RetrogeneDB ID: retro_slyc_1

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:62255293..62256118(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc04g077290.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g084000.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_1
ATGCCTCAAAGCTCATCGACAAAGAAGCACGACCAAGATCCGACGGACAGTACCGGACCCACCCTAAAATCACAGCGTAC
CAAAATGGTGAATACTTCCGATGACAGTGAAAAAAAGAGTTCTGATAAGAAGCTGAAAGAGCTTGAAGTTGGCGTTCCAA
TAGTGTATGGAAATGTTGCATTTTGGCTTGGTAAGAAGGCGAGCGAGTTCCAGTCTCATAAATGGACTATTTATGTTCGT
GGTGCAACTAATGAGGATCTGGGTGTGGTGGTGAAACGTGTTGTTTTTCAATTGCACTCAAGTTTTAACAATCCTACAAG
GGTTGTGGACAACCCTCCTTTTGAGTTATCAGAATCTGGATGGGGTGAATTTGAAATTGTGATGACCCTTCATTTCCACA
CTGATGTTTGCGATAAGCCATTACACTTATATCACCATTTAAAACTATATCCAGAGGATGAATCTGGGGCTCTATCCACT
AAAAAACCTGTTGTAGTAGAGTCATATGATGAAATTGTGTTTGCGGAGCCTTCAGAGTCTTTTTTTGCCCGTGTACAGAA
CAATCCAGCAGTCAATGTGCCTAGACTACCTCCTGGCCTAAATTTGCCTCCTCCTGTACCTATAGAAGATGTTGATCAAA
GGAAACGTGGCGACACCAAAGATCATCCTCTAAGTCAATGGTTCACAAATTTCTCTGAAGCAGATGAATTGTTAAAACTT
ACAGCAGCTCGGCAGCAGGTGCAAGGTCATATCGCAAGATTGAGAAGACAGTTGAGCACGGTAGATGGTCAGCATCAACA
ATTGAAGCCTGCCTCTGACCTGTGA

Alignment

ORF - retro_slyc_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.61 %
• Parental protein coverage: 91.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKIANPSEDFEKKTSSKRLKDVEIYVPIVFGTIAFWLGKKATETQSHRWSVYVRGATNEDLSGVIKKVVF
          TK..N.S.D.EKK.S.K.LK..E..VPIV.G..AFWLGKKA.E.QSH.W..YVRGATNEDL..V.K.VVF
Retrocopy TKMVNTSDDSEKKSSDKKLKELEVGVPIVYGNVAFWLGKKASEFQSHKWTIYVRGATNEDLGVVVKRVVF

Parental  QLHPSFNNPVRVVESPPFELSECGWGEFEIAISLLFHDDVGEKKLDLYHHLKLYAENEPGPQSTKKPIVV
          QLH.SFNNP.RVV..PPFELSE.GWGEFEI...L.FH.DV..K.L.LYHHLKLY.E.E.G..STKKP.VV
Retrocopy QLHSSFNNPTRVVDNPPFELSESGWGEFEIVMTLHFHTDVCDKPLHLYHHLKLYPEDESGALSTKKPVVV

Parental  ETYNEIVFPDPPEDFFSRIQNHPSVVVPRLPTTFKL-PPAPIEDLHALKRGDTKNHPLSQWFINFSEADE
          E.Y.EIVF..P.E.FF.R.QN.P.V.VPRLP....L.PP.PIED....KRGDTK.HPLSQWF.NFSEADE
Retrocopy ESYDEIVFAEPSESFFARVQNNPAVNVPRLPPGLNLPPPVPIEDVDQRKRGDTKDHPLSQWFTNFSEADE

Parental  LLKLTAARQRVQAHIVKLRRQLSVMDELPQTFKLDSD
          LLKLTAARQ.VQ.HI..LRRQLS..D...Q..K..SD
Retrocopy LLKLTAARQQVQGHIARLRRQLSTVDGQHQQLKPASD

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_1 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	Solyc02g084000.2	1 retrocopy	retro_slyc_1 ,