RetrogeneDB ID: retro_slyc_102

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: SL2.40sc03817:4818..5769(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g080770.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_102
AAAGAACACAATTACGAGAAGGCCGTATTGGTAGGTGTTGTTACACAGCATCAGGATGAGGATAAACTTCAGGAATATAT
GGACGAGCTGGAGTTTTTGGCGTACACCGCAGGAGCGACTGTAGACAGACGCTTTACCCAAAAATTAACACAACCGGATT
CCAAAACATTTATCGGAAGCGGGAAAGCACAGGAAATCAAAGAATATGTAAAAGAAAACGAAATAGGAACCGTCATTTTT
GATGATGAACTTTCGCCGTCTCAGCTTAAAAACCTGGAAAGAGAGCTTGAAGTTAAAATTCTCGACAGAACCAATCTGAT
CCTTGATATTTTTGCCCAGCGTGCCACAACATCATACGCAAGAACCCAAGTGGAACTTGCACAATATCAGTACCTGTTGC
CGCGACTTACAAGAATGTGGACCCACCTTGAACGTCAGAAAGGGGGAATCGGGATGAGAGGTCCGGGAGAAACAGAAATT
GAAACCGATAGACGTATCATCCGAGACCGGATTTCCTTATTGAAAGACAAGCTGAAAACCATCGATAAACAGATGGCTAC
CCAGAGAAATAACCGCGGAAAAGTGGTAAGAGTAGCATTGGTAGGATATACCAATGTCGGAAAATCAACTCTGATGAATG
CGCTTTCAAAATCCGAGGTCTTTGCTGAAAATAAATTATTTGCAACGCTGGATACCACGGTAAGAAAAGTGGTAATCGGA
AACCTTCCGTTTCTGCTTACCGATACCGTAGGATTTATCAGAAAACTTCCTACTCAGCTTGTAGAATCTTTCAAATCTAC
ACTGGATGAGGTGCGTGAAGCGGATCTTTTGATCCACGTGGTGGATATTTCCCACGAAAGTTTTGAAGACCATATTGATT
CGGTTAATCAGATTTTAATGGAAATCAATGCCCATCAAAAGCCAATGATCATGATCTTTAATAAAATCGAT

Alignment

ORF - retro_slyc_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.16 %
• Parental protein coverage: 59.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEVFEEKAYLVGVACKGDTEDSFGIEESLKELAQLADTAGLLVVDSTYQKLSSPNPRTYIGSGKVSEIKS
          KE...EKA.LVGV......ED.....E...EL..LA.TAG..V.....QKL..P...T.IGSGK..EIK.
Retrocopy KEHNYEKAVLVGVVTQHQDEDK--LQEYMDELEFLAYTAGATVDRRFTQKLTQPDSKTFIGSGKAQEIKE

Parental  AIRAFDVETVIFDDELSPGQLRNLEKAFGGDVRVCDRTALILDIFNQRAATREASLQVSLAQMEYQLPRL
          ........TVIFDDELSP.QL.NLE......V...DRT.LILDIF.QRA.T..A..QV.LAQ..Y.LPRL
Retrocopy YVKENEIGTVIFDDELSPSQLKNLEREL--EVKILDRTNLILDIFAQRATTSYARTQVELAQYQYLLPRL

Parental  TRMWTHLERQAGG-QVKGMGEKQIEVDKRILRTQIGVLKKELESVRKHRKQYRNRRVSVPVPVVSLVGYT
          TRMWTHLERQ.GG....G.GE..IE.D.RI.R..I..LK..L....K.....RN.R..V....V.LVGYT
Retrocopy TRMWTHLERQKGGIGMRGPGETEIETDRRIIRDRISLLKDKLKTIDKQMATQRNNRGKVVR--VALVGYT

Parental  NAGKSTLLNQLTGADVLAEDQLFATLDPTTRRVQMKNGKEFLLTDTVGFIQKLPTTLVAAFRATLEEIAE
          N.GKSTL.N.L....V.AE..LFATLD.T.R.V...N...FLLTDTVGFI.KLPT.LV..F..TL.E..E
Retrocopy NVGKSTLMNALSKSEVFAENKLFATLDTTVRKVVIGN-LPFLLTDTVGFIRKLPTQLVESFKSTLDEVRE

Parental  SSILVHVVDISHPLAEQQIEAVEKVLSELDTSSIPKLMLWNKVD
          ...L.HVVDISH...E..I..V...L.E......P..M..NK.D
Retrocopy ADLLIHVVDISHESFEDHIDSVNQILMEINAHQKPMIMIFNKID

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_102 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	Solyc04g080770.2	1 retrocopy	retro_slyc_102 ,