RetrogeneDB ID: retro_tcac_10

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 3:29280932..29281586(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_015719
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_015359
• Aliases: None
• Description: None

Sequence

>retro_tcac_10
ATGGCAGACCCAAAACCCGAACCTTCCTCTTCAATGCCCAACCCACGACCCGACTCCGAACCTACCACCCACCACCTCAC
CATCCCCACCGGGTTAACCCACGATGAGTTCTGCGACCTAATCCCTTCCATCACTCAGTTCCACACCTACTCGGTGGGTC
CGGGCAAATGTTCTTCCTTATTAGCCCAACCTATCAAGGCCCCGCACGACGTAGTTTGGTCCGTCGTCCGCCGTTTCGAT
AAACCCCAGACGTACAAACACTTCATCAAGAGCTGCGCGGTGAAAGAAGGTTTCCGAATGGTCGTGGGTTGCACGCGTGA
CGTTAACGTGATCTCCGGGTTACCGGCTGCCACCAGCACCGAGAGACTCGATATTTTAGATGATGACCAACAGGTCACGG
GTTTCAGTATCATTGGAGGGGAGCATCGGTTAAGGAATTACAGGTCGGTGACTACGGTGCATGGTTTCCAGCGTGACGGG
AGGATCTGGACCACCGTTTTGGAATCGTACGTTGTTGATGTTCCGGAAGGGAATACGGAGGAAGACACGCGGCTGTTTGC
TGATACTGTTGTCAAGTTGAACTTGCAGAAGCTGGCCACCGTAACCGAAGGCTTAGCGCGTGATGGTGACGGTCATAAAT
CACAGGTGATGTGA

Alignment

ORF - retro_tcac_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.31 %
• Parental protein coverage: 63.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRRHHRHEIGENQCSSALVKHIKAPVPLVWSLVRRFDQPQKYKPFVSRCVVQGNLE--IGSLREVDVKSG
          ....H....G...CSS.L...IKAP...VWS.VRRFD.PQ.YK.F...C.V........G..R.V.V.SG
Retrocopy ITQFHTYSVGPGKCSSLLAQPIKAPHDVVWSVVRRFDKPQTYKHFIKSCAVKEGFRMVVGCTRDVNVISG

Parental  LPATTSTERLELLDDDEHILSIRIVGGDHRLKNYSSISSLHPEIIDGRPGTLVIESFVVDVPEGNTKDET
          LPA.TSTERL..LDDD.......I.GG.HRL.NY.S....H....DGR..T.V.ES.VVDVPEGNT...T
Retrocopy LPAATSTERLDILDDDQQVTGFSIIGGEHRLRNYRSVTTVHGFQRDGRIWTTVLESYVVDVPEGNTEEDT

Parental  CYFVEALIKCNLKSLADVSEGLA
          ..F.....K.NL..LA.V.EGLA
Retrocopy RLFADTVVKLNLQKLATVTEGLA

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_10 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_015359	1 retrocopy	retro_tcac_10 ,