RetrogeneDB ID: retro_slyc_70

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:53752844..53754362(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g078170.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_70
TGCACCAGTACAAGTCGTAGTTGCTTGTTGTGTGGTAAAATGGAAGAAAAAGATCCATCGATACGAAAAACTTTAATAGC
TCAATGCTTCAAAGATTTGCATCTGATTGAAGATATGGAACTTGTTCTCACCTTAAGATGCCTCTGGAATACTGCTCTTG
CTCAACCTGATGACCCTGAATTCCCATCCCTCGGCGTCTTTAGTTGCATGGCTAGACTTCTCAACAGGTGCACCCGTGAC
CAAAAATGGCTTTCAAGAGGCCATAACGTGTATGTTCCTTATTATGCAGCTCATATCATTGGCTCCTACACCATGAACAA
AGTTAGATTCTCTGTTTTGGCTGTTAAATCAGACGTAATTTCGCCATTAATAGACCTCTTAAGAGGTAAGATAACTTGGG
TCGAACAAAGAGTGGCTGTTAGAGCACTTGGTCACATTGCACGACATAGAAGAACATTTGAAGATATTAAGGTCCATGAA
GTAGAGATTATAAAACTAGCCATTGATATAGCTTCCAAATGCATTTATACAATCTATAGCGAGTTTGTGAGCAAGAGAAG
TGAAAACAGAGTCGAATATCATCGTTATTTGATGATAAAAGGCCTCGGAGAATTCGAAATGGAGAGTAAAAAAGCAGAGT
CTTGGGCTTGCCAAATGCAATGCTGGTCACTGTACCTTCTCAACTGCTTCGTTACAAAGAAAAGAAGCATCAATTTGATA
TGCAAAGAACATTTTCTCAAGAATTTGTGTGATATATGGGGTGGATTACAGAACCAGAATTCTTTCTCTGGAATTGGCCT
AATCCGAAGTCTTTGTGAAAGCGAAGATGGTAGAAAAAACATTGCTCAATTAGTACAAGTCGTAGAAAATATCTGCGACC
TCTCTAGATCATCCGACGAATGGCAATTCATGGCAATTGAATGTCTTTTGTTACTTCTCAAGGATCCAAAAACAAAAAAC
AGAGTAACCAACATTGCAGCTCCTTTTCTTGCTGATTTAGTAGAGCTTAGAACTATCAAAGGAAGACGAAAAATGGGTGA
CATGATAACACAACTACTCTTACAAGATTATGCTAAAATCAAATATGGTCAAGTGGGGTTCTCCGAAACAGGATCAATCA
AAGAGATTTGGGACTTGAAAGTTGAAAAAAGGAAAAGGGATAAAATCATTTCGGAACAAGAAGTGAAGGAAACAGAGCTT
TTGGTTTCCGTTTTAAAACGTGAAGGAAACAAGAAATTTTGGTCAAGTGAGATTGAAGCAGCTGTAAACAAGTACACAAA
GGCTTTAGATTTATGTCCACTGAACTTGAGAAAAGAAAGAATTGTTCTTTATAGCAATAGAGCTCAATGTCATTTAATTT
TAGGAGAAGCAGAGTTAGCTATTAGTGATACAACTCGAGCCTTAAGTTTATCAGGTGAAATGAGACCACATATAAAGAGC
CTATGGCGAAGATCGCAGGCTTATCACATGAAAGGTTTGGCTAGACTAAGTTTAATAGATTGTTTAATGTTCATCAAT

Alignment

ORF - retro_slyc_70 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.35 %
• Parental protein coverage: 78.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CYNNHLGCFFC-IMKETNSSIRSNGIKNYFKKMHLIDEDQELVLVLSGLWTMAMSQPNDKELPSLGIFEC
          C......C..C..M.E...SIR...I...FK..HLI.ED.ELVL.L..LW..A..QP.D.E.PSLG.F.C
Retrocopy CTSTSRSCLLCGKMEEKDPSIRKTLIAQCFKDLHLI-EDMELVLTLRCLWNTALAQPDDPEFPSLGVFSC

Parental  MASLINKGINQKSWLQKDQNIYIPYYASHIIGSYTMNNVEFAIKALDCGVLVPLLDLLRGNMTWVEQRVA
          MA.L.N.......WL....N.Y.PYYA.HIIGSYTMN.V.F...A....V..PL.DLLRG..TWVEQRVA
Retrocopy MARLLNRCTRDQKWLSRGHNVYVPYYAAHIIGSYTMNKVRFSVLAVKSDVISPLIDLLRGKITWVEQRVA

Parental  IRAIGHLASYEKTFKSVAIYEEEIVKLAMNLASTCLDVVYKEFVGVKDLNMRLKYHCDLLTRGVGGLEME
          .RA.GH.A....TF......E.EI.KLA...AS.C....Y.EFV.....N.R..YH..L...G.G..EME
Retrocopy VRALGHIARHRRTFEDIKVHEVEIIKLAIDIASKCIYTIYSEFVSKRSEN-RVEYHRYLMIKGLGEFEME

Parental  NSKAEEWASQLQCWSLHLLNCFAIKQRCLNIICEQSFLKELSEMWGGLANDSSPGGVGLIRVLCYNKDGR
          ..KAE.WA.Q.QCWSL.LLNCF..K.R..N.IC...FLK.L...WGGL.N..S..G.GLIR.LC...DGR
Retrocopy SKKAESWACQMQCWSLYLLNCFVTKKRSINLICKEHFLKNLCDIWGGLQNQNSFSGIGLIRSLCESEDGR

Parental  RCIAESKDVIKNLCNLARSSDDWQYMGIDCLLLLLADSGTRYKVLQVASMCLVDLIELRTLGGRSNVGNT
          ..IA....V..N.C.L.RSSD.WQ.M.I.CLLLLL.D......V...A...L.DL.ELRT..GR...G..
Retrocopy KNIAQLVQVVENICDLSRSSDEWQFMAIECLLLLLKDXXXXXRVTNIAAPFLADLVELRTIKGRRKMGDM

Parental  ITRTLLSDFKQRKVKIKNTGVQQV--LEEIWGLKVDRKKREQNMSDEKLEEKRVMVSLMKQQGNNSFWLG
          IT..LL.D....K.K....G........EIW.LKV...KR....S.....E....VS..K..GN..FW..
Retrocopy ITQLLLQDYA--KIKYGQVGFSETGSIKEIWDLKVEKRKRDKIISEQEVKETELLVSVLKREGNKKFWSS

Parental  KIEEAMMKYSEALELCPLRFRKERIVLYSNRAQCKLLLGEANDAISDTTKALSLSSPTNSHAKSLWRRSQ
          .IE.A..KY..AL.LCPL..RKERIVLYSNRAQC.L.LGEA..AISDTT.ALSLS.....H.KSLWRRSQ
Retrocopy EIEAAVNKYTKALDLCPLNLRKERIVLYSNRAQCHLILGEAELAISDTTRALSLSGEMRPHIKSLWRRSQ

Parental  AYDMKGLAKESLMDCIMFVN
          AY.MKGLA..SL.DC.MF.N
Retrocopy AYHMKGLARLSLIDCLMFIN

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_70 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
Solanum tuberosum	PGSC0003DMG400021536	1 retrocopy	retro_stub_101,
Solanum lycopersicum	Solyc04g078170.1	1 retrocopy	retro_slyc_70 ,