RetrogeneDB ID: retro_tcac_14

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 2:35832043..35832688(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_010821
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_026723
• Aliases: None
• Description: None

Sequence

>retro_tcac_14
ATGATTTCACTCGCCAGCAGATGTGCAAAGCTCCTTAGAATCTCTGTTCCTACAGCACCCAACTCTTCTCTAGGTGTGCA
ACGTACCTCCAAGTTGTGGTGTTCAACTGGTTCGGTTGGTAGCGAAAATGATGAAGGGAAAGGCGATGAAATGGAAGAAG
AGATTGATGATTTTCTTGGCAATAAGTCTGACAAGCTTGAGCCAATGCTCCAAGGTGTCAATCCTGCAAGTGGTTGGAAT
TACCGTGGTGTACACAGGGCAATTATTTGTGGAAAAGTTGGGCAAGCCCCTATACAGAAGATATTGAGGAATGGACGAAC
AGTGACTATGTTTACAGTTGGGACAGGTGGCATGTATGATCAGAAAATCATAAGGGACCAAAACACACCACAACCTGCCC
AATGGCATCGAATTGCTGTGCATAATGATACACTTGGGGCTTATGCGGTTCAACAAATCACCAAAAACTTTTCAGTCTAT
GTTGAGGGTGACATTGAAACTAGAGTTTACAATGACAGCATAAATGGTGAAGTTAAATACATACCAGAAATATGTATCCG
TCGTGATGGAAGAATTCGCCTTATAAAGACTGGTGAAGGTGTTAGCAATATATCATTCGATGACCTGCGAGAGGGATTGC
TGTAG

Alignment

ORF - retro_tcac_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSLASRCAKLLRISVPTAPNSSLGVQRTSKLWCSTGSVGSENDEGKGNEMEEEIDDFLGDKSDKREPML
          M.SLASRCAKLLRISVPTAPNSSLGVQRTSKLWCSTGSVGSENDEGKG.EMEEEIDDFLG.KSDK.EPML
Retrocopy MISLASRCAKLLRISVPTAPNSSLGVQRTSKLWCSTGSVGSENDEGKGDEMEEEIDDFLGNKSDKLEPML

Parental  QGVNPASGWNYRGVHRAIICGKVGQAPIQKILRNGRTVTIFTVGTGGMYDQRIIRDQNTPQPAQWHRIAV
          QGVNPASGWNYRGVHRAIICGKVGQAPIQKILRNGRTVT.FTVGTGGMYDQ.IIRDQNTPQPAQWHRIAV
Retrocopy QGVNPASGWNYRGVHRAIICGKVGQAPIQKILRNGRTVTMFTVGTGGMYDQKIIRDQNTPQPAQWHRIAV

Parental  HNDALGAYAVQQITKNSSVYVEGDIETRVYNDSINGEVKYIPEICIRRDGRIRLIKTGEGVSNISFDDLR
          HND.LGAYAVQQITKN.SVYVEGDIETRVYNDSINGEVKYIPEICIRRDGRIRLIKTGEGVSNISFDDLR
Retrocopy HNDTLGAYAVQQITKNFSVYVEGDIETRVYNDSINGEVKYIPEICIRRDGRIRLIKTGEGVSNISFDDLR

Parental  EGLL
          EGLL
Retrocopy EGLL

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_14 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_026723	1 retrocopy	retro_tcac_14 ,