RetrogeneDB ID: retro_slyc_27

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 4:59557850..59559350(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc04g072580.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc07g045160.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_27
ATGGGATCATTGGTTGATAGTTTTGCTTTGCATAATTTGAACAAGAAAATCGTGATGGGTGACAATGGTTATGTTTTTGA
AGACGTTCCTCATTTGTCTGATTACATTCCTAGTCTTCCTACGTATCCTAATCCATTGAAGAAAAATCCTTCCTATTCAG
TCGTCAATCAGTATTTTGTCGATGAAGATGATACAGTTGCTCAAAATATTGTTGTCCGCAAGAACAGTCCAAGAGGGATA
CATTTTCGTCGAGCTGGTCCTTCCCAAGACGTTTATTTTAAGGCGGATGATGTTAATGCATGTATTGTAACATGTGGAGG
TTTATGCCCTGGTCTCAATACAGTTATCAGGGAAATAGTATGTGGCTTGTACTCTATGTATGGTGTAGCAAGAGTCATGG
GGATAGATGGAGGATATCGAGGTTTCTATTCCAAAAACACGATTCCATTGACACCTAACGTTGTGAATGATATCCATAAA
CGTGGTGGAACGATTCTTGGGTCATCTCGAGGAGGTCATGTTACTAAGAAGATAGTAGATAGCATTCAGGATCGAGGAAT
TAATCAGGTTTATATAATTGGAGGAGATGGAACGCTTAAAGGAGCATCGTTGATATTTGAGGAAATTACGAGGCGTGGTC
TAAATGTTGTAGTTGTTGGAATCCCCAAGACAATAGATAACGATATACCAGTTATTGACAAGTCTTTTGGTTTTGATTCT
GCGGTTGAGGAAGCTCAACGTGCTATTAGTGCTGCTCATGTTGAAGCTACGAGTTTTGAGAATGGAATTGGGGTTGTGAA
GTTAATGGGACGGGATAGTGGGTTTATAGCAATGTATGCTAGTCTTGCTAGTCGAGATGTTGATTGTTGTTTGATTCCAG
AATCCTGTTTCTATCTTGAAGGACGCGGTGGACTGTTTGAGTATATCGAACAAAGGCTGAAAGAGAATGGACACATGGTT
ATCGTTGTAGCTGAAGGTGTTGGACAAGATGATGAGCAAGTTGATGTTGGTTTATGGATATCGACAAGGATAAAGGAGCA
TTTTTCGAAAGAAAAGAAGATGATGATCAATCTGAAGTATATAGATCCAACATACATGATTCGGGCTATTGCAAGTAATG
CATCTGATAATATGTATTGCACTCATCTTGCTCAAAGCGCGGTACATGGAGCAATGGCTGGGTACACAGGCTTTACGGTT
GGTCCTGTCAACAACACACATGCTTACATACCCTTTGATAGAATCACTGAGAAACAAAACAAGGTTGACATTACAGACAT
GATGTGGGCACAACTTCTATCTTCAACTAATCAACCTAGCTTCTTGTCAACAGCGAGATCAGCTGATAATATTGAAGCAA
ACAAGGACGAAGAACCACCTATTCAATTATCAGATGAAGAAACAAATCAACTTAGCTTCTTGACAACCAGAGTCGATATA
AATGAAGCAAACAAGAACAAAGAACCACCTACTGAATTATCAGATGGAGAAACAAATTAA

Alignment

ORF - retro_slyc_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.34 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKIVIGDDGYVLEDVPHLSDYIPNLPTYTNPLQHNPSYSVVKQYFVNEDDTVAEKVVVHKNSPRGIHFRR
          KKIV.GD.GYV.EDVPHLSDYIP.LPTY.NPL..NPSYSVV.QYFV.EDDTVA...VV.KNSPRGIHFRR
Retrocopy KKIVMGDNGYVFEDVPHLSDYIPSLPTYPNPLKKNPSYSVVNQYFVDEDDTVAQNIVVRKNSPRGIHFRR

Parental  AGPCQKVYFEPDDVYACIVTCGGLCPGLNTVIREIVCGLHYMYGVSRVMGIDGGYRGFYSKNTIPLTPKV
          AGP.Q.VYF..DDV.ACIVTCGGLCPGLNTVIREIVCGL..MYGV.RVMGIDGGYRGFYSKNTIPLTP.V
Retrocopy AGPSQDVYFKADDVNACIVTCGGLCPGLNTVIREIVCGLYSMYGVARVMGIDGGYRGFYSKNTIPLTPNV

Parental  VNNIHKRGGTILGTSRGGHVTKKIVDSIQDRGINQVYIIGGDGTQRGAAVIFEEIRRRGLNVAVAGIPKT
          VN.IHKRGGTILG.SRGGHVTKKIVDSIQDRGINQVYIIGGDGT..GA..IFEEI.RRGLNV.V.GIPKT
Retrocopy VNDIHKRGGTILGSSRGGHVTKKIVDSIQDRGINQVYIIGGDGTLKGASLIFEEITRRGLNVVVVGIPKT

Parental  IDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIGLVKLMGRDSGFIAMYATLASRDVDCCLIPE
          IDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIG.VKLMGRDSGFIAMYA.LASRDVDCCLIPE
Retrocopy IDNDIPVIDKSFGFDSAVEEAQRAISAAHVEATSFENGIGVVKLMGRDSGFIAMYASLASRDVDCCLIPE

Parental  SPFYLEGSGGLFEYIEHRLKDNGHMVIVIAEGAGQE
          S.FYLEG.GGLFEYIE.RLK.NGHMVIV.AEG.GQ.
Retrocopy SCFYLEGRGGLFEYIEQRLKENGHMVIVVAEGVGQD

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_27 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
Oryza longistaminata	KN540365.1_FG001	1 retrocopy	retro_olon_23,
Solanum tuberosum	PGSC0003DMG400017413	1 retrocopy	retro_stub_48,
Solanum lycopersicum	Solyc07g045160.2	1 retrocopy	retro_slyc_27 ,