RetrogeneDB ID: retro_slyc_39

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 11:50971491..50973006(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc11g065530.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc09g065890.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_39
ATGTCTTCCTTTCAGTTATCTCTCACCAATCCCAAACACAAAAGAAACCATACTTGTCTAGAAGTTTTTCCATTATGGAA
CACATTCAAATCCAACCTCTCTTTCCCAAACAAAAGACTTTCACCTAGCCTATCTTTGAAAACATCTTCATGTCTTTCAA
ATTTAGAGGACAACAATACTATTGAACTCCAACAATATGATGAAGAAGAGAAAAAACCCCTTCATGAGATGTGGAGAGAA
ATTCAAGGATGTAACAATTGGAAAGGTTTACTTGATCCTATGGATTGTCATCTTAGAAAAGAAATCATTCGTTATGGTGA
ATTTGCTCAATCTTGTTATGACTCATTTGACTATGATCCTCATTCAAAATATTGTGGTACTTGCAAGTATCAACCATCAC
AATTTTTTGACAAGATCAACATGTTGAAAAAAGGGTATGAAATGAAAAGGTACTTATATGCAACCTCAAATATCAACTTA
CCAAATTTCTTCCAAAAATCAAAAATGAGGAACGTTTGGAGCCAACACGCGAACTGGATGGGGTATGTAGCCGTAGCCAC
AGATCCTGAAGAAATAAAACGTTTAGGTAGACGTGACATAGTGGTTGCATGGCGTGGCACGGTCACATACCTAGAATGGA
TCCATGACCTACAAGACATTTTACATCCTGCTCATTTTCGCGATGATCCAAACATCAAGATTGAGACAGGGTTCTTCGAT
ATGTATACTAAAAAAGAAAATAATTGTCACTATGCTTCGTTTTCAGCTCGTGAACAAATTTTAGCGGAGATTAATAGATT
AATCGAAAAATACCAAGGTGAAGAGCTAAGTATCACCATAACAGGACATAGCCTTGGTGCAGCATTGGCTTTGTTAAGTG
CTTATGACATAGCTGAGATGAAATTAAATATTTTACATAATGGTAAGTCTATTACTAAAATTATTCCTATTACTGTTTTT
TCATTTGCTGGACCTAGGGTTGGAAATCTTAAATTTAAAGAAAGATGTGAAGAGCTTGGAATTAAAGTTTTAAGAGTTGT
GAATGTGCATGACAAAGTGCCGAAAGTGCCTGGAATTATTGCAAATGAGAAATTTCAATTCCAAAAGCAATTGGAAGAGA
AATTTTCATTTGCTTGGAGTTATGCTCATGTAGGGGCGGAGTTAGCTTTAGATCATCATCGTTCTCCTTTTCTAAAGCCC
AATAGTGATTTGGGCTCTGCTCATAACCTTGAGGCCCATTTACATCTTGTTGATGGGTACCATGGGAAGGTACGCGCCTT
TCGCTCTGCCACGAGTAGGGATGTTGCCCTAGTCAATAAGGATTCGAGTTTCTTGAAGGAGGAGTATGGTGTGCCACCAT
TTTGGTGGCAAGATGAGAACAAAGGCATGGTGAGAACGAGCGATGGGCAATGGGTGTTGCCGGAGAGGCCCATAATTGAG
GCCCATCCACCCGATACGGCCCATCATTTTCAACAAGTCCTTAAACTTGCGAGAGCTAGGTTAAATTTACCATAA

Alignment

ORF - retro_slyc_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.27 %
• Parental protein coverage: 79.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRWLEIHGQDDWVGMLDPMDPLLRSELIRYGEMAQACYDAFDFDPYSKYCGSCKFPRRKFFDGLGMAEYG
          ..W.EI.G...W.G.LDPMD..LR.E.IRYGE.AQ.CYD.FD.DP.SKYCG.CK.....FFD...M...G
Retrocopy EMWREIQGCNNWKGLLDPMDCHLRKEIIRYGEFAQSCYDSFDYDPHSKYCGTCKYQPSQFFDKINMLKKG

Parental  YDITRYLYATSNINLPNFFKQSRWPKIWSKNANWIGYVAVSND-ETTKRLGRRDITIAWRGTVTRLEWIA
          Y...RYLYATSNINLPNFF..S.....WS..ANW.GYVAV..D.E..KRLGRRDI..AWRGTVT.LEWI.
Retrocopy YEMKRYLYATSNINLPNFFQKSKMRNVWSQHANWMGYVAVATDPEEIKRLGRRDIVVAWRGTVTYLEWIH

Parental  DLMDYLRPISSDNIPCPDPNVKVESGFLDLYTDKDESCRYCKFSAREQILTEVKRLIEMYPDEEMSITVT
          DL.D.L.P......P....N.K.E.GF.D.YT.K...C.Y..FSAREQIL.E..RLIE.Y..EE.SIT.T
Retrocopy DLQDILHPAHFRDDP----NIKIETGFFDMYTKKENNCHYASFSAREQILAEINRLIEKYQGEELSITIT

Parental  GHSLGSALAILSAYDLVETGLNV----KADTSGVPICVFSFSGPRVGNVRFKERIEKLGVKVLRVVNVHD
          GHSLG.ALA.LSAYD..E..LN.....K..T...PI.VFSF.GPRVGN..FKER.E.LG.KVLRVVNVHD
Retrocopy GHSLGAALALLSAYDIAEMKLNILHNGKSITKIIPITVFSFAGPRVGNLKFKERCEELGIKVLRVVNVHD

Parental  IVPKSPGLVLNEHSPSMVMKICEKLPWSYS--HVGVELALDHKNSPFLKPTSDLVCAHNLEAHLHLLDGY
          .VPK.PG...NE..........EK.....S..HVG.ELALDH..SPFLKP.SDL..AHNLEAHLHL.DGY
Retrocopy KVPKVPGIIANEKF-QFQKQLEEKFSFAWSYAHVGAELALDHHRSPFLKPNSDLGSAHNLEAHLHLVDGY

Parental  HGKGRRFVLEKGIDIPLVNK
          HGK.R.F......D..LVNK
Retrocopy HGKVRAFRSATSRDVALVNK

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_39 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	PGSC0003DMG400007545	1 retrocopy	retro_stub_20,
Solanum lycopersicum	Solyc09g065890.2	1 retrocopy	retro_slyc_39 ,