RetrogeneDB ID: retro_tcac_28

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:1762538..1762877(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_030875
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_046859
• Aliases: None
• Description: None

Sequence

>retro_tcac_28
ATGGTTGATATAGGCAGCCAGATCCCCACTACTTTCGATCCATTCGCCGAGGCTGAGGAATTTGGTGGCACTGGAACCAA
GGAGTATGTGCATATACGAATCCAACAGAGGAATGGAAAGAAAAGCTTGACAACTGTTCAAGGGCTGAAACAGGATTTGA
GCTACGAGAAAATTCTCAAGTGTCTCAAGAAGGACTTCTGCTGTAATGGGAATGTCGTGAATGACAAAGAGCTTGGCAAA
ATCATTCAGCTCCAAGGTGATCAGCGCAAAAACGTGTCCCAGTTCCTTGTTAATGCTGGCATCGTGAAGAAGGATCAAAT
CAAGATTCATGGTTTCTAG

Alignment

ORF - retro_tcac_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDLDVQIPTAFDPFADANAEDSGAGAKEYVHIRIQQRNGRKSLTTVQGLKKEFSYNKILKDLKKVFCCN
          M.D...QIPT.FDPFA.A..E..G.G.KEYVHIRIQQRNG.KSLTTVQGLK...SY.KILK.LKK.FCCN
Retrocopy MVDIGSQIPTTFDPFAEAE-EFGGTGTKEYVHIRIQQRNGKKSLTTVQGLKQDLSYEKILKCLKKDFCCN

Parental  GTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKDNIKIHGF
          G.VV.D.ELG..IQLQGDQRKNVS.FLV.AGIVKKD.IKIHGF
Retrocopy GNVVNDKELGKIIQLQGDQRKNVSQFLVNAGIVKKDQIKIHGF

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_28 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_046859	1 retrocopy	retro_tcac_28 ,