RetrogeneDB ID: retro_tcac_58

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: scaffold_36:595..876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_015479
• Aliases: None
• Description: None

Sequence

>retro_tcac_58
AAGAGAGGAAGACACATAAGTAGAAGTAGAGTTAGGAAAATGCAGATCTTCGTGAAAACCCTAATGGGGAAGACCATAAC
CCTAGAGGTCAAATCTTGCAACACTATCAACAATGTTAAGGCTAAGATCTAGGACAAGAAAGGTATCCTAAAGACCAGCA
AAGATTGATCTTCACCAAAAAGCAGCTTGAGGATGGTAGTACTCTTGCCGACTATAACATTCAAAAAGAATCAACTTTGC
ATCTGGTTCTTATTAAAATAGGACTTGCCTTTGAAACCTCA

Alignment

ORF - retro_tcac_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.79 %
• Parental protein coverage: 62.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERERDRSRSRVRKMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGI-PPDQQRLIFAGKQLEDGRTL
          .R.R..SRSRVRKMQIFVKTL.GKTITLEV.S..TI.NVKAKI.DK.GI.P.DQQRLIF..KQLEDG.TL
Retrocopy KRGRHISRSRVRKMQIFVKTLMGKTITLEVKSCNTINNVKAKI*DKKGI<PKDQQRLIFTKKQLEDGSTL

Parental  ADYNIQKESTLHLVLRLRGGIIEPS
          ADYNIQKESTLHLVL...G...E.S
Retrocopy ADYNIQKESTLHLVLIKIGLAFETS

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_58 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_015479	1 retrocopy	retro_tcac_58 ,