RetrogeneDB ID: retro_slyc_37

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:8858834..8860814(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc03g044330.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc06g059880.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_37
ATGGCGGCTGCTGCCTCACCATCTCCATGTTTCTCCAAAACCCTACCTCCATCTTCCTCCAAATCTTCCACCATTCTACC
TAGATCTACCTTCTCTTTCCACAATCACCCACAAAAAGCCTCACCCCTTCATCTCATCCACGCTCAACATAATCGTCGTG
GTTTTGCCGTTGCCAATGTCGTCATATCCACTACCACCCATAACGACGTTTCTGAACCTGAAACATTCGTTTCCCGTTTC
GCCCCTGACGAACCCAGAAAGGGTTGTGATGTTCTTGTGGAGGCACTTGAAAGGGAAGGTGTTACGGATGTATTTGCATA
CCCAGGAGGTGCTTCTATGGAGATTCATCAAGCTTTGACACGTTCGAATATTATTCGTAATGTGCTACCACGTCATGAGC
AAGGTGGTGTGTTTGCTGCAGAGGGTTACGCACGGGCTACTGGGTTCCCTGGTGTTTGCATTGCTACCTCTGGTCCCGGA
GCTACAAATCTTGTTAGTGGTCTTGCGGATGCTTTGTTAGATAGTATTCCGATTGTTGCTATTACAGGTCAAGTGCCAAG
GAGGATGATTGGTACTGATGCGTTCCAGGAAACGCCTATTGTTGAGGTAACGAGATCTATTACGAAGCATAATTATCTTG
TTATGGATGTAGAAGATATTCCTAGGGTTGTTCGTGAAGCATTTTTTCTTGCGAAATCGGGACGGCCTGGCCCAGTTTTG
ATTGATGTACCTAAGGATATTCAGCAACAATTGGTGATACCTAATTGGGATCAGCCAATGAGGTTGCCTGGTTACATGTC
TAGGTTACCTAAATTGCCTAATGAAATGCTTTTGGAACAAATTGTTAGGCTGATTTCCGAGTCGAAGAAGCCTGTTTTGT
ATGTGGGTGGTGGGTGTTCGCAATCAAGTGAGGAGCTGAGACGATTTGTGGAGCTTACAGGTATTCCTGTAGCGAGTACT
TTGATGGGTCTTGGAGCTTTTCCAACTGGGGATGAGCTTTCACTTCAAATGTTGGGTATGCATGGAACTGTGTATGCTAA
TTATGCTGTGGATAGTAGTGATTTGTTGCTTGCATTTGGGGTGAGGTTTGATGATCGAGTTACTGGTAAATTGGAAGCTT
TTGCTAGTCGAGCGAAAATTGTCCACATTGATATTGATTCGGCAGAGATTGGAAAAAACAAGCAACCTCATGTTTCCATT
TGTGCAGATATCAAGTTGGCATTACAGGGTTTGAATTCCATATTGGAGGGTAAAGAAGGTAAGATGAAGTTAGATTTTTC
TGCCTGGAGGCAGGAGTTAACGGAGCAGAAGATGAAGTACCCACTGAATTTTAAGACTTTTGGTGATGCCATCCCTCCAC
AATATGCTATTCAGGTTCTTGATGAGTTAACTAACGGAAATGCCATTATTAGTACTGGTGTGGGGCAACACCAGATGTGG
GCTGCCCAATACTATAAGTACAAAAAGCCACGCCAATGGTTGACATCTGGTGGATTAGGAGCAATGGGATTTGGTTTGCC
TGCTGCTATAGGTGCGGCTGTTGGGAGACCGGGTGAGATTGTGGTTGACATTGACGGTGATGGGAGTTTTATCATGAATG
TGCAAGAGTTAGCAACAATTAAGGTGGAGAATCTCCCAGTTAAGATTATGTTGCTGAATAATCAACACTTGGGAATGGTG
GTTCAATGGGAGGATCGATTCTATAAAGCTAACAGAGCACACACTTACTTGGGTGACCCTTCTAACGAGGAAGAGATCTT
CCCTAATATGTTGAAATTTGCAGAGGCTTGTGGCGTACCTGCTGCAAGAGTGTCACACAGGGATGATCTTAGAGCTGCCA
TTCAAAAGATGTTAGACACTCCTGGGCCATACTTGTTGGATGTGATTGTACCTCATCAGGAGCACGTTCTACCTATGATT
CCCAGCGGTGGTGCTTTCAAAGATGTGATCACGGAGGGCGATGGGAGATGTTCCTATTGA

Alignment

ORF - retro_slyc_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 90.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFTSRFLPDEPRKGCDILVEALERQGVKNVFAYPGGTTLEIHQALTRSPTIRNILPRHEQGGVFAAEGYA
          TF.SRF.PDEPRKGCD.LVEALER.GV..VFAYPGG...EIHQALTRS..IRN.LPRHEQGGVFAAEGYA
Retrocopy TFVSRFAPDEPRKGCDVLVEALEREGVTDVFAYPGGASMEIHQALTRSNIIRNVLPRHEQGGVFAAEGYA

Parental  RATGFPGVCMATSGPGATNLISGLADAMADSIPIIAITGQVPRRMIGSDAFQEIPIVEVTRSITKHNYLV
          RATGFPGVC.ATSGPGATNL.SGLADA..DSIPI.AITGQVPRRMIG.DAFQE.PIVEVTRSITKHNYLV
Retrocopy RATGFPGVCIATSGPGATNLVSGLADALLDSIPIVAITGQVPRRMIGTDAFQETPIVEVTRSITKHNYLV

Parental  MDVHDIPRIVREAFFLARSGRPGPVLIDVPKDVQQQMDIPNWDQPMKLPGYISRLPLPPKKTLLEQIVRL
          MDV.DIPR.VREAFFLA.SGRPGPVLIDVPKD.QQQ..IPNWDQPM.LPGY.SRLP..P...LLEQIVRL
Retrocopy MDVEDIPRVVREAFFLAKSGRPGPVLIDVPKDIQQQLVIPNWDQPMRLPGYMSRLPKLPNEMLLEQIVRL

Parental  ISESKKPVLYVGGGCIQSSNELRRFAQLTGIPVASTLMGLGAFPAGDELSLQMLGMHGTVYSNYAVDRSD
          ISESKKPVLYVGGGC.QSS.ELRRF..LTGIPVASTLMGLGAFP.GDELSLQMLGMHGTVY.NYAVD.SD
Retrocopy ISESKKPVLYVGGGCSQSSEELRRFVELTGIPVASTLMGLGAFPTGDELSLQMLGMHGTVYANYAVDSSD

Parental  LLLAFGVRFDDRVTGKLETFASRAKIVHIDIDSTEIGKNKQPHVSICTDIKLALQGLNSILMDTENALKL
          LLLAFGVRFDDRVTGKLE.FASRAKIVHIDIDS.EIGKNKQPHVSIC.DIKLALQGLNSIL...E...KL
Retrocopy LLLAFGVRFDDRVTGKLEAFASRAKIVHIDIDSAEIGKNKQPHVSICADIKLALQGLNSILEGKEGKMKL

Parental  NFSPWRKELTEQKLKYPLKYKFYGDSIPPQYAIEVLDELTNGNAIITSGVGQHQMWCAQYYKYKNPMQCL
          .FS.WR.ELTEQK.KYPL..K..GD.IPPQYAI.VLDELTNGNAII..GVGQHQMW.AQYYKYK.P.Q.L
Retrocopy DFSAWRQELTEQKMKYPLNFKTFGDAIPPQYAIQVLDELTNGNAIISTGVGQHQMWAAQYYKYKKPRQWL

Parental  TSSGFGAMGFGLPAAIGAAIAIPDAIVVDIDGDGSFMMNVQELATVRAENLPVKMMILNNQHLGMATQWE
          TS.G.GAMGFGLPAAIGAA...P..IVVDIDGDGSF.MNVQELAT...ENLPVK.M.LNNQHLGM..QWE
Retrocopy TSGGLGAMGFGLPAAIGAAVGRPGEIVVDIDGDGSFIMNVQELATIKVENLPVKIMLLNNQHLGMVVQWE

Parental  DRFYKANRAHSYLGNPSNKARIFPNMLKFAEACDIPCAQVIHRNDVRDAIRKMLHTPGPYLLDVIVPHQE
          DRFYKANRAH.YLG.PSN...IFPNMLKFAEAC..P.A.V.HR.D.R.AI.KML.TPGPYLLDVIVPHQE
Retrocopy DRFYKANRAHTYLGDPSNEEEIFPNMLKFAEACGVPAARVSHRDDLRAAIQKMLDTPGPYLLDVIVPHQE

Parental  HVLPMIPSNGAFKDVITEGDGRCSY
          HVLPMIPS.GAFKDVITEGDGRCSY
Retrocopy HVLPMIPSGGAFKDVITEGDGRCSY

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_37 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	Solyc06g059880.2	1 retrocopy	retro_slyc_37 ,