RetrogeneDB ID: retro_slyc_31

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:4203734..4205588(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc12g011370.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc12g096380.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_31
ATGACAATCTCAGAGCTTTCTCAACAACTCAAAATTCCCTTAAATTCTTCCGAAAAATTCAGTCTCACTTCTCCTCCTTC
AGCCTCAACAAAAATGGAGTCTTTACCAAAAATCCAACAACCCCATAAGCGTTATTGGCGTTTTAGCAAACAAGATTTCT
TCCCCGAACCGTCTTTTCACAATTTTGGATCCTACAAAAATGCCCTTTCTCAAACCCCAAATCGTCTCAAGAATCGTCTT
TTTTCACGTTCATCAGATACCAGTGAATTGATTGAGCTTAAGAAAGAATCGGAAAATGAAATGAAATTATGTTTGACTTG
GTGGGATTTAATTTGGCTTGGATTTGGATCTGTTGTTGGTTCAGGGATTTTTAGCATTACGGGTCAAGAAACCCGAAATG
ATGCTGGACCTGCTATTGTTCTTTCGTATGCAATTTCTGGTTTATCTGCTTTGCTTTCTGTGTTTTGTTATACAGAATTT
TCTGTTGATATTCCTGTTGCTGGTGGGTCTTTTTCGTTTTTGAGAATTGAATTGGGTGATTTTGTTGCATTTATAGCTGC
TGCTAATATTCTATTAGAGGCTATGGTGGGTGCTGCTGGGTTAGGACGTTCATGGTCGTCTTATTTTGCTAGTATTATTA
ATAATAACCCGGATTTTTTGAGGATCAAGATTGATTCTTTTGTAGAAGGGTTTAATTTGTTGGATCCAATAGCTGTTGTG
GTTCTTGCACTTGCAAATGTGGTTGCTATAACTGGGACAAAGATGACATCTACTTTGAATTGGATAAGTTCTATAATTAG
TGCTGGGGTGATTGTTTTTATTATAATTGTTGGGTTTGTTAATGGAAAGACTTCAAATTTGGTGCCTTTTTTCCCTTTTG
GGGCTGGAGGGGTGTTTAGAGCTGCAGCAGTTGTGTATTGGTCGTATACTGGTTTTGATATGGTTGCGAATATGGCTGAG
GAGACAAAGAGGCCATCGAGGGATATACCGTTAGGGTTGCTTGGTTCGATGTCTATAATTACTGTTGTTTATTGTTTGAT
GGCCTTGGCGTTGGCAATGATGGTTAAATATACTCAAGTGGATGTTAATGCAGCTTATTCAGTTGCATTTGAAGGTATAG
GTATGAATTGGGCAAAGTATTTGGTGGGGATTTGTGCACTTAAGGGAATGACTACGAGTATGCTTGTTGGGTCATTGGGA
CAATCTCGATACACAACTCAGATTGCAAGAGCACATATGATTCCCCCGTGGTTTGCTTTGGTTCACCCGAAAACTGGAAC
GCCGATTTATGCTACACTCTTGACAACTATAACTAGTTGCATTCTTGCTCTGTTCACGAGCTTGGATGTCTTGTCAAGTG
TGTTCTCATTTAGTACACTTTCCATTTTCATGCTTATGGCTGTTGCATTGCTTGTTAGGCGATACTATGTTACCGATGTT
ACTTTGAAGCAGGATTTGGGTAAATTTCTTGTGTGTTTGTTCATTGTAATTGGTTCATCAGTTGGGGCAACAGTTCTTTG
GAGTACTAATGTAAAAGGTTGGGTTGGGTATGCTGTGACTGGCGTTTTGTGGTTGTTGGGCACTTCAGGGATGGCGCTAC
TTCCAAAACAAAGAATTCCTAAAGTTTGGGGTGTACCTCTTGTGCCATGGGTACCATCATTGTCAATTGGGATGAATATA
TTTTTGATAGGTTCTTTGGGTAAGGAGGCATTTTATCGATTCTTCATATGCAGTGCTGTGATGCTAATTTACTATGTGCT
TGTTGGTGTCCATGCAACATATGATATCGCTCATCCCGATAAGCAGAAGTCTCTTATTGATGAGGGAAAAGATAGTTCTG
ATCAAGTGTCATAG

Alignment

ORF - retro_slyc_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 93.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRVCSCTKDDFLPEESFKSWRNYANALIQTPTRLIDRILTRSEDEEEL-EAKSRSQNEMKKTLTWWDLIW
          .R.....K.DF.PE.SF.....Y.NAL.QTP.RL..R...RS.D..EL.E.K..S.NEMK..LTWWDLIW
Retrocopy KRYWRFSKQDFFPEPSFHNFGSYKNALSQTPNRLKNRLFSRSSDTSELIELKKESENEMKLCLTWWDLIW

Parental  FGLGAVIGAGIFVLTGLEANQEAGPAVVLSYVVSGVSALLSVFCYTEFAVEIPVAGGSFAYLRVELGDFV
          .G.G.V.G.GIF..TG.E....AGPA.VLSY..SG.SALLSVFCYTEF.V.IPVAGGSF..LR.ELGDFV
Retrocopy LGFGSVVGSGIFSITGQETRNDAGPAIVLSYAISGLSALLSVFCYTEFSVDIPVAGGSFSFLRIELGDFV

Parental  AFIAAGNILLEYVIAGAAVARTWTSYFATLLNFSSDKFLIKVDSLAEGYNELDPIAVGVCIIICIIAILS
          AFIAA.NILLE.....A...R.W.SYFA...N...D...IK.DS..EG.N.LDPIAV.V.......AI..
Retrocopy AFIAAANILLEAMVGAAGLGRSWSSYFASIINNNPDFLRIKIDSFVEGFNLLDPIAVVVLALANVVAITG

Parental  TKGSSRLNYIATIVHIFVIFFIIVCGLIKSDTKNYTPFAPFKVRGIFKASAVLFFAYVGFDAVSTMAEET
          TK..S.LN.I..I....VI.FII..G.....T.N..PF.PF...G.F.A.AV....Y.GFD.V..MAEET
Retrocopy TKMTSTLNWISSIISAGVIVFIIIVGFVNGKTSNLVPFFPFGAGGVFRAAAVVYWSYTGFDMVANMAEET

Parental  KNPGRDIPIGLIGSMVITTFLYCLLAMTLCLMQPYQKIDTQAPFSVAFKSVGWSWAQYIVAAGALKGMTS
          K.P.RDIP.GL.GSM.I.T..YCL.A..L..M..Y...D..A..SVAF...G..WA.Y.V...ALKGMT.
Retrocopy KRPSRDIPLGLLGSMSIITVVYCLMALALAMMVKYTQVDVNAAYSVAFEGIGMNWAKYLVGICALKGMTT

Parental  VLLVGAVGQARYLTHISRTHMMPPWFSQVNAKTGTPVNATAVMSCATAIIALFTKLDILSNLLSISTLFI
          ..LVG..GQ.RY.T.I.R.HM.PPWF..V..KTGTP..AT........I.ALFT.LD.LS...S.STL.I
Retrocopy SMLVGSLGQSRYTTQIARAHMIPPWFALVHPKTGTPIYATLLTTITSCILALFTSLDVLSSVFSFSTLSI

Parental  FMLVALALLVRRYYVHGDTTIANRNKLITSLLIILASSIATSTYWGLSKDGWIGYCITLPIWLLATIGLW
          FML.A.ALLVRRYYV...T......K....L.I...SS......W.....GW.GY..T...WLL.T.G..
Retrocopy FMLMAVALLVRRYYVTDVTLKQDLGKFLVCLFIVIGSSVGATVLWSTNVKGWVGYAVTGVLWLLGTSGM-

Parental  YFVPQARKPKLWGVPLVPWLPSASIAINIFLLGSLDRASFMRFGVWTGFLLVYYLFFGLHASYDTAKEFK
          ...P..R.PK.WGVPLVPW.PS.SI..NIFL.GSL....F.RF.......L.YY...G.HA.YD.A...K
Retrocopy ALLPKQRIPKVWGVPLVPWVPSLSIGMNIFLIGSLGKEAFYRFFICSAVMLIYYVLVGVHATYDIAHPDK

Parental  R
          .
Retrocopy Q

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_31 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
Leersia perrieri	LPERR12G15690	1 retrocopy	retro_lper_7,
Solanum lycopersicum	Solyc12g096380.1	1 retrocopy	retro_slyc_31 ,