RetrogeneDB ID: retro_slyc_79

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:25354014..25354609(-)
• Located in intron of: Solyc04g025170.2

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g009620.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_79
ATGTCTGCTATAGTGTGCTGAAAGAGATCGAATTTGTTTTCAGGATTTTCAGCCGTTGTCATCGCCGTATGTGCTGCTGC
TGGTTTCGAAGAGAATTGACCATACTTTTTCTCCGGAGAGGTCTAGTTCTGATTCAGATCGTGTTTTTTCAGGTAATTCG
ATTACATCGTCAGCACTCAATCATCTTCTCATGCTTTTCTCTGACATGGACAAGCAGTTGGTTGAGAGAGCACTTGAAGA
ATCCAGTGATGATCTAGATTCTTCTATAAAACGCCTGAATGAGCTCCGCTTGGGATCTGGTGATAATCTGAGGCCTGAGG
CAGGAAGCTTTGGTGCTACGCATGAGTCCAGCAGCCAGGTTTTTACTCAAGGTGCAGCTACAACTAATGGTGAGACCACA
TCTGCTGAGGATATATCTTCTACAAAAGTGGTGCATTTTCAGGGTACAGAATGGGTGGATCTTTTTGTTAGAGAGATGAT
GAGTGTGTCGAATATAGATGATGCTAAAGTCTGTGCTTCACGAGCTCTTGAGGCTTTTGAGAAGGCCACATGTGCTCGTG
AAACAGATGCGTCCTGCAGTTTCCAGAAGGAGAAT

Alignment

ORF - retro_slyc_79 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 69.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAILCGKRSNLF-EDFQ--SSSSASTPVSKRIRRNFSPARSNSDSDRVLCGNLIASSALDHLLMIFSDT
          MSAI.C.KRSNLF..DFQ..SS......VSKRI...FSP.RS.SDSDRV..GN.I.SSAL.HLLM.FSD.
Retrocopy MSAIVC*KRSNLF>QDFQPLSSPYVLLLVSKRIDHTFSPERSSSDSDRVFSGNSITSSALNHLLMLFSDM

Parental  DKQLVERALEESGDDLDSAIKRLNELCLGSGDNLRPVAGSSGATHEFSSQVFPQGVATTNGETPSAEDLS
          DKQLVERALEES.DDLDS.IKRLNEL.LGSGDNLRP.AGS.GATHE.SSQVF.QG.ATTNGET.SAED.S
Retrocopy DKQLVERALEESSDDLDSSIKRLNELRLGSGDNLRPEAGSFGATHESSSQVFTQGAATTNGETTSAEDIS

Parental  SAEVVHLQGTEWVDLFVGEMMSASNIDDAKARASRALEAFEKTICARATEAACRFQKEN
          S..VVH.QGTEWVDLFV.EMMS.SNIDDAK..ASRALEAFEK..CAR.T.A.C.FQKEN
Retrocopy STKVVHFQGTEWVDLFVREMMSVSNIDDAKVCASRALEAFEKATCARETDASCSFQKEN

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_79 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	Solyc12g009620.1	1 retrocopy	retro_slyc_79 ,