RetrogeneDB ID: retro_slyc_29

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:10402901..10403831(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc03g044720.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g080550.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_29
ATGGAATCAAATAAGAGTAAAATACTGATAATCGGAGTAACAGGCCGTTTGGGTTTTGAACTAGCAAAGGCCAGTCTCAA
TTCCTCTCATCCCACATTCGGACTTGTTAGAGATTCAGCATTCTCTGACACTCATAAATCCCAAAAGATTCATACCCTTA
CCGAAGCGGGCCTCACAGTAATCAAGGGTTCATTGCAAGATGAAGATATCCTGCTTGAAGCACTCAAGCAAGTTGAGATC
GTGATTTCTGCTGTTTCATCTAAGCAAGTCCACGAACAAAAGATTCTGATTTCTGCTATAAAGCGTGCTGGTTGCATTAA
AAGGTTCCTCCCTTCAGAGTTCGGGGCTGACCCTGACAGAACTCAAGTTTCTGATTTGGACCACAACTTCTACTCGAGAA
AATCCGAGATTAGGCGTATTATTGAAGCTGAAGGCATTCCTTACACCTATGTCTGTTGTAACTTATTTACTAGTGTTCTC
CTATCGTCACTTGCTCAACCAGGTCGGAAAGCCCCTCCGAGAGATGAAGTCAGCATATTCGGTGATGGAACTGCTAAAGC
TGTCTTTATGAACGAAAATGATGTTGCTGCCTTTGTCATAAATACAGTGGACGATGCACGGACTCTGAACAAAGTGGTAT
ACATGAGGCCAAAGGGAAATGTGTATTCAATGAATGAGCTAGTAGGGATTTGGGAAGGAAAAATTGAGAAGACGCTAAAA
AAGATTTACATCACTGAAGATGAGCTCTTGAAGAAAATCCGAGATACCCCATATCCTGAGAATATGGAGTTGGTTTTCAT
ATACTCTACATTTGTTAAAGGAGATCAGACATACTTCAGCATAGAGTCTTCTGGTGGTTTGGAAGGGACACAGCTATATC
CACAAATAACATACACCACAGTAAGCGAATTTCTAGACACCTTGTTGTAA

Alignment

ORF - retro_slyc_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.5 %
• Parental protein coverage: 98.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEKSKVLIIGGTGYIGKFVVEASAKSGHPTFALVRETTVSDPDKGKIVENFKNLGVTIINGDLYDHESLL
          ..KSK.LIIG.TG..G.....AS..S.HPTF.LVR....SD..K..........G.T.I.G.L.D...LL
Retrocopy SNKSKILIIGVTGRLGFELAKASLNSSHPTFGLVRDSAFSDTHKSQKIHTLTEAGLTVIKGSLQDEDILL

Parental  KAIKQVDVVISTVGAMQLADQVKIIDAIKEAGNIKRFFPSEFGMDVDKINAVEPAKSTFAVKVQIRRAIE
          .A.KQV..VIS.V...Q...Q...I.AIK.AG.IKRF.PSEFG.D.D..............K..IRR.IE
Retrocopy EALKQVEIVISAVSSKQVHEQKILISAIKRAGCIKRFLPSEFGADPDRTQVSDLDHNFYSRKSEIRRIIE

Parental  AAEIPYTNVSCNYFAGYFLPTLVQPGVTAPPRDKVIIPGDGNVKAVFNEEHDIGTYTIKAIDDPRTLNKT
          A..IPYT.V.CN.F....L..L.QPG..APPRD.V.I.GDG..KAVF..E.D.....I...DD.RTLNK.
Retrocopy AEGIPYTYVCCNLFTSVLLSSLAQPGRKAPPRDEVSIFGDGTAKAVFMNENDVAAFVINTVDDARTLNKV

Parental  LYIRPLKNTLSFNELVAIWEKLIGKTLEKIYVPEEQILKDIQTSPIPINIILAINHSTFVKGDQTNFEIE
          .Y.RP..N..S.NELV.IWE..I.KTL.KIY..E...LK.I...P.P.N..L....STFVKGDQT.F.IE
Retrocopy VYMRPKGNVYSMNELVGIWEGKIEKTLKKIYITEDELLKKIRDTPYPENMELVFIYSTFVKGDQTYFSIE

Parental  PSFGVEASELYPDVKYTTVEEYL
          .S.G.E...LYP...YTTV.E.L
Retrocopy SSGGLEGTQLYPQITYTTVSEFL

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_29 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	Solyc04g080550.2	1 retrocopy	retro_slyc_29 ,