RetrogeneDB ID: retro_slyc_95

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 9:23295938..23296774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g118610.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_95
ACTACACAAGCATTGCAGCTACGGTTATCCTCCGCTATTGCTTCAGCTTCTGCCTTTTTTATTACTAAAACTCAACCTCC
AGAGAAAGGTAGACCTTAGAAATGATAAAATTTACTGCTCTTTGTACCGGGGGTTATCACCTTTGTCCTTTGCTCTGGGA
AGATCATCTTAAGGCAAGATAAGATTGAAATGCTTAATTACAGATGAAATTGATTACGAATGGATCCTCTAAATTGCAAT
GAGCTTATCCCTTCAACTTATAATTGGATTCTTTGTAGTTGTGCAGGGTACTTTATATAGAAGTTTTTGATGAGAAGAAT
TACTTTTTAATAGGACCACACTCTAGAATAATATTAGTGGTGAATGAAAATGGTTACTATGTTATTACTCCTTTCATATT
ATTGGCACATAATCGAAATAGCTTGCAGGCACCAATTATTGTTAATAGGGGCTAAGGTTTTCTGGAATTGGAGAGGCAAG
TCTTTGGAAGTGGATGCATCTAGGGCTGATGAGCAATCTTCATGTGTTGCGCCCCCATCTCAAGAGAGTGGGAAGAGCTC
CTAGTTGATATTTTCTTCAATAAATAAGAAAGTCGAAGAGGATCAAGTTCCAACTCTGAAATCCACAAAAGTAATTAGAC
TTATCTGAGGAAGTGAGAATCAATGTATATTTGTTCCAGCAAATAATCGCACTTCCTTCTAAGGGTTTACGTTGACGTTC
CAGTGATTATTTATGCATTTTGACTCTCTGAGAACATACTCTACATTAAACTCATCAATGATAATGTTGAACCAAACAAT
ACTTATACAATTCCAAAGGATACAAAAACATTGGTT

Alignment

ORF - retro_slyc_95 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 71.76 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTQALQLRLSSAVASAPAISVTETQPPEKGGPSKWSKLLLFIPGVITFGLGSWQIIRRQDKIEMLEYRQN
          TTQALQLRLSSA.ASA.A...T.TQPPEKG.P.K...LLLF.PGVITF.L.S..II.RQDKIEML.YR.N
Retrocopy TTQALQLRLSSAIASASAFFITKTQPPEKGRP*K**NLLLFVPGVITFVLCSGKIILRQDKIEMLNYR*N

Parental  RLQMDPLNCNEVSPSSEN-LDSLEFCRVLCRGVFDEKKSIFIGPRSRSISGVTENGYYVITPLMPLANDP
          .L.MDPLNCNE..PS..N.LDSL..CRVL...VFDEK....IGP.SR.I..V.ENGYYVITP...LA...
Retrocopy *LRMDPLNCNELIPSTYN<LDSL*LCRVLYIEVFDEKNYFLIGPHSRIILVVNENGYYVITPFILLAHNR

Parental  KSVQTP-ILVNRGWVPRNWRDKSLEVAA--ADDQSLSTAPPPQESGKSSWWMFSSKKKKVEEDQVPTLKS
          .S.Q.P..L.....V..NWR.KSLEV.A..AD.QS...APP.QESGKSS...FSS..KKVEEDQVPTLKS
Retrocopy NSLQAP>LLLIGAKVFWNWRGKSLEVDASRADEQSSCVAPPSQESGKSS*LIFSSINKKVEEDQVPTLKS

Parental  TEVIGVIRGSEKPSIFVPANDPSSFQWF-YVDVPAIARASGLPENTLYIEAINDNVDPSNPYPIPKDTNT
          T.VI..I.GSE...IFVPAN...SF..F.YVDVP.I..A..L.EN.LYI..INDNV.P.N.Y.IPKDT.T
Retrocopy TKVIRLI*GSENQCIFVPANNRTSF*GF<YVDVPVIIYAF*LSENILYIKLINDNVEPNNTYTIPKDTKT

Parental  LV
          LV
Retrocopy LV

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_95 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	Solyc03g118610.2	1 retrocopy	retro_slyc_95 ,