RetrogeneDB ID: retro_slyc_46

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 5:64625495..64626548(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc05g054800.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc08g023460.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_46
ATGAACCCTTCATCTTCAACTACTGGGGGTGCTGGATCTGATGATAATACTTCAATTAGAAGAAATTCAAACCGACCCAA
GTATTCAAGATTCACTCAACAGGAACTTCCAGCTTGCAAACCGATTCTAACTCCAAAATGGGTGATTTCTGTTTTTTTAC
TTGTTGGTATTGTGTTTATCCCAATTGGGGTTGTTTCACTTTTAGCATCTAGAGATGTTGTTGAAATTGTTGATCGTTAT
GATTCTGAATGTGTGCCATCGAATATGACAAATGATAAAATTAGGTTTATAACAAATGATAGTTTTGATAAAACATGTAT
TAGGACTTTGACTGTGCCTAAGAAAATGAAGCAGCCTATTTATATTTATTATCAGCTTGAGAATTATTATCAGAATCATC
GTAGGTATGTTAAAAGTCGAAGTGATCAGCAGTTGAAAAGTGCTAGTAGAAGGGATGATACTGGTACTTGTGACCCCGAA
GATCGTGTTAATGGTTTACCAATTGTGCCTTGTGGTTTGATTGCTTGGAGTTTGTTCAATGATACTTATAATTTTAGTAT
TGTTAATAATATTAATAAGCGGTTGGATGTGAACAAAAATGGTATAGCTTGGAAGAGTGATAGGGATCATAAGTTTGGAA
AAGATGTTTTTCCGTCAAACTTTCAGAATGGGACACTAATCGGGGGTGGGAAGCTTACGAATGAATCGTTGGACAAGCAA
GAAAATCTAATTGTTTGGATGAGAACTGCTGCACTTCCGACGTTTAGGAAGTTGTATGGGAAGATAGAAGTGGATCTGGA
GGCGGGTGAACGGTTAAACGTGACGGTGCTGAACAATTACAATACTTATAGTTTCGATGGAAAGAAGAAGCTTGTGCTTT
CTACAACTAGCTGGATTGGCGGAAAGAATGATTTTCTTGGTATTGCTTATCTTACTGTAGGTGGATTGTGTTTCTTTCTG
GCCATGGCTTTCACGATCGTGTATCTAGTTAAGCCAAGGCAGCTTGGAGATCCAACATACTTGTCGTGGAACCGGAACCC
GGGAGGTAACTAG

Alignment

ORF - retro_slyc_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.48 %
• Parental protein coverage: 96.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSTLSGNGAQSVESRSHPVRRHLDDAVY-QFTQQNLPACKPVLTPAWVISMFFLIGVIFIPIGLLCLYAS
          PS.....GA.S....S...RR......Y..FTQQ.LPACKP.LTP.WVIS.F.L.G..FIPIG...L.AS
Retrocopy PSSSTTGGAGSDDNTS--IRRNSNRPKYSRFTQQELPACKPILTPKWVISVFLLVGIVFIPIGVVSLLAS

Parental  ESVIEIVDRYDIDCVPDNLKSQKVAYIKDNSVSKNCTRYLKVPQNMKAPIYIYYQLDNYYQNHRRYVKSR
          ..V.EIVDRYD..CVP.N....K...I...S..K.C.R.L.VP..MK.PIYIYYQL.NYYQNHRRYVKSR
Retrocopy RDVVEIVDRYDSECVPSNMTNDKIRFITNDSFDKTCIRTLTVPKKMKQPIYIYYQLENYYQNHRRYVKSR

Parental  SDKQLLHGLQYNDTSSCNPEGENNGLPIVPCGLIAWSLFNDTY--SFFNGADA-INVNRKNIAWRSDREH
          SD.QL.......DT..C.PE...NGLPIVPCGLIAWSLFNDTY..S..N.......VN...IAW.SDR.H
Retrocopy SDQQLKSASRRDDTGTCDPEDRVNGLPIVPCGLIAWSLFNDTYNFSIVNNINKRLDVNKNGIAWKSDRDH

Parental  KYGKDVYPFNFQSGPLIGGATLDPDIPLSDQENLIVWMRTAALPTFRKLYGKIEVDLEEGDLIMVNLVNN
          K.GKDV.P.NFQ.G.LIGG..L.....L..QENLIVWMRTAALPTFRKLYGKIEVDLE.G....V...NN
Retrocopy KFGKDVFPSNFQNGTLIGGGKLTNE-SLDKQENLIVWMRTAALPTFRKLYGKIEVDLEAGERLNVTVLNN

Parental  YNTYSFGGRKKLVLSTTSWLGGRNNFLGMSYVTVGSSFIFLAFVFLLLHVKNPR
          YNTYSF.G.KKLVLSTTSW.GG.N.FLG..Y.TVG....FLA..F.......PR
Retrocopy YNTYSFDGKKKLVLSTTSWIGGKNDFLGIAYLTVGGLCFFLAMAFTIVYLVKPR

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_46 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	Solyc08g023460.2	1 retrocopy	retro_slyc_46 ,