RetrogeneDB ID: retro_slyc_24

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 8:56488963..56489905(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc08g067450.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc08g005470.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_24
ATGGAAAGGTACTTGATAGTTAAGGAAGTTGGTAATGGTTCATTTGGGAATGTATGGAGAGCTTTGAATAAACAGAGTGG
TGAAGTGGTTGCGATTAAGAAAATGAAGAAGAAGTATTATTCATGGAAAGAATGCATCAACTTGAGAGAAGTCAAGTCAT
TGAGGAGAATGAACCATCCAAATGTAGTTAAGCTCAAGGAAGTGATTAACGAGAATGACATATTATACTTTGTGTTTGAA
TACATGGAGTGCAACTTATATAATCTTATGGAGAATCGGCCTCATTTTTTCGTAGAGTCACAAGTGAGAATTTGGTGCTT
CCAAATATTTCAAGGTCTTGCATCCATCCATCAACAAGGATACTTTCATCGCGATCTTAAGCCAGAGAACTTGTTGGTTT
CAAAAGATTATATGATAAAAATTGCTGATTTTGGTTCTGCTAGGGAGATCAATTCTCAGCCTCCATATACTGAATATGTC
TCAACACGCTGGTATCGTGCCCCTGAAGTTCTTTTAGGATCACCAATATATGGTCCTGCTGTTGATATGTGGGCAATGGG
TGCAATAATGGCGGAGTTATTAACTCTTCGTCCTCTATTCCCTGGTTTGGGTGAAGCAGATGAGATTTACAGAATATGCA
GTGTTATAGGTACTCCATCAAAGAGTGAATGGGCTCATGGACATGAACTTGCTGCTGCTATCAACTACCAGTTTCCACAG
ATACGTGGTGTAACTCTGTCTAACGTACTCCCATATGTTAGCGAGGATGCAATTAATCTAATAACTTGGCTTTGTTCGTG
GGATCCTTGCAAGAGGCCAACAGCGGTGGAGGTTCTTCAGCACAATTTCTTCCAGAGTTGCTTTTATGTACCTCCATCAT
TATGCTCTAACACTGCTGCTGCTCCTCCATCTGTTGGAATTACGGCAAATCCCTTAGTATAA

Alignment

ORF - retro_slyc_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.79 %
• Parental protein coverage: 68.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERYKVIKEVGNGTFGSVWRALNKQSGEVVAIKKMKKKYYSWEECINLREVKSLRKMSHPNIVKLKEVIR
          MERY...KEVGNG.FG.VWRALNKQSGEVVAIKKMKKKYYSW.ECINLREVKSLR.M.HPN.VKLKEVI.
Retrocopy MERYLIVKEVGNGSFGNVWRALNKQSGEVVAIKKMKKKYYSWKECINLREVKSLRRMNHPNVVKLKEVIN

Parental  ENDILYFVFEYMECNLYHLMKDRPKLFLESEVRNWCFQIFQGLANMHQRGYFHRDLKPENLLVSKD-TIK
          ENDILYFVFEYMECNLY.LM..RP..F.ES.VR.WCFQIFQGLA..HQ.GYFHRDLKPENLLVSKD..IK
Retrocopy ENDILYFVFEYMECNLYNLMENRPHFFVESQVRIWCFQIFQGLASIHQQGYFHRDLKPENLLVSKDYMIK

Parental  IADFGLAREINSKPPYTEYVSTRWYRAPEVLLQSPIYGPAVDMWAMGAIMAELLTLRPLFPGSSEADEIY
          IADFG.AREINS.PPYTEYVSTRWYRAPEVLL.SPIYGPAVDMWAMGAIMAELLTLRPLFPG..EADEIY
Retrocopy IADFGSAREINSQPPYTEYVSTRWYRAPEVLLGSPIYGPAVDMWAMGAIMAELLTLRPLFPGLGEADEIY

Parental  KICSVIGTPSKSEWAHGHELAGAINYQFPQMPGVNLSVLLPSASEDAINLITSLCSWDPCKRPTAVEVLQ
          .ICSVIGTPSKSEWAHGHELA.AINYQFPQ..GV.LS..LP..SEDAINLIT.LCSWDPCKRPTAVEVLQ
Retrocopy RICSVIGTPSKSEWAHGHELAAAINYQFPQIRGVTLSNVLPYVSEDAINLITWLCSWDPCKRPTAVEVLQ

Parental  HRFFQSCFYVPPSLRSKTAVSKTPPSAGM
          H.FFQSCFYVPPSL.S.TA....PPS.G.
Retrocopy HNFFQSCFYVPPSLCSNTAAA--PPSVGI

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_24 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400018466	1 retrocopy	retro_stub_34,
Solanum lycopersicum	Solyc08g005470.2	1 retrocopy	retro_slyc_24 ,
Vitis vinifera	VIT_02s0033g01110	1 retrocopy	retro_vvin_73,