RetrogeneDB ID: retro_slyc_20

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 7:63664743..63665799(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc07g055740.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc10g079610.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_20
ATGAATGCTTCAAATATACTATTGTTGATTATCGTTGTACAACTTGTTTCAGTAAATTTAGCCTTTGAGAAAACTCAAAA
CGTTCTCTCAAAATCGAAAATTATCCATCTTAATGGGTCGATTGGACCGGAGAGTGTTGCGTTCGATCCAAATGGCGAAG
GTCCATACATAGGAGTAGCCGATGGACGCATTCTCAAGTTGCAATTAGGGTCAAATAATCGATTATTTTGGGCTGAATTC
GCGGTCACTTCTTCTCATCGAAGGGATTGTACCTCACCATTCGCTCCTAAAATGGAACATATATGTGGTAGGCCATTAGG
CTTACGATTCGATACAAAAACAGGTGAATTATACATTGCAGACGCGTATTTAGGTCTACAAGTTGTTGGACCCAAAGGTG
GACTAGCAACTCCATTAGTTCAAAAATTCGAAGGTAAACCTCTTGTTTTCACAAATGACGTTGACATTGACGATGATGTG
ATTTATTTCACGGATACAAGCACCAAGTATCAACGCTGGCAGTTTCTAACGTCGTTTTCAAGTGGTGATACGACTGGTAG
GTTGATGAAATATGATAAATCTACGAAAAAAGTAACAGTCTTATTAGGTGATCTTGCTTTTGCAAATGGCGTTGCGTTGA
GTAAAAACAAATCGTTTGTTTTAGTGACTGAAACTACAAATTTTAGAATTTTAAGGTATTGGCTTAAAGGCCCCTTAGTA
GGAACACATGATGTATTTGTTGAGTTGCCCGGGTTCCCGGACAACATCAGAATAAACCCTAAAGGGGACTTTTGGGTCGC
GTTACAAGCAATAAGATCAGTACCCAGTGTTTCAGATTCGAAATTTGGAATGTTTAGTTTCAACCCTCAGCAAATGGGAG
ATGACGGGGAGCTACACCCTACCGCCCTCAAGCTAAGTGAGGACGGGCAAGTTTTGGAAGTTCTAGAAGATGTTGAAGGC
AAGACATTAAGGTCTATAAGTGAAATTGAAGAAAAAGATGGGAAGTTATGGATTGGTTCTGTTGTGATGCCTTTTTTGCG
AGTTTATGAAATGTAA

Alignment

ORF - retro_slyc_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.44 %
• Parental protein coverage: 66.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKDLLSKSEVIHLKGAVGPESIAFDPNGEGPYTGVADGRILKWNGDSDG---WVDFAVTSSQRKECVHPF
          ....LSKS..IHL.G..GPES.AFDPNGEGPY.GVADGRILK....S.....W..FAVTSS.R..C..PF
Retrocopy TQNVLSKSKIIHLNGSIGPESVAFDPNGEGPYIGVADGRILKLQLGSNNRLFWAEFAVTSSHRRDCTSPF

Parental  APQMEHVCGRPLGLRFDTRTGDLYIADAYLGLHVVGPSGGLATPLVTEVEGQPLRFTNDLDIDEQEDVIY
          AP.MEH.CGRPLGLRFDT.TG.LYIADAYLGL.VVGP.GGLATPLV...EG.PL.FTND.DID...DVIY
Retrocopy APKMEHICGRPLGLRFDTKTGELYIADAYLGLQVVGPKGGLATPLVQKFEGKPLVFTNDVDIDD--DVIY

Parental  FTDTSTQFQRRQFVASVVSGDKTGRLMKYDKSTKSVTVLLRGLAFANGVALSKDKSFVLVAETSTCRVVR
          FTDTST..QR.QF..S..SGD.TGRLMKYDKSTK.VTVLL..LAFANGVALSK.KSFVLV.ET...R..R
Retrocopy FTDTSTKYQRWQFLTSFSSGDTTGRLMKYDKSTKKVTVLLGDLAFANGVALSKNKSFVLVTETTNFRILR

Parental  HWLKGPHAGKHDTFADLPGYPDNIRRNSRGEFWVGLHSKRSL
          .WLKGP..G.HD.F..LPG.PDNIR.N..G.FWV.L...RS.
Retrocopy YWLKGPLVGTHDVFVELPGFPDNIRINPKGDFWVALQAIRSV

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_20 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	PGSC0003DMG400029857	1 retrocopy	retro_stub_31,
Solanum lycopersicum	Solyc10g079610.1	1 retrocopy	retro_slyc_20 ,