RetrogeneDB ID: retro_slyc_6

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 2:54781158..54782148(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc02g094160.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc01g080210.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_6
ATGCCTCTTATCCCAGAAGAGCCTTTGCTCGCCTCTAACCCAGATCGATTCTGTATGTTCCCAATTCAGTATCCACAGAT
TTGGGAAATGTACAAGAAAGCCATGGCATCTTTCTGGACGGCAGAAGAAGTCGATCTCTCCACCGATACTCGTCACTGGG
AAAACCTAACATCCGGTGAAAGGCATTTCATCACTCATGTTCTTGCCTTTTTTGCCGCCTCAGACGGCATCGTTTTAGAG
AACCTCGCTGGAAGGTTCATGAAAGATGTCCAGGTTGCCGAGGCTCGTGCTTTCTATGGGTTCCAAATCGCCATTGAGAA
TATCCATTCCGAGATGTACAGTTTGCTGTTGGAGTCGTACATCAAGGATTCTGACGAAAAGAGCAAATTGTTCCGTGCAA
TTGAGACAATCCCTTGTGTTGAAAAGAAGGCGAAATGGGCCCTTCGTTGGATCGATGGGTCCGAAACTTTCGCGGAGCGT
TTGGTGGCTTTTGCTTGTGTTGAAGGGATTTTCTTCAGCGGAAGCTTCTGTTCGATATTTTGGTTGAAAAAACGGGGGTT
AATGCCTGGATTAACCTTCTCAAATGAGTTAATTTCAAGAGACGAAGGTTTGCACTGTGATTTTGCGTGTTTGCTTTACA
GTTTGCTAAGGACGAAGCTAACTGAGGAGCGAGTCAGGGGAATTGTTGCAGATGCTGTGGAGATAGAAAGGGAGTTCGTG
TGTGATGCTCTTCCTTGTGCTCTGGTGGGAATGAATGGAGATTTGATGAGTAAATACATAGAGTTTGTAGCTGACAGATT
GTTGGATGCTTTGGGTTATGACAAGATGTACAATGCTCAGAATCCATTCGATTGGATGGAGCTGATTAGTTTACAAGGGA
AGACTAATTTCTTTGAGAAGAGAGTTGGGGAGTATCAGAAAGCCTCAGTTATGTCCAGTTTGAATGGTAATGGTGATACC
CATGAATTCAAGCTGGATGAGGACTTTTAA

Alignment

ORF - retro_slyc_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 95.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEPILKEQSQKYCTFPIRYPQLWEMYKKAVASFWSVEEVDLSEDIQHWEALSESEKHFISHVLAFFAASD
          EEP.L.......C.FPI.YPQ.WEMYKKA.ASFW..EEVDLS.D..HWE.L...E.HFI.HVLAFFAASD
Retrocopy EEPLLASNPDRFCMFPIQYPQIWEMYKKAMASFWTAEEVDLSTDTRHWENLTSGERHFITHVLAFFAASD

Parental  GIVLENLAARFLNDVQIQEARAFYGFQIAMENIHSEMYSLLLDAFIKDPRQKNKLFNAIDSIPCVSQKAK
          GIVLENLA.RF..DVQ..EARAFYGFQIA.ENIHSEMYSLLL...IKD...K.KLF.AI..IPCV..KAK
Retrocopy GIVLENLAGRFMKDVQVAEARAFYGFQIAIENIHSEMYSLLLESYIKDSDEKSKLFRAIETIPCVEKKAK

Parental  WALNWIQSSSSFAERLVAFACVEGIFFSGSFCAIFWLKKRGLMPGLAYSNVLISKDEGLHRDFACLLYSI
          WAL.WI..S..FAERLVAFACVEGIFFSGSFC.IFWLKKRGLMPGL..SN.LIS.DEGLH.DFACLLYS.
Retrocopy WALRWIDGSETFAERLVAFACVEGIFFSGSFCSIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSL

Parental  MRNQLTRQKVHQIVHEAVEIETEFVCDALPCALIGMNAELMSQYIKFVADHLLVALGYDKKYNVGNPFDW
          .R..LT...V..IV..AVEIE.EFVCDALPCAL.GMN..LMS.YI.FVAD.LL.ALGYDK.YN..NPFDW
Retrocopy LRTKLTEERVRGIVADAVEIEREFVCDALPCALVGMNGDLMSKYIEFVADRLLDALGYDKMYNAQNPFDW

Parental  MEFISLQGKSNFFERRVADYQKASVMSSLQDNGKNFEFKLDEDF
          ME.ISLQGK.NFFE.RV..YQKASVMSSL..NG...EFKLDEDF
Retrocopy MELISLQGKTNFFEKRVGEYQKASVMSSLNGNGDTHEFKLDEDF

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_6 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00025p00110680	1 retrocopy	retro_atri_2,
Brassica rapa	Bra014962	1 retrocopy	retro_brap_7,
Prunus persica	PRUPE_ppa008063mg	1 retrocopy	retro_pper_7,
Solanum lycopersicum	Solyc01g080210.2	1 retrocopy	retro_slyc_6 ,
Theobroma cacao	TCM_020494	1 retrocopy	retro_tcac_4,
Vitis vinifera	VIT_05s0020g02560	1 retrocopy	retro_vvin_20,