RetrogeneDB ID: retro_slyc_45

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 7:66685539..66685878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc07g064620.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g064150.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_45
ATGGTTGATATCGACATCCAGATCCCATCTGCTTTCGATCCATTTGCTGAGGCTAAGGACTCCGGTGCACCTGGAGCCAA
GGAGTATGTTCATATTCGTATACAACAAAGGAATGGAAAGAAAAGCTTGACGACTGTTCAAGGACTGAGGAAAGAATTCA
GTTACGAAAAAATCCTCAAAGATCTGAAAAAGGAATTCTGTTGCAACGGGAACGTTGTGCAGGATAAGGAACTTGGCAAA
GTGATACAACTTCAAGGTGATCAAAGGAAGAATGTTTCTCATTTCCTTGTGACTGCTGGTGTTGTCAAGAAGGATCAGAT
CAAGATTCATGGTTTCTAA

Alignment

ORF - retro_slyc_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDLDVQIPTAFDPFAEANADNSGAGSKDYVHIRIQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCN
          M.D.D.QIP.AFDPFAEA..D....G.K.YVHIRIQQRNG.KSLTTVQGL.KEFSY.KILKDLKKEFCCN
Retrocopy MVDIDIQIPSAFDPFAEAK-DSGAPGAKEYVHIRIQQRNGKKSLTTVQGLRKEFSYEKILKDLKKEFCCN

Parental  GTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKEHIKIHGF
          G.VVQD.ELG.VIQLQGDQRKNVS.FLV.AG.VKK..IKIHGF
Retrocopy GNVVQDKELGKVIQLQGDQRKNVSHFLVTAGVVKKDQIKIHGF

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_45 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400019258	1 retrocopy	retro_stub_51,
Solanum lycopersicum	Solyc07g064150.2	1 retrocopy	retro_slyc_45 ,