RetrogeneDB ID: retro_tcac_49

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:10918802..10919120(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_015438
• Aliases: None
• Description: None

Sequence

>retro_tcac_49
GCGAAAGTATGGATTAATTCACCGCATTTCAACTCCAATTCAAGCTCTCAGGTTGTTTCCTACTTCCAAAGTGAAGGTGG
TGGCTGCTGTGTTTGGTGTTGGGGAAAATTGATAAAGAAGAATGAGATGTTGCAGTACAAATTGGAGCCCATCCCTTTCC
TGGAAAAGCAGGTTAAGAGGACAGAGGAATGAGGAAAACTTTTGACAATGGACATCGAGAGACTGTTAGTATCTGACGAC
AACAGGTTTGACTTTATGAATGGTATAGCAGTTGAGGTTAAAGAATATGTTAAGCGTAATCGTGTTGAATATGGAGGT

Alignment

ORF - retro_tcac_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARAGTNSWRLNPNLKCQCRVVSRFESEGGGRRVWRRRKLTKKDEMLQYKLERIPFLEEQVRKIREGGKLL
          A....NS...N.N...Q..VVS.F.SEGGG..VW...KL.KK.EMLQYKLE.IPFLE.QV....E.GKLL
Retrocopy AKVWINSPHFNSNSSSQ--VVSYFQSEGGGCCVWCWGKLIKKNEMLQYKLEPIPFLEKQVKRTEE*GKLL

Parental  TMDIERLLLSEDNRFDFVNDVAAEAKDYIESNRDEYGG
          TMDIERLL.S.DNRFDF.N..A.E.K.Y...NR.EYGG
Retrocopy TMDIERLLVSDDNRFDFMNGIAVEVKEYVKRNRVEYGG

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_49 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_015438	1 retrocopy	retro_tcac_49 ,