RetrogeneDB ID: retro_slyc_41

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 10:63438581..63439268(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc10g083650.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g020860.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_41
ATGGCTGCCACTACAGCTGCTGCCATTTTCACCCTTCCAAAGCTCTGCAAATCCTCCATTAGCCCAAAATCCATATCCCT
TTTTTCCCCAAAATCCACTCTTTCTTCTTCTTTCTCCATTTCATCTGTTCCATTCAAGGTACATCACTCAAAGCGCACCG
TACGACCCCTTTCATACACCACTCCAAGAATCTCCGCCGTCATCTCCGTCGGAGACAAATTACCCAATTCCACACTTTCC
TACTTCGATTCATCCGATGAACTCCAGACCCTTTCCGTCTCTGACCTCACATCTGGGAAAAAGGTTGTTCTTTTCGCCGT
CCCAGGTGCATTTACACCAACATGTTCACAGAAACATCTTCCTGGTTTCGTGGAGAAGTCGAAGGAGCTAAAATCGAAAG
GGGTTGATACAATTGCTTGTATTTCGGTTAATGATGCTTTTGTGATGAAAGCTTGGAAGGAGAATTTGAACATTAGTGAT
GAAGTTTTGCTGTTGAGTGATGGGAATTTGGAGTTTACAAAGGCAATTGGGTGTGAACTTGACCTTACTGATAAGCCTAT
TGGACTTGGTGTTAGGTCTAGAAGATATGCTATGCTTGTGGATGATGGGGTTGTGAAAGTGTTGAATTTGGAAGAAGGTG
GAGCTTTTAATGTTAGCAGTGCAGAAGATATTCTCAAGGCTCTTTAG

Alignment

ORF - retro_slyc_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.58 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APIAVGDVIPDGTVSYFDEQDQMQTVSVYSLAKGKKVIIFAVPGAFTPTCSMKHVPGFIEKAAELKSKGV
          A.I.VGD..P..T.SYFD..D..QT.SV..L..GKKV..FAVPGAFTPTCS.KH.PGF.EK..ELKSKGV
Retrocopy AVISVGDKLPNSTLSYFDSSDELQTLSVSDLTSGKKVVLFAVPGAFTPTCSQKHLPGFVEKSKELKSKGV

Parental  DEILCISVNDPFVMKAWAKTYPENKHVKFLADGAGKYTHALGLELDLSDK--GLGVRSRRYALLVDDLEV
          D.I.CISVND.FVMKAW.........V..L.DG....T.A.G.ELDL.DK..GLGVRSRRYA.LVDD..V
Retrocopy DTIACISVNDAFVMKAWKENLNISDEVLLLSDGNLEFTKAIGCELDLTDKPIGLGVRSRRYAMLVDDGVV

Parental  KVANIESGGEFTVSGADEIVNAL
          KV.N.E.GG.F.VS.A..I..AL
Retrocopy KVLNLEEGGAFNVSSAEDILKAL

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_41 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41 ,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,