RetrogeneDB ID: retro_tcac_45

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 6:17678006..17678525(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_006606
• Aliases: None
• Description: None

Sequence

>retro_tcac_45
ATCTCAAGTAGTCACATTAACCTTACAATGACTTTTGGGTTGTTTTTGGCCCGTAAGTTGTTTCTGATCAAGGTTGTCGC
TTACATGGAAGCTCGGTGCTTGGCTGCTATATGGAGTTAGGTTGGCTAAAGCTTTCATGAAGCATGAGTGCAACTCCCTT
GGTGGTGGTGTTAACGTTGTGGCTTATTGCTACAACAAGGGAACTACTTTGGGAGTTGAGATTATTAGCACTTTCGTGCT
TGTCTACATTGTTTTCTCAGCCATTCACCTTAAGTGGAATGCTTGTGACTCCCACATTCTTGTGTTGGCGCCCCTTGTTA
TTGGGTTTGCCGTTTTCATGGCTACCATTCCCATCACTAGTAGTGGTATCAACCCTTATAGGAGTAATGGTGCTGCTGTT
ATCTACAACAACAAGAAAGCCTAGGATAACCATTGGATTTTTTATGTTGGTCTTTTCGTGGGAATCTTGTAACAATTGCA
TACCACCAATTAACTGCATCTATCAAGGCTTTGGGATCA

Alignment

ORF - retro_tcac_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 64.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ISGGHINPAVTFGLFLARKVSLIRAVAYMVAQC-LGA-ICGVGLVKAFMKHDYNSQGGGANTVASGYNKG
          IS..HIN...TFGLFLARK..LI..VAYM.A.C.LG....GV.L.KAFMKH..NS.GGG.N.VA..YNKG
Retrocopy ISSSHINLTMTFGLFLARKLFLIKVVAYMEARC<LGC<LYGVRLAKAFMKHECNSLGGGVNVVAYCYNKG

Parental  TALGAEIIGTFVLVYTVFSATDPKRSARDSHVPVLAPLPIGFAVFMVHLATIPITGTGINPARSIGAAVI
          T.LG.EII.TFVLVY.VFSA...K..A.DSH..VLAPL.IGFAVFM...ATIPIT..GINP.RS.GAAVI
Retrocopy TTLGVEIISTFVLVYIVFSAIHLKWNACDSHILVLAPLVIGFAVFM---ATIPITSSGINPYRSNGAAVI

Parental  YNNEKAWDDHWIFWVGPFVGA-LAAAAYHQYILRAAAIKALGS
          YNN.KA.D.HWIF.VG.FVG..L...AYHQ.....A.IKALGS
Retrocopy YNNKKA*DNHWIFYVGLFVGI<LVTIAYHQL---TASIKALGS

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_45 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_006606	1 retrocopy	retro_tcac_45 ,