RetrogeneDB ID: retro_tcac_23

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 9:38052720..38054010(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_041506
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_011909
• Aliases: None
• Description: None

Sequence

>retro_tcac_23
ATGCAGGCGGTTTCTCCTACACAAAATCTTAACTCTTCTATAATTCGGCCGTCGAAGCCTCGGCTCAACCAGCTAACTCG
GTTCGCCGTTCGCTGCGTCCACCGGTCTGATTCGGTCCAATTCCCCAATGGAGTCGGTTCAAGCCGCGCCGATTGGCAAA
GCTCCTGTGCCATCCTTTCTAGCAAAGTCTTTTCTCAGGACCAAGGTTCCGGTGACAAATCCACTCCTCCCTCCGCTTCG
GACCACCTCGCCCCCGCCGTTAACGGCCACAAGACCTCCATCGATCTCAACCTAGTCCCAATCGACAAAAACAACAAGCC
TCAACCACCTTCCCCACTGCCTCCACAAAAACCGCTAACCATCACCGACTTGTCCCCGGCTCCGATGCATGGCTCTCAGC
TGCGCGTAGCCTACCAGGGAGTACCTGGCGCGTACTCCGAAGCTGCTGCGGGAAAGGCTTATCCTAACTGTGAAGCCATC
CCTTGTGACCAGTTCGAAGTCGCGTTTCAAGCAGTTGAGCTTTGGATCGCCGACCGAGCCGTGTTACCAGTGGAAAACTC
ACTCGGCGGCTCGATTCATAGGAACTACGATCTACTTCTCCGGCACCGCCTCCACATCGTCGGCGAAGTCCAACTCCCAG
TCCACCACTGCCTGTTAGCTCTCCCAGGAGTCCGCAAAGAGTACCTTACGCGTGTCATTTCTCATCCACAAGCTCTCTCC
CAGTGTGAACACACACTCACCAAACTCGGTCTCAACGTCACGCGCGAAGCTGTCGACGACACAGCCGGAGCGGCGGAGTA
CATCGCAACCAACAACCTTCGCGACACCGCCGCCATAGCAAGCGCACGCGCCGCGGAACTCTACGGACTCCAAGTCCTTG
CCGATGGAATCCAGGACGATTCGGGAAACGTCACGCGCTTCGTCATGCTAGCTCGGGAGCCAATCATCCCGCGTACGGAT
CGGCCATTTAAAACGAGCATCGTTTTCGCGCACGACAAAGGGACGAGCGTGCTTTTCAAAGTGCTGTCTGCGTTTGCGTT
TAGGAACATCAGCCTAACGAAAATCGAGTCGCGGCCGCACCGCAACAGGCCGATCCGGTTGGTCGACGACGCCAATGTGG
GAACTGCCAAGCATTTTGAGTATATGTTTTACGTGGATTTCGAAGCGTCGATGGCGGAGGTCAGGGCCCAAAACGCGTTG
GCTGAGGTCCAGGAGTTCACGTCATTCTTGAGGGTGTTGGGAAGTTACCCCATGGATATGACGCCATGGTGCCCCTCAAG
GGAAGATTAG

Alignment

ORF - retro_tcac_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.56 %
• Parental protein coverage: 81.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPLTVADLSATPDDSSKVRISFKGTLGSYNEDAALKAYPKCKTVPCDEFEDAFKAVELWLAEKAVLPIEN
          KPLT..DLS..P...S..R....G..G.Y.E.AA.KAYP.C...PCD.FE.AF.AVELW.A..AVLP.EN
Retrocopy KPLTITDLSPAPMHGSQLRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVEN

Parental  SSGGSIHRNYDLLLRHRLHIVGEVQLPVNFCLLALPGVRIEQLKRVLSHPQALALSDIFLSKLG--VARE
          S.GGSIHRNYDLLLRHRLHIVGEVQLPV..CLLALPGVR.E.L.RV.SHPQAL......L.KLG..V.RE
Retrocopy SLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVTRE

Parental  NVDDTASAAQYVASNGLRDAAVVASIRAAQVYGLNVLAEKIQDDPDNITRFLVLARDPIISRTDKPFKTS
          .VDDTA.AA.Y.A.N.LRD.A..AS.RAA..YGL.VLA..IQDD..N.TRF..LAR.PII.RTD.PFKTS
Retrocopy AVDDTAGAAEYIATNNLRDTAAIASARAAELYGLQVLADGIQDDSGNVTRFVMLAREPIIPRTDRPFKTS

Parental  IVFTLEEGPGILFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNTGAAKYFDYLFYIDFEASMAEPRA
          IVF....G...LFK.L..FA.R.I.LTKIESRP.R.RP.R.VDD.N.G.AK.F.Y.FY.DFEASMAE.RA
Retrocopy IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYVDFEASMAEVRA

Parental  QNALGHLQEFATFLRVLGCYPMDTT
          QNAL...QEF..FLRVLG.YPMD.T
Retrocopy QNALAEVQEFTSFLRVLGSYPMDMT

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_23 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
Theobroma cacao	TCM_011909	1 retrocopy	retro_tcac_23 ,
Vitis vinifera	VIT_12s0059g00750	1 retrocopy	retro_vvin_5,