RetrogeneDB ID: retro_slyc_94

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:9579688..9580080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc10g018350.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_94
AACAATTCTGATAATTATATTGATTTCAAGGTGAAGACAACAAATTCAAAAATAGTATTGTGTACAACCCAACACTTGAA
TTGGCATGCCTCACACTTCTAGAGATATCATAATTATAATACAACTGTAAAAAGAGGCTCCACCGGTCATGCAAAGCAAG
GATAATTTCTTGCTTCAAACTGTTTTTGCAAGCCCTAGAACTACGGCAAAGGACATTACCCCCCGATATGTTCAATAAAG
GGTCGGGGAATTATGTAAAGGACTGCAAGTTGAAAATGATTTATGTTCCACCTCAAGTTCTAATGCCTATAAAGGAGGGG
TCTGAGGAAAGTTCTTATCATAGGGCTTTAGTATCCGAAAATAAAACTGTAAATATATCTGAGCTTAATGAC

Alignment

ORF - retro_slyc_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.39 %
• Parental protein coverage: 54.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKSDNYVAFKVKTTNPKK-YCVRPNTGIVMPHSSSEVKVTMQAQKEAPPDMQCKDKFLLQSVVASPGAAA
          N.SDNY..FKVKTTN.K..YCV.PNT.I.MPH.S.......Q..KEAPP.MQ.KD.FLLQ.V.ASP...A
Retrocopy NNSDNYIDFKVKTTNSKI>YCVQPNT*IGMPHTSRDIIIIIQL*KEAPPVMQSKDNFLLQTVFASPRTTA

Parental  KDITP-EMFNKESGNYVEDCKLKVVYVPPQLRLPVREGSEEGSSPRASVSENGAVNTSEFNN
          KDITP..MFNK.SGNYV.DCKLK..YVPPQ...P..EGSEE.S..RA.VSEN..VN.SE.N.
Retrocopy KDITP>DMFNKGSGNYVKDCKLKMIYVPPQVLMPIKEGSEESSYHRALVSENKTVNISELND

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_94 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc10g018350.1	1 retrocopy	retro_slyc_94 ,