RetrogeneDB ID: retro_slyc_38

Retrocopy location

• Organism: Tomato (Solanum lycopersicum)
• Coordinates: 5:1496348..1496828(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Solyc05g006890.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Solyc04g005510.2
• Aliases: None
• Description: None

Sequence

>retro_slyc_38
ATGTCTGACGAAGAGCACCAATTTGAATCAAAAGCAGATGCCGGAGCTTCCAAAACTTACCCTCAACAAGCTGGTACTAT
TCGGAAGAACGGTTACATTGTAATCAAAGCTCGTCCTTGCAAGGTTGTGGAAGTCTCCACTTCCAAGACTGGCAAGCATG
GACACGCCAAATGTCACTTTGTAGCAATTGACATTTTCACTGGCAAGAAACTTGAGGATATTGTTCCCTCTTCGCACAAT
TGTGATGTCCCCCATGTTAATCGTACAGATTACCAGCTTATTGACATCTCCGAGGATGAATTTGTGAGTCTCCTCACTGA
CAGTGGTAATACTAAGGATGACCTGAGGCTTCCAACAGATGAGAATCTTCTCTCACTGATCAAGGATGGATTCGCGGAGG
GCAAAGACCTTGTTGTGTCTGTCATGTCTTCCATGGGAGAGGAACAGATTAATGCACTGAAGGATATTGGTCCCAAGTAA

Alignment

ORF - retro_slyc_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDEEHQFESKADAGASKTYPQQAGTIRKNGYIVIKARPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKK
          MSDEEHQFESKADAGASKTYPQQAGTIRKNGYIVIKARPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKK
Retrocopy MSDEEHQFESKADAGASKTYPQQAGTIRKNGYIVIKARPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKK

Parental  LEDIVPSSHNCDVPHVNRTDYQLIDISEDGFVSLLTDNGNTKDDLRLPTDENLLSLIKDGFAEGKDLVVS
          LEDIVPSSHNCDVPHVNRTDYQLIDISED.FVSLLTD.GNTKDDLRLPTDENLLSLIKDGFAEGKDLVVS
Retrocopy LEDIVPSSHNCDVPHVNRTDYQLIDISEDEFVSLLTDSGNTKDDLRLPTDENLLSLIKDGFAEGKDLVVS

Parental  VMSAMGEEQINALKDIGPK
          VMS.MGEEQINALKDIGPK
Retrocopy VMSSMGEEQINALKDIGPK

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_38 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	Solyc04g005510.2	1 retrocopy	retro_slyc_38 ,