RetrogeneDB ID: retro_tcac_55

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 9:14945731..14946178(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_023563
• Aliases: None
• Description: None

Sequence

>retro_tcac_55
ATACACACCATGTGTAGAAGATGTGGTAGTCTCGATACCTCTCATAGTGATAGCGAGGGATCTCTAGATTTTACGGCTAG
AAGCAAATGGCACGTTGATTTAGGTGATTCGGAAGGTGGTCCATCCTGAATTCCTAATAATAGAATTCCTCTGAATGTAA
CAGAATGGGTTCATAATAAGGAAAGCTTTGAGAGTAGCCAGAATTTTGAAAGTGAGAGTAGCTCTAATATTCTGAAAACT
GAAATAGATTTCCTTTTGAAACAATCCGAAGAGTACCATAGAGAACATACGAGGAAGGCAATTGCAAGGGGAGATATTCG
TCTTAGGAAGGGGGTGAACGTTGTACGCCATTTTCCTCCTAGATGTGGAAGAAATGCTGAATCGGTGAGTGCGGAGGAAA
TTAGGAGAAGACAACAAGCCTGGAATGAAGAACAAAGGAGAAAATCT

Alignment

ORF - retro_tcac_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.48 %
• Parental protein coverage: 68.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQKLCLETGIRSTSTPRTPWQTRLDALRK--VSPSDSEGGPSQIPNNRIHRNLAEWVHNKESFESSQNFE
          ....C...G...TS...........A..K..V...DSEGGPS.IPNNRI..N..EWVHNKESFESSQNFE
Retrocopy IHTMCRRCGSLDTSHSDSEGSLDFTARSKWHVDLGDSEGGPS*IPNNRIPLNVTEWVHNKESFESSQNFE

Parental  SESSSNILKTGIDFLLKQSEEYHREHTRKAIARGDIRLRKGVNVVRHFPLGYGRNAAPVSAEEIRRRQQA
          SESSSNILKT.IDFLLKQSEEYHREHTRKAIARGDIRLRKGVNVVRHFP...GRNA..VSAEEIRRRQQA
Retrocopy SESSSNILKTEIDFLLKQSEEYHREHTRKAIARGDIRLRKGVNVVRHFPPRCGRNAESVSAEEIRRRQQA

Parental  WIKEQRRKS
          W..EQRRKS
Retrocopy WNEEQRRKS

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_55 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_023563	1 retrocopy	retro_tcac_55 ,