RetrogeneDB ID: retro_slyc_34

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 10:2121095..2122571(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc10g007960.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g109150.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_34
ATGGCTAATACCAAAGACTCATACCACATAATTACAATGGATACCAAAGAATCTTCAATTCCAAGTCTTCCTATGAAAGA
AATTCCTGGTGATTATGGTGTCCCATTCTTCGGGGCGATAAAAGATCGTTACGATTTTCATTACAATCAAGGTGCTGATG
AATTTTTCAGGTCTCGCATGAAAAAGTACGATTCCACTGTCTTTAGAACCAATGTCCCTCCTGGTCCTTTCAATGCTCGT
AACTCTAAAGTTGTTGTCCTTGTAGACGCGGTTAGTTATCCCATCCTTTTCGATAACTCCCAAGTCGACAAGGAAAACTA
CTTTGAAGGTACTTTTATGTCCTCTCCATCTTTCAATGGTGGTTATAAGGTTTGTGGTTTTCTTGGTACTAGTGACCCTA
AACACACCACTCTAAAAGGTCTTTTCTTGTCCACACTAACTAGATTGCATGACAAGTTCATCCCTATCTTTACTACATCA
ATCACTTCAATGTTTACCAGTCTTGAAAAAGAACTGTCTGAGAAAGGAACGTCTTACTTCAATCCCATCGGTGACAACTT
GTCATTCGAATTCCTCTTTCGATTGTTTTGTGAAGGGAAAAATCCAATTGATACAAGTGTTGGCCCTAATGGACCAAAAA
TTGTAGACAAATGGGTTTTTCTTCAACTAGCTCCATTGATTTCACTAGGGCTTAAATTTGTACCAAACTTTCTTGAAGAT
TTAGTCTTGCACACTTTCCCTCTACCTTACATCCTTGTAAAACGCGATCATCAGAAGCTATACAACGCGTTCTACAACTC
CATGAAGGATATCTTAGATGAAGCTGAGAAACTTGGAGTTAAAAGAGATGAAGCTTGTCATAACTTTGTTTTCCTAGCAG
GATTCAATTCGTATGGCGGTTTGAAAGTGTTCTTCCCATCTTTGATCAAATGGATAGGTACATCAGGACCTAGTTTACAT
GCTAGGCTTGTTAAAGAGATCAGGACCGCGGTTAAAGAGGCTGGAGGGGTAACTCTTTCAGCTATAGATAAAATGCCTCT
TGTTAAGTCTGTGGTTTATGAAACCCTAAGGATGGATCCTCCGGTTCCATTCCAAACCGTTAAGGCTAGGAAGAATATAA
TCATTACTAATCACGAATCATCGTTCTTGATCAAGAAAGATGAATTGATATTTGGATATCAACCCTTAGCTACAAAGGAT
TCAAAAGTATTTAAGAACGCGGAGGAGTTCAATCCAGATAGATTTGTGGGGGGTGGAGAGAAGTTGCTTAAGTATGTGTA
TTGGTCAAATGGTAAAGAGATTGATAATCCAAGTGTGAATGATAAACAATGTCCTGGTAAAGATTTGATAGTGTTGATGG
GAAGGTTATTGGTTGTGGAGTTTTTCATGCGTTATGATACTTTTGAAGTTGAATTTGGAAAACTTTTGCTTGGTTCAAAG
GTGACTTTTAAGTCATTAACTAAAGCAACATCATGA

Alignment

ORF - retro_slyc_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 97.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IASSSDNESCKPLLQVREIPGDYGFPFFGAIKDRYDYYYSLGADEFFRTKSLKYNSTIFRTNMPPGPFIA
          I......ES..P.L...EIPGDYG.PFFGAIKDRYD..Y..GADEFFR....KY.ST.FRTN.PPGPF.A
Retrocopy IITMDTKESSIPSLPMKEIPGDYGVPFFGAIKDRYDFHYNQGADEFFRSRMKKYDSTVFRTNVPPGPFNA

Parental  KDPKVIVLLDAISFPILFDCSKVEKKNVLDGTYMPSTDFFGGYRPCAFLDPSEPSHATHKGFYLSIISKL
          ...KV.VL.DA.S.PILFD.S.V.K.N...GT.M.S..F.GGY..C.FL..S.P.H.T.KG..LS....L
Retrocopy RNSKVVVLVDAVSYPILFDNSQVDKENYFEGTFMSSPSFNGGYKVCGFLGTSDPKHTTLKGLFLSTLTRL

Parental  HTQFIPIFENSVSLLFQNLEIQISKDGKANFNDISDAMSFDFVFRLLCNNTNPLDTKLGTTGPKCFDLWM
          H..FIPIF..S....F..LE...S..G...FN.I.D..SF.F.FRL.C...NP.DT..G..GPK..D.W.
Retrocopy HDKFIPIFTTSITSMFTSLEKELSEKGTSYFNPIGDNLSFEFLFRLFCEGKNPIDTSVGPNGPKIVDKWV

Parental  LPQLAPLVTLGLKFVPNFLEDLMLHTFQLPFFIIKSKYQKLYDAFNEHAGSTLDDAEKSGIKRDEACHNL
          ..QLAPL..LGLKFVPNFLEDL.LHTF.LP....K...QKLY.AF.......LD.AEK.G.KRDEACHN.
Retrocopy FLQLAPLISLGLKFVPNFLEDLVLHTFPLPYILVKRDHQKLYNAFYNSMKDILDEAEKLGVKRDEACHNF

Parental  VFLAGFNAYGGMKILFPSLMKWVASGGKSLHTPLANEIRTIIKEEGGSITLSAINKMSLVKSTVYEVLRI
          VFLAGFN.YGG.K..FPSL.KW....G.SLH..L..EIRT..KE.GG..TLSAI.KM.LVKS.VYE.LR.
Retrocopy VFLAGFNSYGGLKVFFPSLIKWIGTSGPSLHARLVKEIRTAVKEAGG-VTLSAIDKMPLVKSVVYETLRM

Parental  EPPIPFQYGKAKEDIMVQSHDSNFLIKKGEMIFGYQTFATKDAKIFENPEEFIAERFMGSEGEKLLKYVY
          .PP.PFQ..KA...I....H.S.FLIKK.E.IFGYQ..ATKD.K.F.N.EEF...RF.G..GEKLLKYVY
Retrocopy DPPVPFQTVKARKNIIITNHESSFLIKKDELIFGYQPLATKDSKVFKNAEEFNPDRFVGG-GEKLLKYVY

Parental  WSNARETDSPTVDNKQCAGRDLAVLLCRLLLVEFFMRYDTFTVESSKYLAGPLITFKTLEK
          WSN..E.D.P.V..KQC.G.DL.VL..RLL.VEFFMRYDTF.VE..K.L.G...TFK.L.K
Retrocopy WSNGKEIDNPSVNDKQCPGKDLIVLMGRLLVVEFFMRYDTFEVEFGKLLLGSKVTFKSLTK

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_34 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	Solyc01g109150.2	1 retrocopy	retro_slyc_34 ,