RetrogeneDB ID: retro_tcac_26

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 1:31820967..31821303(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_004481
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_019441
• Aliases: None
• Description: None

Sequence

>retro_tcac_26
ATGGATACATCAAGGAAGAAGATCCACAAGGACAAAGATGCTGAACCTACTGAATTTGAAGAGACATTTGCTCAGGCATT
GTTTGATTTGGAGAATACTAACCAATATTTTAAGGCTGAGTTGCAAGATCTGTATATAAACTCAGCAGTTCAAATGGATG
TTTCTGGAAACCGCAAGGCAGTTGTCATTTATGTACCCTATAGATTGAGGAAGGCATTCTGTAAGGTTCATTTACGTCTT
GTTAGAGAACTGGAGAAAAAGTTCAGTGGAAAGGATGTTGTCCTGCTTGCCACCCGGAGGATATTGAGGCCACCAAAGAA
AGGCTTTGCTGTTTAG

Alignment

ORF - retro_tcac_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYTSRKKIHKDKDAEPTEFEETVAQALFDLENTNQDFKAELQDLYINSAVQMDVSGNRKAVVIYVPYRLR
          M.TSRKKIHKDKDAEPTEFEET.AQALFDLENTNQ.FKAELQDLYINSAVQMDVSGNRKAVVIYVPYRLR
Retrocopy MDTSRKKIHKDKDAEPTEFEETFAQALFDLENTNQYFKAELQDLYINSAVQMDVSGNRKAVVIYVPYRLR

Parental  KAFRKVHLRLVRELEKKFSGKDVVLLATRRILRPPKKGSAV
          KAF.KVHLRLVRELEKKFSGKDVVLLATRRILRPPKKG.AV
Retrocopy KAFCKVHLRLVRELEKKFSGKDVVLLATRRILRPPKKGFAV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Theobroma cacao was not studied using RNA-Seq expression data.

ChIP-Seq

Theobroma cacao was not studied using ChIP-Seq data.

EST

Theobroma cacao was not studied using EST data.

TSS

Theobroma cacao was not studied using FANTOM5 data.

Lab

retro_tcac_26 was not experimentally validated.

Homology

Retrocopy orthology:

Theobroma cacao 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
Theobroma cacao	TCM_019441	1 retrocopy	retro_tcac_26 ,