RetrogeneDB ID: retro_slyc_26

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:62946876..62949177(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc04g078110.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g044150.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_26
ATGGAAAGACTCAGGCTCATGTTTCTTTTAATACTAATGGTAGTGTTGTTTCATGTGTTTGTTGATGCAAGACAGAACCA
GAAGAAGACTTATATAATTCACATGGACAAGTTCAACATGCCTGCTGATTTTGATGATCATACTCAGTGGTATGACTCAT
CATTGAAGTCAGTATCCAAGAGCGCCAACATGCTTTACACCTACAACAGTGTCATCCATGGCTACTCAACACAGCTAACA
GCTGATGAAGCCAAAGCACTTGCACAGCAACCGGGAATTCTCTTGGTCCACGAGGAAGTGATATACGAGCTTCACACCAC
TCGATCCCCTACGTTTCTGGGACTTGAAGGACGTGAAAGTAGATCATTCTTTCCTCAGACTGAAGCAAGGAGTGAGGTCA
TTATTGGTGTGCTGGACACAGGTGTTTGGCCTGAATCAAAAAGTTTTGATGACACTGGACTAGGTCCAGTCCCTGCGAGC
TGGAAGGGTAAGTGTCAAACTGGCAAGAACTTCGACGCATCAAGCTGTAATCGGAAACTTATTGGTGCGAGGTTTTTCTC
ACAAGGTTATGAAGCAGCTTTTGGGGCAATCGATGAGACCATTGAATCCAAGTCACCAAGGGACGATGAAGGCCATGGCA
CACACACTGCAACTACAGCAGCTGGCTCGGTTGTAACCGGAGCTAGCCTCTTGGGTTATGCAACTGGTACAGCACGTGGG
ATGGCTTCACACGCAAGGGTGGCAGCGTACAAGGTATGTTGGACCGGAGGATGTTTTAGCAGCGACATACTGGCAGGGAT
GGACCAGGCTGTCATAGATGGTGTAAATGTGCTCTCACTGTCCCTTGGTGGCACAATTTCTGATTATCATAGGGACATAG
TTGCAATCGGAGCATTTTCTGCAGCATCTCAAGGGATCTTTGTCTCATGCTCAGCGGGGAATGGTGGTCCAAGCTCTGGG
ACGCTATCCAACGTTGCACCATGGATAACTACTGTAGGTGCTGGAACCATGGACCGTGAATTTCCAGCATACATTGGCAT
TGGAAATGGGAAAAAACTCAATGGAGTATCACTTTACAGTGGAAAGGCATTGCCTAGTTCTGTGATGCCACTGGTGTATG
CTGGAAATGTCAGCCAATCATCTAATGGAAATTTATGCACCAGTGGTAGTCTAATTCCAGAAAAAGTTGCTGGAAAAATT
GTCGTCTGTGACCGGGGGATGAATGCAAGGGCACAAAAGGGTTTGGTTGTGAAGGATGCTGGTGGAATAGGGATGATTCT
GGCAAACACAGACACTTACGGAGATGAGTTGGTTGCTGATGCACACCTCATACCTACAGCTGCAGTTGGTCAAACTGCGG
GCAACTTGATCAAGCAGTACATAGCTTCTAACAGCAATCCAACTGCCACAATTGCATTTGGAGGAACCAAGTTGGGTGTT
CAACCATCGCCAGTTGTTGCAGCTTTTAGTTCCAGAGGGCCAAACCCAATCACACCAGATGTACTCAAACCTGATTTGAT
AGCACCAGGTGTCAATATTCTTGCTGGCTGGACAGGGAAAGTTGGACCAACTGGCTTGCAAGAAGACACCAGGAATGTAG
GCTTCAACATCATCTCTGGAACTTCCATGTCATGTCCCCATGTAAGTGGGCTAGCAGCACTACTCAAAGCTACCCATCCA
GAATGGAGTCCAGCAGCTATAAGGTCAGCACTGATGACTACAAGTTATAGCACATACAAAAACGGAAAAACAATCGAGGA
TGTTGCAACAGGAATGTCATCTACACCATTTGATTATGGTGCTGGACATGTGAATCCAACAGCAGCTGTCAGTCCTGGTT
TAGTGTATGATCTAACAGTTGATGACTATATAAACTTTCTATGTGCCTTGGACTACAGCCCGAGTATGATCAAGGTCATT
GCAAAAAGAGACATCTCCTGTGACGAAAATAAGGAGTATAGAGTTGCTGATCTTAATTACCCATCTTTTTCCATTCCTAT
GGAAACGGCCTGGGGTGAACATGCAGATAGTAGTACCCCCACCGTGACCAGATACACAAGGACTCTAACAAATGTGGGAA
ACCCAGCTACATACAAGGCCTCAGTCTCTTCTGAAACACAGGACGTGAAGATTCTGGTTGAGCCACAAACACTTACTTTC
AGCCGAAAGAACGAAAAGAAAACCTACACTGTGACATTCACTGCTACTTCCAAGCCATCAGGCACAACCAGCTTCGCTCG
ACTGGAGTGGTCAGATGGACAACACGTTGTTGCAAGCCCAATTGCTTTCAGCTGGACATGA

Alignment

ORF - retro_slyc_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.01 %
• Parental protein coverage: 98.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRFVVLSLLFLLGLCHFSAGMNMMKSNFIVHMAKSQMPESFEDHTHWYDSSLRSVSGSAEMLYVYNNAVH
          LR...L..L.......F.......K...I.HM.K..MP..F.DHT.WYDSSL.SVS.SA.MLY.YN...H
Retrocopy LRLMFLLILMVVLFHVFVDARQNQKKTYIIHMDKFNMPADFDDHTQWYDSSLKSVSKSANMLYTYNSVIH

Parental  GFAARLTAEEAESLQNQPGILSVLPEMKYELHTTRTPSFLGLD--VSADYFPESNAMGDVIVGVLDTGVW
          G....LTA.EA..L..QPGIL.V..E..YELHTTR.P.FLGL....S...FP...A...VI.GVLDTGVW
Retrocopy GYSTQLTADEAKALAQQPGILLVHEEVIYELHTTRSPTFLGLEGRESRSFFPQTEARSEVIIGVLDTGVW

Parental  PESKSFDDTGFGPIPASWKGECESGTNFTSKNCNRKLIGARYFAKGYESTLGPIDVSKESKSPRDDDGHG
          PESKSFDDTG.GP.PASWKG.C..G.NF....CNRKLIGAR.F..GYE...G.ID...ESKSPRDD.GHG
Retrocopy PESKSFDDTGLGPVPASWKGKCQTGKNFDASSCNRKLIGARFFSQGYEAAFGAIDETIESKSPRDDEGHG

Parental  THTSTTATGSVVQGASLLGYASGNARGMATHARVAVYKVCWVGGCFSSDILAALDKAIDDNVNVLSLSLG
          THT.TTA.GSVV.GASLLGYA.G.ARGMA.HARVA.YKVCW.GGCFSSDILA..D.A..D.VNVLSLSLG
Retrocopy THTATTAAGSVVTGASLLGYATGTARGMASHARVAAYKVCWTGGCFSSDILAGMDQAVIDGVNVLSLSLG

Parental  GGNSDYYRDSVAIGAFAAMEKGILVSCSAGNAGPSPYSLSNVAPWITTVGAGTLDRDFPAYVSLGNGKNF
          G..SDY.RD.VAIGAF.A...GI.VSCSAGN.GPS...LSNVAPWITTVGAGT.DR.FPAY...GNGK..
Retrocopy GTISDYHRDIVAIGAFSAASQGIFVSCSAGNGGPSSGTLSNVAPWITTVGAGTMDREFPAYIGIGNGKKL

Parental  SGVSLYKGASSLSKMLPFVYAGNASNMTNGNLCMSGTLIPEEVKGKIVLCDRGINPRVQKGSVVKAAGGA
          .GVSLY.G....S...P.VYAGN.S...NGNLC.SG.LIPE.V.GKIV.CDRG.N.R.QKG.VVK.AGG.
Retrocopy NGVSLYSGKALPSSVMPLVYAGNVSQSSNGNLCTSGSLIPEKVAGKIVVCDRGMNARAQKGLVVKDAGGI

Parental  GMVLANTAANGDELIADAHLIPATSVGQTTGEAIKNYLTSNPNPTATILFEGTKVGIKPSPVVAAFSSRG
          GM.LANT...GDEL.ADAHLIP...VGQT.G..IK.Y..SN.NPTATI.F.GTK.G..PSPVVAAFSSRG
Retrocopy GMILANTDTYGDELVADAHLIPTAAVGQTAGNLIKQYIASNSNPTATIAFGGTKLGVQPSPVVAAFSSRG

Parental  PNSITQEILKPDIIAPGVNILAGWTGAAGPTGLAEDDRRVEFNIISGTSMSCPHVSGLAALLKGAHPDWS
          PN.IT...LKPD.IAPGVNILAGWTG..GPTGL.ED.R.V.FNIISGTSMSCPHVSGLAALLK..HP.WS
Retrocopy PNPITPDVLKPDLIAPGVNILAGWTGKVGPTGLQEDTRNVGFNIISGTSMSCPHVSGLAALLKATHPEWS

Parental  PAAIRSALMTTAYTVYKKGGALQDVVTGKPSTPFDHGAGHVDPVAALNPGLVYDLKADDYLNFLCALNYT
          PAAIRSALMTT.Y..YK.G....DV.TG..STPFD.GAGHV.P.AA..PGLVYDL..DDY.NFLCAL.Y.
Retrocopy PAAIRSALMTTSYSTYKNGKTIEDVATGMSSTPFDYGAGHVNPTAAVSPGLVYDLTVDDYINFLCALDYS

Parental  SIQINSVARRPFSCATNKKFRVADLNYPSFAVVFPEQMTASSGSGSSSI-KHTRTLTNVGPAGTYKVNVI
          ...I...A.R..SC..NK..RVADLNYPSF.............S........TRTLTNVG...TYK..V.
Retrocopy PSMIKVIAKRDISCDENKEYRVADLNYPSFSIPMETAWGEHADSSTPTVTRYTRTLTNVGNPATYKASVS

Parental  KPSNSVKVVVEPETLAFTRMNEQKSYTVTFTAPSMPSTENVYARIEWSDGKHVVSSPVAISWT
          .....VK..VEP.TL.F.R.NE.K.YTVTFTA.S.PS.....AR.EWSDG.HVV.SP.A.SWT
Retrocopy SETQDVKILVEPQTLTFSRKNEKKTYTVTFTATSKPSGTTSFARLEWSDGQHVVASPIAFSWT

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_26 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400014862	2 retrocopies	retro_stub_57, retro_stub_9,
Solanum lycopersicum	Solyc03g044150.2	1 retrocopy	retro_slyc_26 ,
Solanum lycopersicum	Solyc06g083720.1	1 retrocopy	retro_slyc_9,