RetrogeneDB ID: retro_tcac_40

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 3:10868114..10868358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_003770
• Aliases: None
• Description: None

Sequence

>retro_tcac_40
AAAAGATTTTATAAATCAAGTGGTAGATAAAAGATTAGCTATTGCAGTGGCGGGGTTCAATGGGCCAGCCTATTAGAGGG
GCACGGTAAACTCCTTTATATTCTCACCTCGATCGTAGAGGCGCGTAGGGTATCTCCTGAGGTGGGCATTTTGAGTGCAC
TTCACGTGGACCACCGTGTGAGAGTGAGACTCAGCCAACGCCAAGGAACGGCTATGTTTTAAAATAAAAATATGGTTTAT
GCGA

Alignment

ORF - retro_tcac_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRLHPKAEDRSISTPNTGVPWTNLLEGHGKLHYIITSNGEARRVSPGVKLR-VHFTPNHHVKGNSANAKE
          KR.........IS....GV.W..LLEGHGKL.YI.TS..EARRVSP.V....VHFT........SANAKE
Retrocopy KRFYKSSGR*KISYCSGGVQWASLLEGHGKLLYILTSIVEARRVSPEVGIL>VHFTWTTV*E*DSANAKE

Parental  RLLKTVCIWSSR
          RL.....IW..R
Retrocopy RLCFKIKIWFMR

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_40 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_003770	1 retrocopy	retro_tcac_40 ,