RetrogeneDB ID: retro_tcac_6

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 3:31391308..31392379(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_016119
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_042615
• Aliases: None
• Description: None

Sequence

>retro_tcac_6
ATGGTGGAAGCGCAAACATGGACGACAAGGAGGATGAGCAACCCAAGATTGGACTCAACCGCCACTGCCGACCACCAGGT
GTTGGACATTCCGGCAACCCCAACTGGTGATGATAGAAATAGCTTTTACAGCGTTGGATCTCATCTCTCTCCTAACCTTT
TAACTGCCCTGATCATTGCTTCATGGTTCATGTCCAACATTGGGGTCCTTTTACTTAACAAGTATCTCCTCAGCTTTTAT
GGCTACCGTTATCCAATCTTTCTCACTATGCTTCACATGATCTCATGTGCTTGTTACAGTTACGTAGCCATTAACTTCCT
TGAAATAGTTCCAAGGCAACACATTTTGTCAAGAAAGCAGTTTTTCAAGATCTTTGCTTTGAGTTGTATTTTTTGTTTCT
CTGTGGTGTGTGGGAACACTTCGTTAAGGTACATTCCGGTGTCGTTTAACCAAGCTATTGGTGCGACGACCCCTTTTTTC
ACTGCCATTTTCGCTTTCTTAATCACTTGCAAGAAGGAATCTGCTGAGGTTTATTTTGCGCTTTTGCCTGTGGTTTTTGG
GATTGTTTTGGCTAGCAATAGTGAGCCTTTGTTTAACCTGTTTGGCTTCTTGGTTTGCATTGGTTCTACTGCTGGTCGTG
CTTTGAAATCTGTGGTTCAAGGGATCTTGTTGACTAGTGAAGCTGAGAAGCTACATTCCATGAACTTGTTGTTGTATATG
GCGCCTATGGCAGCAATGATTTTGTTACCATTTACCCTATATATTGAAGGGAATGTTGCAAGAGTCACACTCGAGAAAGC
TAGGAGTGATTCTTTTATTATTTTCTTGTTGCTAGGGAATGCTACGGTGGCTTATTTGGTGAATTTGACAAATTTTTTGG
TTACCAAGCATACAAGTGCCCTTACTTTGCAGGTTTTGGGCAATGCCAAAGCTGCAGTGGCAGCGTTTGTGTCGGTTATG
ATCTTCAGGAATCCGGTGACCGTGATGGGGATGACTGGATTCGCTGTTACAGTTATGGGAGTTGTGCTTTACAGTGAGGC
AAAGAAGAGATCTAAAGTCACAACACACTGA

Alignment

ORF - retro_tcac_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 96.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVTAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLLSYIAIAWMKMVPMQTIRSRVQFFKISAL
          ....W..SNIGVLLLNKYLLS.YG..YPIFLTM.HM..C...SY.AI.....VP.Q.I.SR.QFFKI.AL
Retrocopy IIASWFMSNIGVLLLNKYLLSFYGYRYPIFLTMLHMISCACYSYVAINFLEIVPRQHILSRKQFFKIFAL

Parental  SLVFCVSVVFGNISLRFLPVSFNQAIGATTPFFTAVFAYLMTFKREAWLTYLTLVPVVTGVIIASGGEPS
          S..FC.SVV.GN.SLR..PVSFNQAIGATTPFFTA.FA.L.T.K.E....Y..L.PVV.G...AS..EP.
Retrocopy SCIFCFSVVCGNTSLRYIPVSFNQAIGATTPFFTAIFAFLITCKKESAEVYFALLPVVFGIVLASNSEPL

Parental  FHLFGFIMCVAATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVFLLPATLIMEENVVGITLALA
          F.LFGF..C...TA.RALKSV.QGILL.SE.EKL.SMNLLLYMAP.A...LLP.TL..E.NV...TL..A
Retrocopy FNLFGFLVCIGSTAGRALKSVVQGILLTSEAEKLHSMNLLLYMAPMAAMILLPFTLYIEGNVARVTLEKA

Parental  RDDIKIIWYLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVSILIFRNPVSVTGMLGYSLT
          R.D..II..LL.N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA..VS..IFRNPV.V.GM.G...T
Retrocopy RSDSFIIFLLLGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAFVSVMIFRNPVTVMGMTGFAVT

Parental  VFGVILYSEAKKRSK
          V.GV.LYSEAKKRSK
Retrocopy VMGVVLYSEAKKRSK

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_6 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6 ,
Vitis vinifera	VIT_13s0019g03270	1 retrocopy	retro_vvin_10,