RetrogeneDB ID: retro_slyc_69

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:53370713..53371838(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g043920.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_69
GTTTCATTAGGCTTCAATTTACGGTACGACCCGCCCGACCCGACTTTCTATGACGACCCGGATTTGAGTTACACTATGGA
GAAGCCGATTAAGAAGTGGGACGAGAAACGAAGGCAATGGCTGAATTTGCATCCCTCTTTCATCCCCGGAGCAGAGGAAC
GGATTCTGATGGTTTCCGGTTCACAGTCGACGCCGTGTAAGAACCCAATAGGCGACCATTTGCTGCTTAGATTCTTCAAG
AACAAAGTAGACTACTGCCGAATCCACGGGTACGATATTTTTTACAACAACGTTTTACTTCAGCCTAAGATGTGGTCGTT
TTGGGCGAAAATGCCGGCGATTAAAGCTGCCATGATAGCTCATCCTGAAACTGAGTGGATCTGGTGGGTCGATTCAGATG
CTGCGTTCACCGACATGGACTTCAAACTTCCTTTGGATCGTTACAAAGACCATAATTTCGTACTTCATGGTTGGGAAAAG
TTATTATACGAGCAACAAAGCTGGACAAGCATCAATGCCGGAGTTTTCTTGATTCGGAACTGTCAATGGTCCATGGACTT
AATGGAAACTTGGGCGAAAATGGGGCCACAGTCACCGGAATACGACAAGTGGGGTGAAATCTTACATACAACTTTCAAAG
ACAAGATATTCCAGGAATCGGATGACCAATCCGGTCTAGCATATCTACTTTTGAAGGAAAAGGAAAAATGGGGTAACAAA
ATATACGTAGAAGGGGGATATTACTTCGAGGGGTATTGGGTGGAAATCGTGGGAACGTACGATAACATCACCGACAGGTA
TTTAGCAATAGAGAAAAGTGAAGGGAGGCTAAGAAGAAGACACGCAGAGAGGGTGAGTGAGAGTTATGCTAGTGTATGGG
AAGAACACCTTAAGGAAGCTGGGTATGGGAGATACAGTTGGAGAAGGCCATTCATCACACATTTCACAGGGTGTCAGCCA
TGTAGTGGAGATCATAATCAGATGTATTCTGGTGAAACTTGTTTTGATGCTATGCAGAAAGCTTTGAATTTTGCTGATAA
TCAGGTGTTGAGAAAGTATGGGTATATGCATAAGGATCTGCTTGATTCTTCCTCTGTTTTTCCTGTTCCTTTTAACTTTC
CTGCC

Alignment

ORF - retro_slyc_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.61 %
• Parental protein coverage: 89.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INLDFNLDQEG-STNFYDEPNLSYTIEKPIQNWDDKRRQWFNLHPSFKLEGEKDRVLIVSGSQSTPCKNP
          ..L.FNL........FYD.P.LSYT.EKPI..WD.KRRQW.NLHPSF...G...R.L.VSGSQSTPCKNP
Retrocopy VSLGFNLRYDPPDPTFYDDPDLSYTMEKPIKKWDEKRRQWLNLHPSF-IPGAEERILMVSGSQSTPCKNP

Parental  IGDHLLLRFFKNKVDYSRIHGYDIFYNNVLLEPKMFFFWAKLPAIRAAMVAHPEAEWIWWVDSDAAFTDM
          IGDHLLLRFFKNKVDY.RIHGYDIFYNNVLL.PKM..FWAK.PAI.AAM.AHPE.EWIWWVDSDAAFTDM
Retrocopy IGDHLLLRFFKNKVDYCRIHGYDIFYNNVLLQPKMWSFWAKMPAIKAAMIAHPETEWIWWVDSDAAFTDM

Parental  DFKLPLEKYKNHNFVVYGWPKLIYEKKSWTGINAGVFLIRNCQWSMDLIEAWAKMGPQSPEYNRWGEILR
          DFKLPL..YK.HNFV..GW.KL.YE..SWT.INAGVFLIRNCQWSMDL.E.WAKMGPQSPEY..WGEIL.
Retrocopy DFKLPLDRYKDHNFVLHGWEKLLYEQQSWTSINAGVFLIRNCQWSMDLMETWAKMGPQSPEYDKWGEILH

Parental  TTFKDKNFPQSDDQSGLSYLLLKEKDKWGDKIYIESEYYFQGYWVDIIDTLDNITNKYFEIEKKIPILRR
          TTFKDK.F..SDDQSGL.YLLLKEK.KWG.KIY.E..YYF.GYWV.I..T.DNIT..Y..IEK....LRR
Retrocopy TTFKDKIFQESDDQSGLAYLLLKEKEKWGNKIYVEGGYYFEGYWVEIVGTYDNITDRYLAIEKSEGRLRR

Parental  RHAEKV-VSEIKVWEEYLIKDSY---SIRRPFVTHFTGCEPCSGDYNPIYSWETCYNAMQKALNFADNQV
          RHAE.V..S...VWEE.L....Y...S.RRPF.THFTGC.PCSGD.N..YS.ETC..AMQKALNFADNQV
Retrocopy RHAERVSESYASVWEEHLKEAGYGRYSWRRPFITHFTGCQPCSGDHNQMYSGETCFDAMQKALNFADNQV

Parental  LRKYGFVHNNLLDSSSVRPLPFDYPS
          LRKYG..H..LLDSSSV.P.PF..P.
Retrocopy LRKYGYMHKDLLDSSSVFPVPFNFPA

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_69 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc03g043920.2	2 retrocopies	retro_slyc_42, retro_slyc_69 ,