RetrogeneDB ID: retro_slyc_47

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 3:70067763..70069326(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc03g122110.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g079920.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_47
ATGGAAGAAAGCCTAGAGTACCAAAAGAAGAGTTGGATTGCTTTAAAAAAGAGCATAAATGGGCTGCTCAATAAAATCAA
TAAAGCGAACATAAAACACATCATTCCTGAATTGTTTGAAGAAAATTTGATTCGTGGTAGGGGCTTGTTTTGCAGATCAA
TTATGAAATCACAATTGAATTCTGTTATTTTCACAGATGTTTTTGCAGCATTGATAGCCGTTGTTAACACAAAATTCCCA
CAAATTGGTGAACTTTTGTGTAAGAGGATCATTCTGCAATTGCGGAGAGCTTATAACAATAATAATAAACCTCAGATGTT
AGCATCGGTTAAATTTATTGGTCATCTTGTCAATCAGCAAGTTGTTCATGAACTTGTAGCTTTGGAATTAGTTACTCTTT
TACTTGAGAAACCTACTGATGATAGTGTTGATGTTGCTGTTGGTTTCGTTAAGGAATGTGGTTCGATGCTTCAGGATCTG
TGTCCCTTAGGGTTGCACGCTATTTTTGAGAGATTCAGAGGAATACTTCATGAAGGAGAAATAGATAAAAGGGTTCAGTT
CTTAATTGAAGAACTTTTTGCATTGCGGAAACAGAAGTTTCAGCCAGCTGTTCCTCCAGAACTTGACCTTGTTGAGGAGG
AAGATCGATTAACACATGAAATCTCTCTCGGAGACATGGTGGACGAGCAAATTGAATTGGATGTTTTCAAGCCCGATCCT
AATTTTGTTGAAAATGAAAATAAGTATGAACAACTACAGAATAGGATTCTAGGTGGGAGTGATGAGGACGAAGAATCTGA
TCTTCTAGTTGGTGGTGATCAGGACGAGGATGAATCTGAGGACGAGGACGAGCACGAAATGAAAATTGAAGATGAGACAG
AGACAAACTTGATCAATCTTCGGAGGACGATTTACTTAACGATTATGTCAAGTGGTGGGTTTGAAGGAGCAGGGCATAAG
CTGTTGAAAATCAGACTAGAGCCTGGTCAGGAGATGGAACTATGCATAATGTTATTGGAGTGCTGCAGTCAGGAGAAGAC
TTTTCTCCATTACTATGCACTTTTGGCGCAGCGGTTATGCATGATCAACAAAGTTCACCAGAAGAATTTTGAGAAATTAT
TCATGCAACAATACTCGATGATCCACCAACTTGAAACTAATAAACTGCGTAATGTGGCAAAGTTTTTTGCTCAATTACTA
GGCACTGATGCACTGCCTTGGCATGTTTTGGCTTATTTAAGATTGACAGAAGAGGATACTACATCTTCTTCTCGTATATT
CATCAAAATTTTATTCCAGGAGTTGTCAGGGCACCTTGGCATCCATAAGCTGAATGAGCGTCTTAGTGACCCCTCTATGC
AAGAGTCGTTTGAGTCGATATTTCCAAAGGATAATCCTAAAAATGTGAGGTTTGCTATCAACTTTTTCACATCCATTGGT
CTAGGTGGGATAACTGAAAATCTGCGAGACTATCTGAAGAACATGCCAAGGCTCATCTTGCAGCAAGAGAAACGTGTTTC
CAGAGATGATGATCGTCCAAGGAAGAGGAGGAGGAGAAGTTAG

Alignment

ORF - retro_slyc_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.43 %
• Parental protein coverage: 86.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSSVEYQRMTWDALRKSINGLVNKVNAANLKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAAL
          ..S.EYQ...W.AL.KSINGL.NK.N.AN.K.IIPELF.ENLIRGRGLFCRS.MKSQ..S..FTDVFAAL
Retrocopy EESLEYQKKSWIALKKSINGLLNKINKANIKHIIPELFEENLIRGRGLFCRSIMKSQLNSVIFTDVFAAL

Parental  VAVVNTKFPEVGDLLLRRIILQLQRAYKRNDKPQLLAAVKFIAHLVNQQIVHELIALELLTVLLEKPTDD
          .AVVNTKFP..G.LL..RIILQL.RAY..N.KPQ.LA.VKFI.HLVNQQ.VHEL.ALEL.T.LLEKPTDD
Retrocopy IAVVNTKFPQIGELLCKRIILQLRRAYNNNNKPQMLASVKFIGHLVNQQVVHELVALELVTLLLEKPTDD

Parental  SVEVAVGFVTECGSMLQDLCPRGLHGIFERFRGILHEGEIDKRVQFLIESLFALRKAKFQGYQAVRPELD
          SV.VAVGFV.ECGSMLQDLCP.GLH.IFERFRGILHEGEIDKRVQFLIE.LFALRK.KFQ...AV.PELD
Retrocopy SVDVAVGFVKECGSMLQDLCPLGLHAIFERFRGILHEGEIDKRVQFLIEELFALRKQKFQ--PAVPPELD

Parental  LVEQEDQLTHEVSLSDTIDPEIALDIFKPDPNFLENERKYEELKKAILGEESEEEGDSDAESEDEDEDEE
          LVE.ED.LTHE.SL.D..D..I.LD.FKPDPNF.ENE.KYE.L...ILG...E.E........D.DEDE.
Retrocopy LVEEEDRLTHEISLGDMVDEQIELDVFKPDPNFVENENKYEQLQNRILGGSDEDEESDLLVGGDQDEDES

Parental  SDEEEDEEQMKIKDETETNLINLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERT
          ..E.EDE..MKI.DETETNLINLRRTIYLTIMSS..FE.AGHKLLKI.LEPGQEMELCIMLLECCSQE.T
Retrocopy --EDEDEHEMKIEDETETNLINLRRTIYLTIMSSGGFEGAGHKLLKIRLEPGQEMELCIMLLECCSQEKT

Parental  YLRYYGLLGQRFCMINKIHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTDALPWHCLAYIRLTE
          .L.YY.LL.QR.CMINK.HQ.NFEK.F.QQYSMIH.LETNKLRNVAKFFA.LLGTDALPWH.LAY.RLTE
Retrocopy FLHYYALLAQRLCMINKVHQKNFEKLFMQQYSMIHQLETNKLRNVAKFFAQLLGTDALPWHVLAYLRLTE

Parental  EDTTSSSRIFIKILFQEMSEHLGIRLLNERLNDPTMQESLESIFPKDNPKNTRFAINFFTSIGLGGITES
          EDTTSSSRIFIKILFQE.S.HLGI..LNERL.DP.MQES.ESIFPKDNPKN.RFAINFFTSIGLGGITE.
Retrocopy EDTTSSSRIFIKILFQELSGHLGIHKLNERLSDPSMQESFESIFPKDNPKNVRFAINFFTSIGLGGITEN

Parental  LREYLKNMPRLIMQQQKPVSDSDE
          LR.YLKNMPRLI.QQ.K.VS..D.
Retrocopy LRDYLKNMPRLILQQEKRVSRDDD

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_47 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G39400	1 retrocopy	retro_bdis_57,
Medicago truncatula	MTR_3g434840	1 retrocopy	retro_mtru_18,
Sorghum bicolor	Sb03g029810	1 retrocopy	retro_sbic_32,
Arabidopsis lyrata	scaffold_202963.1	1 retrocopy	retro_alyr_10,
Solanum lycopersicum	Solyc04g079920.2	1 retrocopy	retro_slyc_47 ,