RetrogeneDB ID: retro_tcac_19

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 1:6929880..6930495(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_001402
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_026453
• Aliases: None
• Description: None

Sequence

>retro_tcac_19
ATGGCAGATTCAGAGTCAGGGATCAGTAACCAAGTTTTGGAGCCTTCCAGTACTCACCCTCTCGGGTCTCCCCTTGTCCC
TACCCTTCAGAACGTGGTTTCCACTGTGAACTTGGGTTGCAAGCTGGACCTCAAGTTCATTGCGCTTCATGCACGAAATT
CCGAATACAACCCCAAAAGATTTGCTGCTGTGATAATGAGGATCAAAGAACCCAAGACCACCGCACTCATATTTTCATCT
GGAAAGATTGTTTGCACTGGAGCCAAAACCGAGCAACAATCCCTACTGGCTGCTCGCAAGTTCGCTCGAATCATTCAAAA
AATTGGTTTTGATATTCAGTTCAAGGATTTCAAGATTCAGAACATTGTTGCTTCTTGTAATATGAAGTTCCCCATCAGTC
TTGTGCAGCTTGCAGCTTTTCATGGGAAGTTCACAATATATGAGCCAGAGTTATTTCCGGGATTAATATATCGAATGAAA
ACACCTAAAGTTGCCATCCTTGTTTTTCCTTCGGGAAATATTGTTATTGCTGGAGCTCAAAAGAGAGATCATATTTTCCA
AGCTTTCGAGAACATATATCCTGTTTTGACGTCTTTCAAGAGAAATTACAAGTGA

Alignment

ORF - retro_tcac_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRNIVSTVNLDCKLDLKQIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEQQSKLAA
          L.N.VSTVNL.CKLDLK.IAL.ARN.EYNPKRFAAVIMRI.EPKTTALIF.SGK.VCTGAK.EQQS.LAA
Retrocopy LQNVVSTVNLGCKLDLKFIALHARNSEYNPKRFAAVIMRIKEPKTTALIFSSGKIVCTGAKTEQQSLLAA

Parental  RKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLI
          RK.ARIIQK.GF...FKDFKIQNIV.SC..KFPI.L..LA..HG.F..YEPELFPGLIYRMK.PK...L.
Retrocopy RKFARIIQKIGFDIQFKDFKIQNIVASCNMKFPISLVQLAAFHGKFTIYEPELFPGLIYRMKTPKVAILV

Parental  FVSGKIVITGAKVRDETYTAFENIYPVLTEFRKN
          F.SG.IVI.GA..RD....AFENIYPVLT.F..N
Retrocopy FPSGNIVIAGAQKRDHIFQAFENIYPVLTSFKRN

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_19 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra027434	2 retrocopies	retro_brap_12, retro_brap_9,
Brassica rapa	Bra030855	1 retrocopy	retro_brap_53,
Theobroma cacao	TCM_026453	1 retrocopy	retro_tcac_19 ,