RetrogeneDB ID: retro_tcac_29

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 1:3739991..3740831(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_000843
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_001201
• Aliases: None
• Description: None

Sequence

>retro_tcac_29
ATGGATGAGCCTAAGGTTGTTCTCGTCACCGGCTGTGCCAAAGGGGGCATTGGATATGAATATTGCCGGGCATTAGCAGA
GCACAACTGCCGGGTGGTTGCCTCTGACATCCCTCGACGAATGGATGACATGTTGGACTTCAATGCCGATAACATTGAAA
CGATAGAGCTCGATGTTTCATCAAACGAGAGCGTGTCATCAGCTGTGAATTCTGTTATATCCAAGTATGGTCACATTGAT
GTACTGATAAACAATGCTGGCATAGGAAGCACCGGCCCCTTAGCTGAGCTTTCTCTAGATGCAATCAAGAAAGCTTGGGA
AATCAACACATTGGGGCAGCTGAGAATGGTGCAACAAATTGTTCCCCACATGGCTTCGCGGCGCAGGGGGTGTATAGTCA
ATGTAGGGAGTGTGGTCGGGAGAGTGCCAACCCCATGGGCAGGGTCCTATTGTTCTAGCAAGGCAGCTGTTCATGCCATG
ACCAATTCTTTGCGTGTTGAGTTAAGGCCCTTCGGTATCAATGTGGTACTTGTGGTGCCTGGTGCTGTGAGATCAAATTT
TGGAAGCTCTAGCCTGGAGAGGCTGGGAGATCATGATTGGAAACTTTATAAGGAATTCAAGGAGGCCATTGCTGAGCGAG
CCAGGGCTTCCCAAGGTTCCAAGGCAACGGATGCCACAATGTTTGCAAGACATGTGGCAAAGAAGGTTTTGAGTCCTAAA
CCACCGAAGCAGATAGTATTTGGTCACATGACTGGTTTGTTTGCTGTGCTTTCATTGTCTCCACTTTGGGTCAGAGATCT
GTTCTTTAGTACTCGTTTCAATCTAAACAAGAGGGTCTAA

Alignment

ORF - retro_tcac_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.56 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQNPVVLITGCSQGGIGHALARAFADNNCKVVAT--ARSLSSMSDLQQDPRFYLQELDVLSEQSVQRVMS
          D...VVL.TGC..GGIG....RA.A..NC.VVA....R....M.D...D......ELDV.S..SV.....
Retrocopy DEPKVVLVTGCAKGGIGYEYCRALAEHNCRVVASDIPRRMDDMLDFNAD-NIETIELDVSSNESVSSAVN

Parental  NVLDKFGRVDVLVNNAGIQCIGPLAEIPLVAMENTFNTNVFGSMRLVQAVVPHMASRKKGKIVNVGSVAA
          .V..K.G..DVL.NNAGI...GPLAE..L.A.......N..G..R.VQ..VPHMASR..G.IVNVGSV..
Retrocopy SVISKYGHIDVLINNAGIGSTGPLAELSLDAIKKAWEINTLGQLRMVQQIVPHMASRRRGCIVNVGSVVG

Parental  MAPGPWSGVYTASKAALHALTDTLRLELKHFGIDVINVVPGAVRSNIGDSAV
          ..P.PW.G.Y..SKAA.HA.T..LR.EL..FGI.V..VVPGAVRSN.G.S..
Retrocopy RVPTPWAGSYCSSKAAVHAMTNSLRVELRPFGINVVLVVPGAVRSNFGSSSL

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_29 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_001201	1 retrocopy	retro_tcac_29 ,