RetrogeneDB ID: retro_tcac_16

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 1:30349610..30350450(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_004219
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_041518
• Aliases: None
• Description: None

Sequence

>retro_tcac_16
ATGGCGGAGCACTTGGCCTCAATCTTCGGGACCGAGAAGGACCGCGTGAATTGTCCCTTCTATTTCAAGATTGGAGCGTG
CCGGCACGGGGACAGGTGCTCACGGCTTCACAACCGGCCGACGATCTCACCAACTCTCCTGCTGTCGAACATGTACCAGC
GCCCGGACATGATCACCCCCGGAGTGGACGCCCAGGGCCAGCCTATCGACCCCCACAAGATCCAGGAGCACTTCGAGGAC
TTCTACGAGGACATCTTCGAGGAGCTCAGCAAGTTCGGTGAGATCGAGAGCCTCAACGTCTGTGACAACCTTGCTGACCA
CATGATTGGAAACGTGTATGTTCAGTTCAGGGAGGAGGACCAGGCTGCAGCCGCCCTCCAGGCACTTCAAGGAAGGTTCT
ACTCCGGTCGGCCTATCATCGCGGATTTCTCCCCAGTCACTGATTTTCGAGAGGCCACTTGTCGGCAATTTGAGGAGAAT
AACTGTAACCGCGGGGGTTACTGTAATTTTATGCATGTCAAGGTAATTGGGAGGGAGCTAAGAAGGAAGCTGTTTGGGAG
GTACCGCAAGTTCAGAGGGAGTCGGAGCAGGAGCAGGAGCGCCAGTCCACGCCACAGGCGTGATAAGGAGTTTAGGGACC
GGGACCGGGACCGGGACCGTGGTGATTATCGCGATAGAAATGGGCGAAGACCTGATAGGCACGATAGGGACAGCGGTAGT
AGGAGAAAGCTTGGGAGTCCTAGGCGAAGCAGAAGTCCCGCACCTCCTGCTAGAGAAGGGAGCGAGGAGCGGAGAGCCAG
GATTGAACAGTGGAATCGAGAGAGGGAAGAGAAGGTGTAA

Alignment

ORF - retro_tcac_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 88.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHTKPSISPTLLLSNMYQRPDMITPGVENQGNPID
          MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLH..P.ISPTLLLSNMYQRPDMITPGV..QG.PID
Retrocopy MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHNRPTISPTLLLSNMYQRPDMITPGVDAQGQPID

Parental  PRKIQEHFEEFYEDLFEELSKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLSGRYYSGRPII
          P.KIQEHFE.FYED.FEELSK.GEIESLN.CDNLADHM.GNVYVQFREE..AA.AL..L.GR.YSGRPII
Retrocopy PHKIQEHFEDFYEDIFEELSKFGEIESLNVCDNLADHMIGNVYVQFREEDQAAAALQALQGRFYSGRPII

Parental  VDFSPVTDFREATCRQYEENTCNRGGYCNFMHLKTISRELRRQLFGRYRRRRSHSQSRSRS-PPKHRGSH
          .DFSPVTDFREATCRQ.EEN.CNRGGYCNFMH.K.I.RELRR.LFGRYR..R..S.SRSRS..P.HR...
Retrocopy ADFSPVTDFREATCRQFEENNCNRGGYCNFMHVKVIGRELRRKLFGRYRKFRG-SRSRSRSASPRHRRDK

Parental  EERSHGGRGHIRRYGDRDHYHESRSKRHRSTSPGHRRGRSRSPGGKRNRSPVREGSEERRAKIEQWNRER
          E.R....R...R..GD.......R..RH...S.G.RR.............P.REGSEERRA.IEQWNRER
Retrocopy EFRD---RDRDRDRGDYRDRNGRRPDRHDRDS-GSRRKLGSPRRSRSPAPPAREGSEERRARIEQWNRER

Parental  EQE
          E..
Retrocopy EEK

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_16 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00040p00218420	1 retrocopy	retro_atri_1,
Theobroma cacao	TCM_041518	1 retrocopy	retro_tcac_16 ,
Vitis vinifera	VIT_08s0007g03950	1 retrocopy	retro_vvin_15,