RetrogeneDB ID: retro_tcac_31

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:900369..900894(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_021712
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_015401
• Aliases: None
• Description: None

Sequence

>retro_tcac_31
ATGTCGAAGCTAACTCCAAACAAAGCAAACGGTCTTGACATGGAGAATCATTCATGGGGCCAAAATCTGCAAGAGGTGAC
TGTTAGCATCCCAGTTTCTCAGGGAACCAGATCAAGGGACGTTATCTGCGATATAAAGAAGAAGTATCTGAAGATTGAGT
TAAAGGGTCAGGCTCCGATTCTTGACGGGGAGTTGTTCGGGACCGTGAAACCCGATGAATGTTACTGGAGCTTGGAGGAC
CAAAGCATGATCTCTGTGTTTCTGACCAAGTGTGATAAGTCCAACTGGTGGAAATCCTTGTTGAAGGGAGGTCCCGAGAT
TGATACTCAGAAGGCAGAACCTGAGCCGAGCAAGTTGTCGGATTTGGACTTTGAAACGAGGTCAGCTGTCGAGAAGATGA
TGTTTGATCAGAGACAGAAACAGTTGGGGCTTCCCACCAGCCAGGAGATCGAGAACCAAGAGATGCTCAAGAAATTCATG
GCTCAGAATCCCAATTTCGACTTCTCCAATGCAAAGATGATGTAA

Alignment

ORF - retro_tcac_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.27 %
• Parental protein coverage: 57.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PNKGNGLDLEKYSWTQTLQEVTVNVPVPSGTRSRFVVCEIKKNHLKVGLKGQPPVIDGELLQSVKPDDCY
          PNK.NGLD.E..SW.Q.LQEVTV..PV..GTRSR.V.C.IKK..LK..LKGQ.P..DGEL...VKPD.CY
Retrocopy PNKANGLDMENHSWGQNLQEVTVSIPVSQGTRSRDVICDIKKKYLKIELKGQAPILDGELFGTVKPDECY

Parental  WSIEDNCSLSILLTKHNQMEWWKSLVKGDPEIDTQKVEPENSKLSDLDPETRQTVEKMMFDQRQKAMGLP
          WS.ED....S..LTK.....WWKSL.KG.PEIDTQK.EPE.SKLSDLD.ETR..VEKMMFDQRQK..GLP
Retrocopy WSLEDQSMISVFLTKCDKSNWWKSLLKGGPEIDTQKAEPEPSKLSDLDFETRSAVEKMMFDQRQKQLGLP

Parental  TSDELQKQEILKKFMSEHPEMDFSRAKLM
          TS.E...QE.LKKFM...P..DFS.AK.M
Retrocopy TSQEIENQEMLKKFMAQNPNFDFSNAKMM

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_31 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_53047	1 retrocopy	retro_hvul_58,
Theobroma cacao	TCM_015401	1 retrocopy	retro_tcac_31 ,