RetrogeneDB ID: retro_slyc_42

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:53365050..53366382(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g092210.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_slyc_42
ATGGCCCATAACGTGTTTCGGGCCAAACAGCAATCGTCTTCTCCGAGAGACAAATCTCTGTTCGCGGCCGTCATAGTTGC
GGTTCTACTTGTCTGTGCTATTTGGTCATTTACTGATCCTTTGCCTAATTTATCAGGTTTATTATACAATCAGAATATTA
GTTCACCCGAATATTGCCCACCGGGACGGGAAGCTGTTGACCGGAGTTCCGACCCGCCGGAGAAAACATTCTACAATGAC
CCGGAACTCAGTTACACTATTGACAAACCAATAAAAAATTGGGACGAAAAGAGAGTTCAGTGGCTGCAGCTTCATCCTTC
GTTCGCCGCCGGAAGAGTTAACCGTGTGCTCCTCCTCTCAGGATCACAGCCCACACCATGCAAAAACCCTAGAGGTGATC
ATTTACTGTTAAGGTTTTTTAAAAACAAAGTTGACTACTGTAGAATCCATGGCTACGATATTTTCTACGGAAACACGTTT
TTTCACCCTAAAATGCGTTCTTATTGGGCGAAAATACCGCTTGTTCGGGCCGCCATGCTGGCTCATCCTGAATCCGAGTG
GATTCTATGGGTTGACTCAGATGCAATCTTCACTGACATGGATTTCAAAATTCCATTACACAAATATAATGACTACAACT
TCATCGTCCACGGCTGGCCTGATTTGATTTTTAAGAAGAAAAGCTGGGTCGCTATAAATGCTGGGATTTTTCTTATTCGA
AACTGTCAATGGTCCATGGATTTCTTAGATGTTTGGGCTAATATGGGCCCGAAAAGCCCAGAATACAAGCAATGGGGCAA
AATCTTACGAACAACTTTCAAGGACAAAACGTTCCCGGAGTCCGACGACCAATCCGCACTGAGCTATTTAATACTGAAAG
GAGAACAAAAATGGCGGAGCAAAATTCACGCAATTACTGATTACTCTCTACACGGATACTGGCTAGGAATAGTAAACAGA
TTTGAAAACATAACAGCGAATTACATGAAGATAGAGAGAGATGTACCCAAGTTACGGAGGAGACACGCGGAGGCTGTGAG
CCACAGCTACGCGGCCGCGTGGGAGCCCTTGTTGGCGGAGGGCGCTGACGAAAAGGGCGGATGGAGGCGGCCGTTTATCA
CGCACTTCACGGGGTGTCAGCCATGTAGTGGGGACCACGCGACGGAGTATGTGGGTGATTCATGTTGGGTGGGAATGGAA
CGAGCGTTGAACTTTGCGGATAATCAGGTGCTACGTAACTTTGGGTTCATGCATGATGACATCAAAAGTAATTCCCCTGT
CTCTCCCTTAAATTTCGATTTTCCGGCTGAAGACAGTGAAGAATTCGTGTGA

Alignment

ORF - retro_slyc_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.94 %
• Parental protein coverage: 77.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVTLSIILALWSFISPKYPKFSTINLDFNLDQEGSTNFYDEPNLSYTIEKPIQNWDDKRRQWFNLHPSFK
          L..LS..L......SP.Y........D...D....T.FY..P.LSYTI.KPI.NWD.KR.QW..LHPSF.
Retrocopy LPNLSGLLYNQNISSPEYCPPGREAVDRSSDPPEKT-FYNDPELSYTIDKPIKNWDEKRVQWLQLHPSFA

Parental  LEGEKDRVLIVSGSQSTPCKNPIGDHLLLRFFKNKVDYSRIHGYDIFYNNVLLEPKMFFFWAKLPAIRAA
          ..G...RVL..SGSQ.TPCKNP.GDHLLLRFFKNKVDY.RIHGYDIFY.N....PKM...WAK.P..RAA
Retrocopy A-GRVNRVLLLSGSQPTPCKNPRGDHLLLRFFKNKVDYCRIHGYDIFYGNTFFHPKMRSYWAKIPLVRAA

Parental  MVAHPEAEWIWWVDSDAAFTDMDFKLPLEKYKNHNFVVYGWPKLIYEKKSWTGINAGVFLIRNCQWSMDL
          M.AHPE.EWI.WVDSDA.FTDMDFK.PL.KY...NF.V.GWP.LI..KKSW..INAG.FLIRNCQWSMD.
Retrocopy MLAHPESEWILWVDSDAIFTDMDFKIPLHKYNDYNFIVHGWPDLIFKKKSWVAINAGIFLIRNCQWSMDF

Parental  IEAWAKMGPQSPEYNRWGEILRTTFKDKNFPQSDDQSGLSYLLLKEKDKWGDKIYIESEYYFQGYWVDII
          ...WA.MGP.SPEY..WG.ILRTTFKDK.FP.SDDQS.LSYL.LK...KW..KI.....Y...GYW..I.
Retrocopy LDVWANMGPKSPEYKQWGKILRTTFKDKTFPESDDQSALSYLILKGEQKWRSKIHAITDYSLHGYWLGIV

Parental  DTLDNITNKYFEIEKKIPILRRRHAEKVV-SEIKVWEEYL
          ....NIT..Y..IE...P.LRRRHAE.V..S....WE..L
Retrocopy NRFENITANYMKIERDVPKLRRRHAEAVSHSYAAAWEPLL

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_42 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,