RetrogeneDB ID: retro_tcac_27

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:35593030..35593477(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_025935
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_036681
• Aliases: None
• Description: None

Sequence

>retro_tcac_27
ATGAACAAAGGTACGGGAGTGGGAACTGGGCCAACGGCGGCGGCTGCAGCGGCAGCGGCACAGAAGCAAAAAACTATGAT
GCAGAGAGTGGAAACCGACATCGTCAACATCGTCGACAATTTCACCCAGCTTGTTAATGTTGCCCGGGTAAATGATCCAC
CAGTTCGAAATTCACAAGAAGCTTTCATGATGGAGATGCGTGCAGCCAGAATGGTCCAGGCAGCTGATTCTTTGCTTAAG
TTGGTGTCGGAGCTGAAGCAGACGGCAATCTTTTCAGGATTTGCATCTCTTAATGACCATGTGGAGCAAAGAAGTGTTGA
GTTTGACCAGCAAGCAGAAAAAACAGACCGAATGCTGGCCAGGATTGGAGAGGAGGCAGCAGCGAGCCTCAAGGAGCTTG
AATCTCATCATTATTCTTCTGCACGGAGGACAGCCGAATCTCCTTAG

Alignment

ORF - retro_tcac_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.6 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNKGTGVGTGPTAAAAAAAAQKQKTMMQRVETDIGNIVENFTQLVNVARVNDPPVGNSQEAFMMEMRAAR
          MNKGTGVGTGPTAAAAAAAAQKQKTMMQRVETDI.NIV.NFTQLVNVARVNDPPV.NSQEAFMMEMRAAR
Retrocopy MNKGTGVGTGPTAAAAAAAAQKQKTMMQRVETDIVNIVDNFTQLVNVARVNDPPVRNSQEAFMMEMRAAR

Parental  MVQAADSLLKLVSELKQTAIFSGFASLNDHVEQRSVEFDQQAKKTDRMLARIGEEAAASLKELESHYYSS
          MVQAADSLLKLVSELKQTAIFSGFASLNDHVEQRSVEFDQQA.KTDRMLARIGEEAAASLKELESH.YSS
Retrocopy MVQAADSLLKLVSELKQTAIFSGFASLNDHVEQRSVEFDQQAEKTDRMLARIGEEAAASLKELESHHYSS

Parental  ARRTAES
          ARRTAES
Retrocopy ARRTAES

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_27 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_036681	1 retrocopy	retro_tcac_27 ,