RetrogeneDB ID: retro_tcac_43

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 4:5446081..5446327(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_002781
• Aliases: None
• Description: None

Sequence

>retro_tcac_43
ATGATTTTAGTGTGTTCATCTTAGATTTTTGAAAGTTTTGGAAGCTTCAAACTGCCTACAAGGGAAAATGTATCGATACA
TACCCTCATTTATCGATACATTCTTGGTGTCACGACTCGGTACTCTCCTCGAGCCCGTGACAACCATCACGATGTTCCGA
TAGACATTCACTACCCAAAATGCCAACCGAAACCCCGTAAGGCTTTAATATCAGTTTTTACACCTCCCCTGTGAGCAACA
GTTATT

Alignment

ORF - retro_tcac_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.19 %
• Parental protein coverage: 57.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVIATSNASANLGDRGLPKVVDMTTILAVVDRFSNGIVTTQYSPRARDNHRDVSIDIHCSKCQPEPRKA
          ......S......G...LP.......I.....R...G.VTT.YSPRARDNH.DV.IDIH..KCQP.PRKA
Retrocopy MILVCSS*IFESFGSFKLP-TRENVSIHTLIYRYILG-VTTRYSPRARDNHHDVPIDIHYPKCQPKPRKA

Parental  LISVFAPPLGILVI
          LISVF.PPL...VI
Retrocopy LISVFTPPL*ATVI

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_43 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Theobroma cacao	TCM_002781	1 retrocopy	retro_tcac_43 ,