RetrogeneDB ID: retro_slyc_19

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 5:5906879..5908127(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc05g012730.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g042360.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_19
ATGAGAAATTGGAACTTTATTGTGTTTCTCTGTCTTGCTTTCGTATTGAGAGTTGAATCCTTCAAGTTTCATAGGATTGA
TCAACACGTTGAAAGGATCTCCGGAAGTGCTGGTGATGTGTTGGAGGATGATCCTACAGGTAGGTTGAAAGTTTTTGTAT
ATGAGCTTCCAAGCAAATATAACAAGAAAACTGTGCAGAGGGACTCGCGATGCCTCAGTCATATGTTTGCTGCTGAGATA
TATATGCATCAGTTTCTGTTATCCAGTCCTGTTCGAACACTTGATCCAGAGGAAGCAGATTGGTTTTACACTCCAGTTTA
CACAACTTGTGAGTACTTGACACCACATGGTCATCCTTTACCTTTCAACTCACCACGTATGATGAGAAGCGCGATTCAGC
TTATTGCTTCTAGCTGGCCATACTGGAACAGGACACAAGGGGGTGATCATTTCTTCATTGTACCACATGATTTTGGTGCA
TGTTTCCATTTTCAAGAAGAGAAAGCTATTGGAAGAGGTATTCTTCCGTTGCTCCATCGTGCTACCTTGGTTCAAACTTT
TGGACAACGGAATCATGTTTGTTTGAAGGAAGGATCGATAACTATTCCTCCGTATGCTCCTCCACAGAAAATTCAGTCTC
ATTTGATCTCTCCTGATACACCAAGATCCATATTTGTCTATTTCCGTGGCTTGTTTTATGACAAAAGAAATGATCCTAAA
GGCGGGTACTATGCAAGAGGCGCTCGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTCTTTGATATTTCTACAGA
TCATCCAACTACATACTACGAAGACATGCAACGAGCTATCTTTTGCTTGTGCCCTCTCGGATGGGCTCCATGGAGTCCTA
GATTGGTTGAAGCTGTTGTATTCGGATGCATCCCCGTTATAATAGCAGATGACATTGTCTTGCCATTTGCTGACGCGATC
CCATGGGAAGATATAGGATTGTTCGTAGCGGAGAAGGATGTCCCATATTTGGATAACATTCTTACTTCTGTTCCACCACA
AGAAATACTGAGGAAGCAGAGATTGCTCGCCAATCCTTCAATGAAGCAGGCTATGTTATTTCTACAACCTGCTCAACCAG
GTGATGCTTTCCACCAAATCTTGAATGGACTTGCTCGTAAATTACCCAATCATCACAAGACTATATACGGAGACAACAAC
GTCTTAAACTGGACTGCTGGTCCAGTTGCTGATCTAAAACCTTGGTAG

Alignment

ORF - retro_slyc_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFAAEIYMHRFLLSSPVRTLNPEEADWFYTPVYTTCD-LTPNGLPLPFKSPRMMRSAIQLIASNWPYWNR
          MFAAEIYMH.FLLSSPVRTL.PEEADWFYTPVYTTC..LTP.G.PLPF.SPRMMRSAIQLIAS.WPYWNR
Retrocopy MFAAEIYMHQFLLSSPVRTLDPEEADWFYTPVYTTCEYLTPHGHPLPFNSPRMMRSAIQLIASSWPYWNR

Parental  TEGADHFFIVPHDFAACFHYQEEKAIGRGILPLLQRSTLVQTFGQRNHVCLKDGSITIPPYAPPQKMQSH
          T.G.DHFFIVPHDF.ACFH.QEEKAIGRGILPLL.R.TLVQTFGQRNHVCLK.GSITIPPYAPPQK.QSH
Retrocopy TQGGDHFFIVPHDFGACFHFQEEKAIGRGILPLLHRATLVQTFGQRNHVCLKEGSITIPPYAPPQKIQSH

Parental  FIPPDIPRSIFVYFRGLFYDVGNDPEGGYYARGARAAVWENFKDNPLFDISTEHPTTYYEDMQRAIFCLC
          .I.PD.PRSIFVYFRGLFYD..NDP.GGYYARGARAAVWENFKDNPLFDIST.HPTTYYEDMQRAIFCLC
Retrocopy LISPDTPRSIFVYFRGLFYDKRNDPKGGYYARGARAAVWENFKDNPLFDISTDHPTTYYEDMQRAIFCLC

Parental  PLGWAPWSPRLVEAVIFGCIPVIIADDIVLPFADAIPWEEIGVFVDEKDVPNLDTILTSIPPEEILRKQR
          PLGWAPWSPRLVEAV.FGCIPVIIADDIVLPFADAIPWE.IG.FV.EKDVP.LD.ILTS.PP.EILRKQR
Retrocopy PLGWAPWSPRLVEAVVFGCIPVIIADDIVLPFADAIPWEDIGLFVAEKDVPYLDNILTSVPPQEILRKQR

Parental  LLANPSMKQAMLFPQPAQSGDAFHQILNGLARKLP-HDRTVFLTPGQKILNWTAGPVGDLKPW
          LLANPSMKQAMLF.QPAQ.GDAFHQILNGLARKLP.H..T.........LNWTAGPV.DLKPW
Retrocopy LLANPSMKQAMLFLQPAQPGDAFHQILNGLARKLPNHHKTIY--GDNNVLNWTAGPVADLKPW

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_19 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538848.1_FG012	1 retrocopy	retro_olon_4,
Oryza brachyantha	OB01G51480	1 retrocopy	retro_obra_20,
Solanum tuberosum	PGSC0003DMG400014472	1 retrocopy	retro_stub_120,
Solanum lycopersicum	Solyc12g042360.1	1 retrocopy	retro_slyc_19 ,