RetrogeneDB ID: retro_slyc_49

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 1:3717262..3718214(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc02g064540.1
• Aliases: None
• Description: None

Sequence

>retro_slyc_49
ATCGTCAGCTTCCTTCTTCATTAGTAGCACATAATCCTTGGAAGAACGGTTGATGTTAAATTGGTGATACCTAAAGGTGC
AATTAGTCAATGCCAACCTTATTTAGAATGCCCACATTTTCAAAGACAAAATAGCGAAACTAGCAATAACAACAGAAGAA
AGATTTTTGTTGGTAGATTGCCTCTTAATTTATCGGAAGAAGAATTTAAAACATATTTTAAAAAATTTGAAATAATTTCA
CAAGTGAACCTCATCTTCAATAAAGAAATCAAAATAACCCCGAGGATTTGAGTTTGTCACTTATGATTCAAAAGAATTTG
TAACACATGTATTGTAAGAGAAATTCACTAGTTGAATAATAAATATGTTGAGGTTAAAAAAGTAGAGCCAAGGGAACGAA
GAGTTATGAATATTATTATCATAATTTTTACCCTTCGAATTCCGGCTATGGAATGTGGAAAATTTATAATTGTTATAATG
GGATTATCGCCCCTCATTATTGTCACAATCATACTATGCGACCTACTAATTGAACTAGTTTGTTTAATCATTTGGGTACA
AATCTATTTATTTCCCCACAACTTCTGGTACTATATTTGACCCCTACATATCCAATCAACTGCTACGGTTCAACTCGTAG
ATATTCAGTCAAGTGTTACAGTTCAACGCATAATCAAGTGAATGATAACAAGTGCTCTTACTGGGTTTTATCAACTTTTG
CCCAGAATAATGTGATAAATGAAGGAAATGACCAAAAATGCAATGATACTGAGGTTCAATATGTTGGAAATGGTTCATAT
CTAGCTAATGAGAGTACAAAATCACCAGAGAAAGAAATAAACAATGGTGAAACGACGACTTGGAGAAAATTCCCCAAGAC
AATACAAAAGAAAACAATGGTGAAAAAGATCACTTGGTGAAAATTTTCCAGGTTAATACTAAAGATGACACC

Alignment

ORF - retro_slyc_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.35 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LIEQLIHQQHIILGRTVDVKLAIPKGASGQCQLGSECPNFQRQD---SNNNRRKIFVGGLPLNLSEEEFK
          ....L.H..HIILGRTVDVKL.IPKGA..QCQ...ECP.FQRQ....SNNNRRKIFVG.LPLNLSEEEFK
Retrocopy IVSFLLH**HIILGRTVDVKLVIPKGAISQCQPYLECPHFQRQNSETSNNNRRKIFVGRLPLNLSEEEFK

Parental  TYFEKFGTISQVNLISNKEIKT-PRGFGFVTYDSEESVTHALQEK-LHWLINKYVEVKKAEPRERRVINS
          TYF.KF..ISQVNLI.NKEIK..PRGF.FVTYDS.E.VTH.L.EK..H.L.NKYVEVKK.EPRERRV.N.
Retrocopy TYFKKFEIISQVNLIFNKEIKI>PRGFEFVTYDSKEFVTHVL*EK<IH*LNNKYVEVKKVEPRERRVMNI

Parental  -NYHNFYP---GYGMWQIYDCNNEIFAPQYCHNHTMVPTNWTSSFNHLGTNQFVHPQPIVPYFTPTYPVN
          ..YHNFYP...GYGMW.IY.C.N.I.AP.YCHNHTM.PTN.TS.FNHLGTN.F..PQ..V.Y.TPTYP.N
Retrocopy <YYHNFYPSNSGYGMWKIYNCYNGIIAPHYCHNHTMRPTN*TSLFNHLGTNLFISPQLLVLYLTPTYPIN

Parental  YYGSTHRYPINCYCSTQNQVDHNRGSY---STFTQNNVINEENGQECNNIEVQLVGDGSLPANESAKSLE
          .YGST.RY...CY.ST.NQV..N..SY...STF.QNNVINE.N.Q.CN..EVQ.VG.GS..ANES.KS.E
Retrocopy CYGSTRRYSVKCYSSTHNQVNDNKCSYWVLSTFAQNNVINEGNDQKCNDTEVQYVGNGSYLANESTKSPE

Parental  KETDNGGE-KDDLKEILYDNTKEDNGEIDHLVKILQVNSEDDT
          KE..N.GE..DDL..I..DNTKE.NGE.DHLVKI.QVN..DDT
Retrocopy KEINN-GE<NDDLEKIPQDNTKENNGEKDHLVKIFQVNTKDDT

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_49 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum lycopersicum	Solyc02g064540.1	1 retrocopy	retro_slyc_49 ,