RetrogeneDB ID: retro_slyc_4

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 6:48340000..48342565(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc06g082560.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g115230.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_4
ATGATGAATAATCCTGAAAATTTTACTGACAAGACAAATGAGGCTGTTGGTGAGGCACATGAACTGGCTGTATCAGCAGG
GAATGCTCAGTTGACACCTCTGCATATTGCTTTGGTTTTATTATCTGATCACAGTGGTATTTTCTGGCAAGCAATCGTAA
ATGCTGCTGGCATAGAAGATACAGCTAATGGTGTTCAAAGGGTGTTTAATCAAGCTAAGAAGAAAATCCCTTCTCAGTTA
CCACCACCTGATCAAGTTCCACCAAGTACTTCACTTAATAAGGTGCTGCTACGAGCACAATCGTTGCAGAAGTCTCGTGG
TGATAGCCATTTGGCAGTTGATCTGTTGATTTTAGGCCTTCTGGAAGATTCACAAATTGTTCATCTTTTGAACGACTCTG
GTCTTAGTGCAGCAGGAGTGAAATCAGAAGTTGAGAAACTTAGAGGAAAAGATGGAAAGGATGTGGAAAGTGCGACCACA
TTCCAAGCTCTTAACACCTATGGTCGTGATCTCGTGGAACAAGCAGGAAAACTTGATCCTGTGATTGGTAGGGATGAAGA
AATTCGAAGAGTGATTCGGATTCTATCGAGGAGGACAAAGAACAATCCGGTGCTTATTGGTGAGCCTGGTGTTGGTAAAA
CAGCTGTAGTTGAAGGGCTAGCACAAAGGATTGTTCGAGGCGATGTTCCAAGTAATTTGGCTGATGTCAGGGTGATCGCA
TTGGATATGGGAGCACTCATTGCTGGAACAAAGTACAGAGGTGAATTTGAAGAGAGGTTGAAGGATGTTCTCAAGGAAGT
GGAAGATGCACAAGGGAAAGTAACTCTCTTCATTGATGAGATACACTTGGTTTTAGGTGCTGGTAGGATTGAAGGGTCAA
TGGATGCTGCTAATTTGTTCAAGCCAATGCTTGCTAGGGGCCAATTAAGGTGCATTGGTGCGACAACTATGGAAGAGTAT
AGCAAGTATGTGGAGAAGGATGCTGCATTTGAAAGGCGTTTCCAGCAGGTATATGTCGCTGAGCCTAGCATTCCCGATAC
TATAAGTATCCTTAGAGGGTTGAAGGAGAAGTATGAAGGCCATCATGGTGTCAAAATTCAGGATAGGGCTCTTGTTATTG
CAGCTCAGCTTTCATCTCGATACATTACAGGTCGACATTTGCCTGATAAGGCTATTGACTTAGTTGATGAGGCTAGTGCA
AATGTGAGGGTTCAGCTTGATAGTCAGCCAGAAGAAATAGATAATCTTGAAAGGAAGAGGATTCAGCTACAAGTTGAACA
CCATGCTCTTGAAAAGGAAAAAGATAAGGCTAGCAAAGCTCGACTTGTTGAAGTGAGGAAAGAGCTTGATGATTCGAGGG
ACAAACTCCAGCCTTTGATGATGAGGTATAACAAGGAGAAGGAACGGATTGATGAGCTTCGAAGGCTTAAGCAAAAGCGC
GATGCACTGACCTATGCTTTACAAGACGCTGAAAGGAGATATGATCTTGCCAGAGCAGCAGATCTTAGATATGGTGCCAT
CCAAGATGTGGAAGCTGCAATAGCCAATCTTGAGAGTAGCACAGATGAGAGTAGAATGTTAACAGAGACTGTTGGACCCG
ATCAGATTGCGGAAGTAGTTAGTCGCTGGACTGGAATTCCTGTCTCTAGGCTTGGGCAGAATGAGAAGGAGAAATTGATT
GGTCTTGCTGATAGATTGCACCAAAGAGTTGTGGGGCAAGATGAAGCTGTAAAAGCTGTTACTGAGGCTGTGTTGAGGTC
TAGAGCTGGATTAGGAAGGCCACAACAACCAACTGGTTCATTCCTTTTCTTGGGGCCAACTGGTGTTGGAAAGACAGAAC
TTGCTAAAGCTCTTGCTGAGCAGCTCTTTGATGATGACAAATTGATGGTCAGAATCGACATGTCCGAATACATGGAGCAA
CATTCTGTTGCCAGGTTGATTGGGGCTCCACCAGGTTATGTCGGACATGAGGAAGGAGGACAACTTACCAAAGCTGTAAG
GAGGCGACCTTACAGTGTTGTGCTTTTCGACGAAGTTGAAAAAGCTCATCCAACTGTGTTTAATGCCTTGCTTCAAGTGT
TGGATGATGGTAGATTAACTGATGGTCAAGGTCGTACTGTTGATTTCACCAACACTGTGATCATTATGACCTCAAATTTG
GGAGCGGAATATCTCTTGTCAGGTACCCGCGAAATGGTCATGCAGGATGTGAGGAAGCAATTTAAGCCTGAGTTACTGAA
CAGGCTCGATGAGGTTCTAGTGTTTGATCCTTTATCACACGATCAGTTGAGGCAAGTCTGCCGTCACCAACTGAAAGATG
TGGCAGGCCGTTTAGCTGAGAGGGGTATTGCATTGGGCGTTACTGAGGCCGCATTAGATGTCGTACTTGCACAAAGCTAT
GATCCGGTGTACGGTGCAAGGCCTATTAGGAGGTGGTTGGAGAAGAAAGTTGTAACGGAGTTATCAAAGATGCTTGTCAA
GGAGGAAATTAATGAGAATTCCACCGTGTACATAGATGCCAGACGTGGCGACAAAGATCTAACTTATAGGGTGCATGGAG
AATAA

Alignment

ORF - retro_slyc_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.42 %
• Parental protein coverage: 81.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPEKFTHKTNEAIAEAHELAVSAGHAQLTPLHMALALLSDHSGIFWQAIVNAAGSEETANGVERVFNQAK
          NPE.FT.KTNEA..EAHELAVSAG.AQLTPLH.AL.LLSDHSGIFWQAIVNAAG.E.TANGV.RVFNQAK
Retrocopy NPENFTDKTNEAVGEAHELAVSAGNAQLTPLHIALVLLSDHSGIFWQAIVNAAGIEDTANGVQRVFNQAK

Parental  KKIPSQSPAPDQVPASTSLIKVLRRAQSLQKSRGDSHLAVDLLILGLLEDSQIADLLKDSGLSAARVKSE
          KKIPSQ.P.PDQVP.STSL.KVL.RAQSLQKSRGDSHLAVDLLILGLLEDSQI..LL.DSGLSAA.VKSE
Retrocopy KKIPSQLPPPDQVPPSTSLNKVLLRAQSLQKSRGDSHLAVDLLILGLLEDSQIVHLLNDSGLSAAGVKSE

Parental  VEKLRGKDGKKVESATGDTTFQALKTYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG
          VEKLRGKDGK.VESA...TTFQAL.TYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG
Retrocopy VEKLRGKDGKDVESA---TTFQALNTYGRDLVEQAGKLDPVIGRDEEIRRVIRILSRRTKNNPVLIGEPG

Parental  VGKTAVVEGLAQRIVRGDVPSNLADVRLIALDMGALIAGAKYRGEFEERLKAVLKEVEDAEGKVILFIDE
          VGKTAVVEGLAQRIVRGDVPSNLADVR.IALDMGALIAG.KYRGEFEERLK.VLKEVEDA.GKV.LFIDE
Retrocopy VGKTAVVEGLAQRIVRGDVPSNLADVRVIALDMGALIAGTKYRGEFEERLKDVLKEVEDAQGKVTLFIDE

Parental  IHLVLGAGRTEGSMDAANLFKPMLARGQLRCIGATTLEEYRKYVEKDAAFERRFQQVYVAEPSVPDTISI
          IHLVLGAGR.EGSMDAANLFKPMLARGQLRCIGATT.EEY.KYVEKDAAFERRFQQVYVAEPS.PDTISI
Retrocopy IHLVLGAGRIEGSMDAANLFKPMLARGQLRCIGATTMEEYSKYVEKDAAFERRFQQVYVAEPSIPDTISI

Parental  LRGLKEKYEGHHGVKIQDRALVIAAQLSARYITGRHLPDKAIDLVDEACANVRVQLDSQPEEIDNLERKR
          LRGLKEKYEGHHGVKIQDRALVIAAQLS.RYITGRHLPDKAIDLVDEA.ANVRVQLDSQPEEIDNLERKR
Retrocopy LRGLKEKYEGHHGVKIQDRALVIAAQLSSRYITGRHLPDKAIDLVDEASANVRVQLDSQPEEIDNLERKR

Parental  IQLEVEHHALEKEKDKASKARLVEVRKELDDLRDKLQPLMMRYKKEKERVDELRRLKQKRDELTYALQEA
          IQL.VEHHALEKEKDKASKARLVEVRKELDD.RDKLQPLMMRY.KEKER.DELRRLKQKRD.LTYALQ.A
Retrocopy IQLQVEHHALEKEKDKASKARLVEVRKELDDSRDKLQPLMMRYNKEKERIDELRRLKQKRDALTYALQDA

Parental  ERRYDLARAADLRYGAIQEVESAIANLESSTDESTMLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI
          ERRYDLARAADLRYGAIQ.VE.AIANLESSTDES.MLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI
Retrocopy ERRYDLARAADLRYGAIQDVEAAIANLESSTDESRMLTETVGPDQIAEVVSRWTGIPVSRLGQNEKEKLI

Parental  GLADRLHLRVVGQDQAVKAVAEAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV
          GLADRLH.RVVGQD.AVKAV.EAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV
Retrocopy GLADRLHQRVVGQDEAVKAVTEAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDDKLMV

Parental  RIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLTEAVRRRPYSVVLFDEVEKAHPAVFNALLQVLDDGRLT
          RIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLT.AVRRRPYSVVLFDEVEKAHP.VFNALLQVLDDGRLT
Retrocopy RIDMSEYMEQHSVARLIGAPPGYVGHEEGGQLTKAVRRRPYSVVLFDEVEKAHPTVFNALLQVLDDGRLT

Parental  DGQGRTVDFTNTVIIMTSNLGAEYLLSGLSGKCTMEKAREMVMQEV
          DGQGRTVDFTNTVIIMTSNLGAEYLLSG......M...R.....E.
Retrocopy DGQGRTVDFTNTVIIMTSNLGAEYLLSG-TREMVMQDVRKQFKPEL

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_4 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc03g115230.2	1 retrocopy	retro_slyc_4 ,