCTCCTCACACCAAAAAAAAAT
GTGTGCGAGGAGAAAGGGGAAAAAGATGAAAAGGAAGAAGAGTCTAGCAAGGAACAACAAGGCTTACAACCCCCCATGAT
TCCTGAGACACAGGTATCTTCATCTTCGTTTTGTCCACCGGATTTTTTCCTCACCTCCGAGAGTTTAGGCTTGGATTCGC
ATCGTGCCTCCTCATTGGATAGCAGCCATGGATGCTTCAGTATTTCAAGCAGGACTTCAGGTGGTGCTCAAAGAAGCAGA
CGCGATAGTGCTGAATCAATAGGCACGCTTCCTAGAAGAAGCTGGAAGAGAAGACATCGCAAACCAACCTCCCAGAAGCC
CTTCAAACTTATAACTGAGGAAAGGGGAAAAAACAAGTAG

Alignment

ORF - retro_slyc_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.77 %
• Parental protein coverage: 68.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESNCKSTRLTPKKCSKNTENLNPNVENSPGFSKSCKSPMMAKSAMKTQKSVSRNPNTSQLASPSPKNKI
          MESNCKSTRLTPKKCSKNT.NLNPNVENSPGFSKSCKSPMMAKSAMKTQKSVSRNPNTSQLASPSPKNKI
Retrocopy MESNCKSTRLTPKKCSKNTKNLNPNVENSPGFSKSCKSPMMAKSAMKTQKSVSRNPNTSQLASPSPKNKI

Parental  RQRKFVIAKKKKSNRDEVNASMVCKCNKVGDEKKKCLCVAYETLRASQEEFFKNRSGNEQEEDNEVEKLD
          RQRKFVIAKKKKSNRDEV.ASMVCKCNKVGDEKKKCLCVAYETLRASQEEFFKNRSGNEQEEDNEVEKLD
Retrocopy RQRKFVIAKKKKSNRDEVSASMVCKCNKVGDEKKKCLCVAYETLRASQEEFFKNRSGNEQEEDNEVEKLD

Parental  RDDESLISNVQSVTGCMGDLPVRNNQEVTVPVSISEGELVELAETSKEGVGSGGMNVVGTVKRGRERLLE
          RDD.SLISNVQS.TGCMGDLPVRNNQEVTVPVSISEGELVELAETSKEGVGSGGMNVVGT.KRGRERLLE
Retrocopy RDDKSLISNVQSITGCMGDLPVRNNQEVTVPVSISEGELVELAETSKEGVGSGGMNVVGTIKRGRERLLE

Parental  EARQSVPDSSSGKVLNLVKAFEKLLTPKKNVCEEKGEKDEKEEESSKEQQGLQPPKIPETQVSSSSFCPP
          EARQSVPDSSSGKVLNLVKAFEKLLTPKKNVCEEKGEKDEKEEESSKEQQGLQPP.IPETQVSSSSFCPP
Retrocopy EARQSVPDSSSGKVLNLVKAFEKLLTPKKNVCEEKGEKDEKEEESSKEQQGLQPPMIPETQVSSSSFCPP

Parental  DFFLTSESLGLDSRRASSLDSSHGCFSISSRTSGGGQRSRRDSAESIGTLPRRSWKRRHRKPTSQKPFKL
          DFFLTSESLGLDS.RASSLDSSHGCFSISSRTSGG.QRSRRDSAESIGTLPRRSWKRRHRKPTSQKPFKL
Retrocopy DFFLTSESLGLDSHRASSLDSSHGCFSISSRTSGGAQRSRRDSAESIGTLPRRSWKRRHRKPTSQKPFKL

Parental  ITEERGKNK
          ITEERGKNK
Retrocopy ITEERGKNK

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_14 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	Solyc02g067100.2	1 retrocopy	retro_slyc_14 ,