RetrogeneDB ID: retro_tcac_9

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 8:3515206..3515791(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_034533
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_036352
• Aliases: None
• Description: None

Sequence

>retro_tcac_9
ATGACCATTTCTTTTCCTATATATATCTCCAAACTCTTCACCTCTTTCGTCAAACAATTAGCAAGTGAACAGATACAGAA
ATACTTCTTTTTTTCCAATACCCAAGCAAGCAAAGCAACCATGTCGGCGAGAACTAAGCGGATACAAAAGGAGTGGGCAA
ATGTTCAAAAGGATAAGGAGATAAACAATATGTGCAGTGTTGGTCTAGTTGGGAACAACCTTGACGAGTGGCAAGCCACG
ATCTTTGGCCAACCTGGTACTCCTTACGAAGGGGGTTTATTCAATTTATCCATTGTCTTGCCAAGCAATTACCCATTTGC
ACCACCCAAGGTTACCTTCAAAACTAAGATTTATCACCCCAACATTAATGAACAGGGTAGCATTTGTCTTGATATTCTTA
AATTCAAAGATAAGTGGACTCCGGCATATGAAGTAAGGGCTGTGATTATAGCAATATGCTCGCTGATGAATGATCCAAAC
CCAGATGATCCGCTCGTGCCTAAGATTGGTGCTGAGTACAAGAATAACCGGTCCAGCTTCGAGGCTACTGCTCGCCAATG
GACAATGCAGTTTGCTCTACCTTAG

Alignment

ORF - retro_tcac_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.95 %
• Parental protein coverage: 70.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMASKRITKELKDLQKDPPVS--CSAGPIGDGMFHWQATIMGPADSPYAGGVFLVSIHFPPDYPFKPPKV
          S...KRI.KE....QKD......CS.G..G.....WQATI.G....PY.GG.F..SI..P..YPF.PPKV
Retrocopy SARTKRIQKEWANVQKDKEINNMCSVGLVGNNLDEWQATIFGQPGTPYEGGLFNLSIVLPSNYPFAPPKV

Parental  AFKTKVYHPNINSNGSICLDILK--EQWSPALTVSKVLLSICSLLTDPNPDDPLVPEIAHTYKTDRAKYE
          .FKTK.YHPNIN..GSICLDILK....W.PA..V..V...ICSL..DPNPDDPLVP.I...YK..R...E
Retrocopy TFKTKIYHPNINEQGSICLDILKFKDKWTPAYEVRAVIIAICSLMNDPNPDDPLVPKIGAEYKNNRSSFE

Parental  STARSWSQKYAM
          .TAR.W....A.
Retrocopy ATARQWTMQFAL

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_9 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_036352	1 retrocopy	retro_tcac_9 ,