RetrogeneDB ID: retro_slyc_7

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 12:39878865..39879957(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc12g042640.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g098460.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_7
ATGAATTCATCGTCGAAAGGATTGGAATGGAAAGAATGGTTACAAGGATGGCTTCGTTTAACATATGAGACACTGTTTCA
GAAAATTCATGCTAAACATTTACAAGAACCTTTGCCTTTACCTCCTCTCAATGGCCTAAATTGCATTGTCACAGGAGCCA
CTAGTGGCATTGGACTTGAAATTGCTAAACAATTGGCTGAGTCAGGTGCACATCTTGTTATGGCTGTAAGAAACACAAAT
CTTGCTCATCAACTCATTGAAAAATGGCAAAGAAATGAAACTGTATCGAGGCCCTTAAGCATCGATGTTATAGAACTTGA
TCTCTTTTATCTCGAGTCAGTTGTAAAATTTGCAAAAGAATGGAATTCGAGATCAAAACCTCTTCATATTCTCATCAATA
ATGCTGGAATCTATTCTATAGGACAACCACAAAAATTTACCAAAGACGGATATGAAACACATATACAAGTGAACCATCTT
GCACCTGCATTACTATCTCTTCTGCTTTTGCCTTCTTTGAAAAGAGGCTCTCCAAGCAGGATTATCAATATGAATTCCCT
TATGCATGTAATTGGCGTTGTGGATCCTCAAGATATGAATTTCTTAACCAAGAAGAATAAGTTCACAAGTAGAAAGGCAT
ACTCGAGTAGCAAATTGGCACAAATGAAGTTTAGCAGTATACTTCAAAAACTCCTAATTAATACTAATATTCATGTAATG
TGTGTAGAGCCAGGAGCTGTACGTACAAATGTTACGCGAGATCTTCCAAGAATTCTGAACATTCTTTATCAGAAAATGTT
CTTTTTCATGTTCGATGCTCAACAGGGTTCAAGAAGTGCACTTTTTGCAGCTACTGATGCTGAGATCTTGGATTATTGTG
GTGTGTTGAAAGCAGAAGGGTGTATTGGTTGTGCCTTCATTGGTTGCCATTGTAGAATTAGTGAACCTAGCAAACAAGTA
GATAATGAGAGAACCTCTTTTGAAATATGGGATAAGACTATGGAAATGGTTGGTCTTCCTGCAGGGTGTGTTGACATGAT
TCTTCAAGGTGAAGAAATTCATTGCCGCTATGGAGCTGTTAATGATCGTTAA

Alignment

ORF - retro_slyc_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.1 %
• Parental protein coverage: 92.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKKKTLGWMEWLRGWFYLVYEMLFQRILASHLQNPMPLPPINDVTCIVTGSTSGIGREIARQLAEAGAHV
          ...K.L.W.EWL.GW..L.YE.LFQ.I.A.HLQ.P.PLPP.N...CIVTG.TSGIG.EIA.QLAE.GAH.
Retrocopy SSSKGLEWKEWLQGWLRLTYETLFQKIHAKHLQEPLPLPPLNGLNCIVTGATSGIGLEIAKQLAESGAHL

Parental  VMAVRSTNRAQELIRKWQEEWSGKGLPLNIEVMELDLLSLDSVARFAEAWNARMAPVHVLINNAGIFSIG
          VMAVR.TN.A..LI.KWQ........PL.I.V.ELDL..L.SV..FA..WN.R..P.H.LINNAGI.SIG
Retrocopy VMAVRNTNLAHQLIEKWQRNET-VSRPLSIDVIELDLFYLESVVKFAKEWNSRSKPLHILINNAGIYSIG

Parental  EPQKFSKDGYEEHMQVNHLAPAMLSILLLPSLIRGSPSRIVNVNSTMHYVGFVDPEDMNVVSGKRKYTSV
          .PQKF.KDGYE.H.QVNHLAPA.LS.LLLPSL.RGSPSRI.N.NS.MH..G.VDP.DMN....K.K.TS.
Retrocopy QPQKFTKDGYETHIQVNHLAPALLSLLLLPSLKRGSPSRIINMNSLMHVIGVVDPQDMNFLTKKNKFTSR

Parental  VGYGGSKLAQIMFSSILHKRLPAESGISVVCNTPGIVLTNVARDLPQFLQVGYRLIPYFIFNAEEGSRST
          ..Y..SKLAQ..FSSIL.K.L.....I.V.C..PG.V.TNV.RDLP..L...Y.....F.F.A..GSRS.
Retrocopy KAYSSSKLAQMKFSSILQKLL-INTNIHVMCVEPGAVRTNVTRDLPRILNILYQKMFFFMFDAQQGSRSA

Parental  LFAATDPQISEYCEMLKADDWPVCAYISHDCRPTNASEEAHNIETSYKVWEKTLELVGLPSDAVERLIEG
          LFAATD..I..YC..LKA.....CA.I...CR....S....N..TS...W.KT.E.VGLP...V.....G
Retrocopy LFAATDAEILDYCGVLKAEGCIGCAFIGCHCRISEPSKQVDNERTSFEIWDKTMEMVGLPAGCVDMILQG

Parental  EEIKCRYG
          EEI.CRYG
Retrocopy EEIHCRYG

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_7 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400010157	1 retrocopy	retro_stub_22,
Populus trichocarpa	POPTR_0015s05560	1 retrocopy	retro_ptri_15,
Solanum lycopersicum	Solyc03g098460.2	1 retrocopy	retro_slyc_7 ,