RetrogeneDB ID: retro_tcac_4

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 4:2337275..2338265(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_017203
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_020494
• Aliases: None
• Description: None

Sequence

>retro_tcac_4
ATGCCTTCAATTCCAGAAGAGCCACTGCTCGCCTCGAACCCGGACCGGTTTTGCATGTTCCCGATCCAATACCCGGAAGT
ATGGGAAATGTACAAGAAAGCCGAAGCCTCCTTTTGGACCGCCGAGGAAGTCGATCTCTCGTCGGATCTACGCCACTGGG
AAACTCTTACCGATGGCGAACGCCACTTCATCACTCACGTCCTCGCCTTCTTCGCAGCCTCCGATGGCATCGTCCTCGAA
AATCTCGCCGTTCGGTTCATGAAGGAAGTCCAAATCGCCGAGGCTCGTGCGTTCTATGGCTTCCAAATCGCCATCGAAAA
TATCCACTCCGAGATGTATAGTCTCCTCCTTGAAACTTACATCAAGGACTCCAACGAAAAGAACCGGCTCTTCCACGCCG
TCGAAACAGTGCCGTGTGTGGCTAAGAAAGCCGAGTGGGCGTTGAAATGGATCGACGGTTCGGAAACTTTCGCCGAACGG
CTAATCGCTTTTGCTTGCGTGGAAGGGATTTTCTTCTCTGGAAGTTTCTGCGCTATATTTTGGTTAAAAAAGCGCGGGTT
AATGCCTGGATTAACTTTCTCGAACGAGTTAATCTCACGAGATGAAGGTCTCCATTGCGATTTCGCTTGCTTGCTGTACT
CCCTCCTCCGGTCAAAGCTGAGCGAAGAGCGCGTGAGAGGGTTAGTGAGGGACGCAGTGGATATAGAGAGGGAGTTTGTA
TGTGATGCTCTGCCGTGCGCATTGGTTGGGATGAACGGAGAGCTGATGAGTCAGTACATCGAGTTCGTCGCAGATCGGTT
GTTGGGAGCGTTGGGGTACGGGAAGATGTACAATGTGGCTAACCCTTTTGATTGGATGGAACTGATTTCGTTGCAAGGCA
AAACTAATTTCTTCGAGAAAAGAGTTGGAGAGTACCAGAAAGCGGCGGTCATGTCGAGTTTGAATGGAAATGGTGGGACC
CATGAGTTCAAGATGGATGAAGATTTTTAG

Alignment

ORF - retro_tcac_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 69.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEPILKKQNQRFCMFPIRYQTLWEMYKKAEASFWTAEEVDLSQDVQHWDALSNSEKHFISHVLAFFAASD
          EEP.L.....RFCMFPI.Y...WEMYKKAEASFWTAEEVDLS.D..HW..L...E.HFI.HVLAFFAASD
Retrocopy EEPLLASNPDRFCMFPIQYPEVWEMYKKAEASFWTAEEVDLSSDLRHWETLTDGERHFITHVLAFFAASD

Parental  GIVLENLAARFLNDVQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAVESIPCVSKKAK
          GIVLENLA.RF...VQI.EARAFYGFQIA.ENIHSEMYSLLLETYIKDS.EK.RLF.AVE..PCV.KKA.
Retrocopy GIVLENLAVRFMKEVQIAEARAFYGFQIAIENIHSEMYSLLLETYIKDSNEKNRLFHAVETVPCVAKKAE

Parental  WALDWIQSSSLFAERLVAFACVEGIFFSGSFCSIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYGL
          WAL.WI..S..FAERL.AFACVEGIFFSGSFC.IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLY.L
Retrocopy WALKWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSL

Parental  LQKQLKWQKVHCIVHEAVEIETEFVCEALPCALIGMNSTLMSQYIKFVADHLLVALGCQRKYNVENPFDW
          L...L....V...V..AV.IE.EFVC.ALPCAL.GMN..LMSQYI.FVAD.LL.ALG....YNV.NPFDW
Retrocopy LRSKLSEERVRGLVRDAVDIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGALGYGKMYNVANPFDW

Parental  MEFISLQGKANFFERRVGDYQKASVMSSLQNGGNKNYVFKLDEDF
          ME.ISLQGK.NFFE.RVG.YQKA.VMSSL.NG......FK.DEDF
Retrocopy MELISLQGKTNFFEKRVGEYQKAAVMSSL-NGNGGTHEFKMDEDF

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_4 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00025p00110680	1 retrocopy	retro_atri_2,
Brassica rapa	Bra014962	1 retrocopy	retro_brap_7,
Prunus persica	PRUPE_ppa008063mg	1 retrocopy	retro_pper_7,
Solanum lycopersicum	Solyc01g080210.2	1 retrocopy	retro_slyc_6,
Theobroma cacao	TCM_020494	1 retrocopy	retro_tcac_4 ,
Vitis vinifera	VIT_05s0020g02560	1 retrocopy	retro_vvin_20,