RetrogeneDB ID: retro_tcac_30

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 10:23359245..23359974(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_045243
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_026035
• Aliases: None
• Description: None

Sequence

>retro_tcac_30
ATGGGAGTGATCAAGGCAGCCATAGGAGATGCCCTGTTGACATCCATGTGGGTGTTTAGCATGCCTACGCTAAGGATTTT
TACAGGCAAAATAGCAACTTTCCTTGGTGTCCAAGCCCTCCCCTTGGCTCCTCTCTTTATCACCACCATCCTTGTCAGTT
GTTTAGTTTTCCTCTTCAGCTTGATTGGAGAAGCTTTGGGTGGTGCCAGCTTCAACCCCACAGCTTCTCTCACTTTCTAT
GCCGCCGGTCTCAAGAAAAACTCCTCTCTCCTCTCCATGGCCGTACGTTTTCCTGCTCAGGCTGCGGGTGGAGTTGCTGG
TGTCAAGGCAATCCTGCAAGTGATTCCGGGGGAATACAAGAAATTCATCAAAGGACCTTCCCTGAATGTGGATTTGCATA
CAGGGGCAATTGCTGAAGGGGTTTTGACTTTTGGGCTCAGCCTTGCTCTCCTTGTGATTCTGGTCAGAGGTCCTAAAAAC
CCTTTGATTAAGCTGTGGTTAATGGCTGCGTCAACTGTGGGATTGGTTACAACAGGTTCCAAATACACTGGACCTTCCAT
GAATCCAGCCAATGCCTTTGGATGGGCATATCAGAACAACTGGCACAATTCTTGGGAGCTTTACTATGTTTATTGGATTG
GTCCTTTGACTGGGGCAACTTTGGCTGCTTGGGTTTTCAGATTCCTGCTTTCTCCTCCTCCACCACCATCCAAGGAGAAG
AAAGCTTGA

Alignment

ORF - retro_tcac_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGPIKMAIWDMLITFMWVFFASTFGLLTSLIATAIGVQTVTWAPIVITTVIIFVFVFIFNIIGGYLGGAS
          MG.IK.AI.D.L.T.MWVF...T....T..IAT..GVQ....AP..ITT......VF.F..IG..LGGAS
Retrocopy MGVIKAAIGDALLTSMWVFSMPTLRIFTGKIATFLGVQALPLAPLFITTILVSCLVFLFSLIGEALGGAS

Parental  FNPTGTASFYAAGVG-DDSLISMALRFPAQAAGAVGGALAIMEVIPEQYKHMIGGPSLQVDTHTGAIAEG
          FNPT....FYAAG.....SL.SMA.RFPAQAAG.V.G..AI..VIP..YK..I.GPSL.VD.HTGAIAEG
Retrocopy FNPTASLTFYAAGLKKNSSLLSMAVRFPAQAAGGVAGVKAILQVIPGEYKKFIKGPSLNVDLHTGAIAEG

Parental  VLTFLITFAVLLIILRGPHSEMFKAWLLAIATVALVLAGTSYTGPSMNPANAFGWAYVNSWHNTWDQFYV
          VLTF....A.L.I..RGP.....K.WL.A..TV.LV..G..YTGPSMNPANAFGWAY.N.WHN.W...YV
Retrocopy VLTFGLSLALLVILVRGPKNPLIKLWLMAASTVGLVTTGSKYTGPSMNPANAFGWAYQNNWHNSWELYYV

Parental  YWICPFIGAILAAWVFRLFF--PPSPVKVKKA
          YWI.P..GA.LAAWVFR.....PP.P.K.KKA
Retrocopy YWIGPLTGATLAAWVFRFLLSPPPPPSKEKKA

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_30 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g085070	1 retrocopy	retro_mtru_16,
Populus trichocarpa	POPTR_0013s05030	1 retrocopy	retro_ptri_8,
Prunus persica	PRUPE_ppa010591mg	1 retrocopy	retro_pper_47,
Theobroma cacao	TCM_026035	1 retrocopy	retro_tcac_30 ,