RetrogeneDB ID: retro_slyc_25

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:5548701..5550171(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc01g010530.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc03g005140.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_25
ATGTCAAATAACTTTGAGATGAATAACTCTAAGATGACGTTATACGTGGTGTCTTGTTGGATTTTTGCTGCTTTTGGTGG
ATTGATGTTTGGTTACGATATTGGTATTTCTGGCGGAGTTTCTGGTATGGATGATTTCTTGATTAAATTTTTCCCACATA
TTTATGAAACAAAGTTACATGCTATAGAAAATAACTATTGCAAATATGATAGTATGCTTCTCCAACTCTTCACTTCATCC
TTATACATATCCGCTCTTTTCGCGAGTTTTTTTGCTTCAAAAGCGGCTACTAAATTAGGAAGAAGGCTTACCATTTCAAT
GGCGTCAATCTTTTTCATTGTTGGAGCTGTATTGAGTGCAGCCGCGGAGAACAAATCGATGCTTATTTTTGGTAGAATTT
TGTTTGGTATTGGTGTTGGATTTGGAAACGAGACTGTTCCTCTGTTTTTAACTGAAGTTGCACCAATCCAACACAGAGGA
GCTGTGAATATTATGTTTCAATTGTTTGTAACTATAGGTATATTCATTGCAAATCTTGTCAACTATGGAACTTCAACGGT
ACATCCATATGGTTGGAGAATGTCACTTGGACTCGCAGCTATTCCCGCGGTGATTCTGTTTATTGGTACTTTTGTTATCA
CTGACACCCCTACGAGTCTAATTGAGCGTGGTAATGAGGAACAGGGGAAGTCCACGCTCATGAAGATTAGGGGTGTCAAT
GACGTTGAGGATGAGTATAAAGAAATCGTGATAGCGTGTCAACAAGCCAAGCAAGTTAAGCAGCATTCGTTAAAGAAGTT
GTTAAAGCCTGCTAGCATTCCACCACTTGTGATTGGTGTGTTGTTGCAAGTCTTTCAGCAATTTACTGGAATCAACGCTA
TTATGTTTTACGCGCCTGTTCTGTTTCAGACTATGGGATTCAAGGCTAATGCCTCGCTTCTATCCTCTGTCATTACTGGA
ATTGTTAATGTTGGAAGCACATTCGTTTCAATTTACCTTGTTGACAAGGTTGGAAGGAGGAAATTGCTTCTTCAAGCTTG
TTGTCAGATGTTAATTTCTCAGTTAGCAATCGGGGCAATTTTGTTAACAAGTTTATCCGATACAGGAACGTTGAACAAAA
CACTAGCATTGATAGTGGTGGTGTTGGTGTGTACGTATGTAATGTCGTTTGCGTGGTCATGGGGACCCCTTGGTTGGTTA
ATTCCTAGTGAGACATTCCCATTGGAAACAAGGACAACTGGTTTTGCATTCGCGGTTAGCACAAACATGCTCTTCACATC
TATCATTGCACAACTTTTCTTGACTATGCTTTGCACTATGAAAGCCTATATTTTCTTCTTTTTCTCCGGATGGATTGTTG
TCATGGGATTAGTCGTTTACTTCTTCTTGCCTGAAACAAAGGGAGTTCCGATTGATTCCATGGTCGAAAGAGTGTGGATG
CAACACCCTATTTGGAAGAAACTATTCTAA

Alignment

ORF - retro_slyc_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.92 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERNNSKITIYVLSCWIFAAFGGLMFGYDIGISGGVSGMDDFLKKFFPKVYERKSHAKENNYCKYDDQLLQ
          E.NNSK.T.YV.SCWIFAAFGGLMFGYDIGISGGVSGMDDFL.KFFP..YE.K.HA.ENNYCKYD..LLQ
Retrocopy EMNNSKMTLYVVSCWIFAAFGGLMFGYDIGISGGVSGMDDFLIKFFPHIYETKLHAIENNYCKYDSMLLQ

Parental  LFTSSLYLSALVASFFASKSATKFGRRLTICMASIFFLAGAVLSAAAKNKLMLIFGRILFGVGVGFGNET
          LFTSSLY.SAL.ASFFASK.ATK.GRRLTI.MASIFF..GAVLSAAA.NK.MLIFGRILFG.GVGFGNET
Retrocopy LFTSSLYISALFASFFASKAATKLGRRLTISMASIFFIVGAVLSAAAENKSMLIFGRILFGIGVGFGNET

Parental  VPLFLTEVAPIQHRGAVNILFQLFVTIGIFIANLVNYGTSMIHPHGWRLSLGLAAVPAIVLFVGSFVITD
          VPLFLTEVAPIQHRGAVNI.FQLFVTIGIFIANLVNYGTS..HP.GWR.SLGLAA.PA..LF.G.FVITD
Retrocopy VPLFLTEVAPIQHRGAVNIMFQLFVTIGIFIANLVNYGTSTVHPYGWRMSLGLAAIPAVILFIGTFVITD

Parental  TPSSLIERGKDEQGKTVLKKIRGVNDVEVEYQEIVAACEQAKLVK-YPFRNLAKAASIPPLVIAILLQIF
          TP.SLIERG..EQGK..L.KIRGVNDVE.EY.EIV.AC.QAK.VK......L.K.ASIPPLVI..LLQ.F
Retrocopy TPTSLIERGNEEQGKSTLMKIRGVNDVEDEYKEIVIACQQAKQVKQHSLKKLLKPASIPPLVIGVLLQVF

Parental  QQFTGINAIMFYAPVLFQTMGFKSEGSLLSSVITGLVNVGSTFVSIYLVDKVGRRKLLLQACCQMLISQL
          QQFTGINAIMFYAPVLFQTMGFK...SLLSSVITG.VNVGSTFVSIYLVDKVGRRKLLLQACCQMLISQL
Retrocopy QQFTGINAIMFYAPVLFQTMGFKANASLLSSVITGIVNVGSTFVSIYLVDKVGRRKLLLQACCQMLISQL

Parental  AIGAILVTNLEETGTLNKKLAAIVVLLVCTYVMSFAWSWGPLGWLIPSETFPLETRTAGFAFAVSTNMLF
          AIGAIL.T.L..TGTLNK.LA.IVV.LVCTYVMSFAWSWGPLGWLIPSETFPLETRT.GFAFAVSTNMLF
Retrocopy AIGAILLTSLSDTGTLNKTLALIVVVLVCTYVMSFAWSWGPLGWLIPSETFPLETRTTGFAFAVSTNMLF

Parental  TSLIAQAFLTMLCTMQAYIFFFFSAWIVVMGLFVIFFLPETKGVPIDSMVERVWMQHPVWKKLF
          TS.IAQ.FLTMLCTM.AYIFFFFS.WIVVMGL.V.FFLPETKGVPIDSMVERVWMQHP.WKKLF
Retrocopy TSIIAQLFLTMLCTMKAYIFFFFSGWIVVMGLVVYFFLPETKGVPIDSMVERVWMQHPIWKKLF

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_25 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400013384	1 retrocopy	retro_stub_81,
Solanum lycopersicum	Solyc03g005140.1	1 retrocopy	retro_slyc_25 ,