RetrogeneDB ID: retro_slyc_44

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 10:55272672..55273503(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc10g054400.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g032090.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_44
ATGGCGGAGAAAATCACCGGAGCGAACCCTAAAACCACCGTGCACGGTGTTACAACCAACAACAATTTGGATACGAGAAA
TGCAGACCGACGTGTATGGTTGATGAAATGCCCTACCGTGGTCTCTCGATTCTTCGAACAGCATCAACACTCTACTTCCG
TTGAAACTGATCTTTCTTTTAATCCTCCGAGACCTGTTGCCAAAGTCACCGTCGTCGTTGATCCTCTAATCGCCAATGAT
TCAACTCAATTCACCATGGAATTGGCCGGAACTTCATCTGGAAACATGCCGACTCACTACTCGATGGATATGTCAACAGA
TTTTATCCCAATGTCGATATTTTCCGAATCGGGTCAAGGAAGGGTTTCGGTTGAAGGGAAGATATATCACAAATTTGACG
TGAAGCCTCATCATGAAAACATTGAGAATTACGGGAAATTATGTCGAGAAAGGACGAATAAATACATGACGAAAAGTAGA
CAAATTCAGGTTATTGATAATGATAATGCTAAACATATGAGGCCTATGCCTGGATTTTTCGCAACTAAGGCTTCTGGATC
TACTGCAGAGAAGAAGAAGGTGCCTAGTAAAGGATTAGAAATGAAAAGAACAAGAAGAGATCGTGATGAAATGGAAGAAA
TTATGTTCAAACTGTTTGAGAGGCAATCAAATTGGACGCTGAAACAGCTCGTCCAAGAGACGGACCAGCCCGAGCAATTT
ATGAAAGACATGCTCAAACTACTCTGCATTTACAATAATAAGGGTGCTCATCAAGGCACTTATGAGCTGAAGCCGGAGTA
TAAGAGAGCAGAAGACAAGACTGATTCTTGA

Alignment

ORF - retro_slyc_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.56 %
• Parental protein coverage: 97.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HGNSNSSITVDTTKWDRSVWLMKCPLVVSKSWQ----SQAAASSSSSDSPQ-VAKVIVSVDPLRSDDSSA
          HG........DT...DR.VWLMKCP.VVS........S.......S...P..VAKV.V.VDPL...DS..
Retrocopy HGVTTNN-NLDTRNADRRVWLMKCPTVVSRFFEQHQHSTSVETDLSFNPPRPVAKVTVVVDPLIANDST-

Parental  LQFTMEMGGNDVGNMPKSYSLNMFQDFVPMCVLSETGQGRVTMEGKVEHKFDMTPHTRNMEEYRKMCRER
          .QFTME..G...GNMP..YS..M..DF.PM...SE.GQGRV..EGK..HKFD..PH..N.E.Y.K.CRER
Retrocopy -QFTMELAGTSSGNMPTHYSMDMSTDFIPMSIFSESGQGRVSVEGKIYHKFDVKPHHENIENYGKLCRER

Parental  TNKSMIKNRQIQVIDNDRGVNMRPMPGMIGMIASSSKDKKKAVPVKGPEVKRTRRDRGELEDIMFKLFER
          TNK.M.K.RQIQVIDND....MRPMPG.....AS.S...KK.VP.KG.E.KRTRRDR.E.E.IMFKLFER
Retrocopy TNKYMTKSRQIQVIDNDNAKHMRPMPGFFATKASGSTAEKKKVPSKGLEMKRTRRDRDEMEEIMFKLFER

Parental  QPNWTLKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVEET
          Q.NWTLKQLVQETDQP.QF.K..L..LC.YN..G..QGTYELKPEYK.....T
Retrocopy QSNWTLKQLVQETDQPEQFMKDMLKLLCIYNNKGAHQGTYELKPEYKRAEDKT

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_44 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400027984	1 retrocopy	retro_stub_7,
Solanum lycopersicum	Solyc07g032090.2	1 retrocopy	retro_slyc_44 ,