RetrogeneDB ID: retro_slyc_3

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:50066877..50067924(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc04g051200.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g089170.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_3
ATGTTTCAAGTTAGCGTCAGAGATGATGAGGTAGATATTGTGATAGCTGCAATTGAACCAGATCTTACTTCATTTCTGGA
AGAATGGAGAGCAGTATTCTCCCGATTTCACCTGATAATTATCAAAGATCCTGACATCAAAGGAGAACTTAAAATTCCAG
GTGGATTTAATTATGATACCTATACAAAAGCTGATATTCAACAAATTATTGGACCTTCAAATGCTGCAACTTTTTCTGGT
TATTCGTGCCGATATTTTGGCTATCTCTTGTCAAAGAAGAAATATATCATCTCAATTGATGATGACTGCATTCCAGCTAA
GGATACTAAGGGTATCCAAGTCGATGCCATAGCACAACATATCAATAACCTCTCGACTCCTGCCACCCCATTTTTCTTTA
ATACCCTCTATGATCCTTTCTGTAAAGGAGCTGATTTTGTTCGTGGCTACCCATTTAGCCTGCGAAATGGTGTCTCGTGT
GCTCTATCATGTGGACTGTGGCTTAATTTAGCAGATCTTGATGCACCTACACAAGCCCTCAAGCCGGAGCTGAGAAACAC
TCGATATGTTGACGCTGTCCTCACTGTACCAGCTAGGGCCATGATGCCTATGAGCGGAATCAATATAGCGTTTGATCGTG
AATTGGTGGGACCTGCTTTGCTGCCATCTTTCAAGTTGGCAAAGGAAGGAAAGTTCAGGTGGGAAACTGTGGAGGATGTA
TGGACTGGAATGTGTGTTAAGGTAGTATGTGATCACTTAGGATATGGTGTGAAAACTGGGCTTCCATATGTGTGGAGGAA
AGAAAGAGGTAATGCCATAGGGAGTTTGAAGAAAGAGTGGGAGGGGGTGAAGCTGATGGAAGAAGTTGTTCCATTCTTCC
AATCAATGAAATTGACTCCGGCAGCAAAAACAGCAGAAGATTGTGTGATTGAGATTGCAGCAGCCGTGAAGGAGCAACTG
GGACGAATAGATCCTGTGTTCACCCGTGCAGCTGATTCCATGGTGGAGTGGGTGCAGCTGTGGAAGGCTGTGAAAACCCG
AACATAG

Alignment

ORF - retro_slyc_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.75 %
• Parental protein coverage: 59.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELDIVIPTIRN--LDFLEMWRPFFEQYHLIIVQDGDPSKTIKVPDGFDYELYNRNDINKILGPRASCIS
          DE.DIVI..I......FLE.WR..F...HLII..D.D.....K.P.GF.Y..Y...DI..I.GP......
Retrocopy DEVDIVIAAIEPDLTSFLEEWRAVFSRFHLIIIKDPDIKGELKIPGGFNYDTYTKADIQQIIGP-SNAAT

Parental  FKDSACRCFGYMVSKKKYIYTIDDDCFVAKDPSGKDINALEQHIKNLLCPSTPYFFNTLYDPFRDGADFV
          F....CR.FGY..SKKKYI..IDDDC..AKD..G....A..QHI.NL..P.TP.FFNTLYDPF..GADFV
Retrocopy FSGYSCRYFGYLLSKKKYIISIDDDCIPAKDTKGIQVDAIAQHINNLSTPATPFFFNTLYDPFCKGADFV

Parental  RGYPFSLREGVSTAVSHGLWLNIPDYDAPTQLVKPLERNTRYVDTVLTIPKGTLFPMCGMNLAFDRDLIG
          RGYPFSLR.GVS.A.S.GLWLN..D.DAPTQ..KP..RNTRYVD.VLT.P.....PM.G.N.AFDR.L.G
Retrocopy RGYPFSLRNGVSCALSCGLWLNLADLDAPTQALKPELRNTRYVDAVLTVPARAMMPMSGINIAFDRELVG

Parental  PAM
          PA.
Retrocopy PAL

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_3 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	PGSC0003DMG400001375	1 retrocopy	retro_stub_4,
Solanum lycopersicum	Solyc02g089170.2	1 retrocopy	retro_slyc_3 ,
Vitis vinifera	VIT_14s0083g01100	1 retrocopy	retro_vvin_27,