RetrogeneDB ID: retro_slyc_75

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:46801334..46801783(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g082000.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_75
ATGGGGGGAGTTAAAGATGAAGTTGCTACCTGACAGCCAAGAAAGAGAACATTCAAAAAGTTCAGCTATAGAGAAATAGA
TTTGAATTACTACTTGACATGTCTACCTGTGAGCTTGTTAAGATTTTCCTTTCTCGTCCTCACAAAATATTCCATCCAAT
TTTGAAGAGGAATCATATGGCTTTCATCAAGATGCTCCTCAATGAGAAATATGAGGCCCTTGCTAGTGAGAAGCTAGAGG
TTGTGAGAACACATATGAGGAACTTGGTCATTGTTCCTGAGATCATTTGATATATAATGAAATTTACTAAGGAAAAAATT
TAATTTCAATCATATTGAGGTCAAGCCTTAGATTATTCGACACTACTTAGATGAGTTATCTATCTCTTACCAACCTGCAA
GCACGTTAGGGATGGTATTTGTGCTACTCATTCTTCAATGTTCAGTCCA

Alignment

ORF - retro_slyc_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAEVEADVATGQPRKRTFKKFSYRGVDL-DSLLDMSTDELVKLYPARPRRRFQRGLKRKPMALIKKLRKA
          M..V...VAT.QPRKRTFKKFSYR..DL...LLDMST.ELVK....RP...F...LKR..MA.IK.L...
Retrocopy MGGVKDEVAT*QPRKRTFKKFSYREIDL<ELLLDMSTCELVKIFLSRPHKIFHPILKRNHMAFIKMLLNE

Parental  KREAPPGEKPEVVRTHLRNMIIVPEMIGSVI-GIYNGKT-FN--QIEVKPEMISHYLAEFSISYKPV-KH
          K.EA...EK.EVVRTH.RN..IVPE.I......IY.GK..FN...IEVKP..I.HYL.E.SISY.P..KH
Retrocopy KYEALASEKLEVVRTHMRNLVIVPEII*YIM<EIY*GKN<FNFNHIEVKP*IIRHYLDELSISYQPA<KH

Parental  GRPGIGATHSSRFIP
          .R.GI.ATHSS.F.P
Retrocopy VRDGICATHSSMFSP

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_75 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G04270	1 retrocopy	retro_atha_20,
Brassica oleracea	Bo5g004420	1 retrocopy	retro_bole_33,
Brassica rapa	Bra032519	1 retrocopy	retro_brap_20,
Arabidopsis lyrata	fgenesh2_kg.1__358__AT1G04270.1	1 retrocopy	retro_alyr_8,
Medicago truncatula	MTR_1g070450	1 retrocopy	retro_mtru_46,
Solanum tuberosum	PGSC0003DMG400007336	1 retrocopy	retro_stub_80,
Solanum lycopersicum	Solyc02g082000.2	1 retrocopy	retro_slyc_75 ,