RetrogeneDB ID: retro_tcac_5

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 8:3232362..3233670(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_034491
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_045111
• Aliases: None
• Description: None

Sequence

>retro_tcac_5
ATGGACTTCACTGCCACACTTCTCTTTTTTGCGCTTCTCATCTCATCCACCAAGGCTTTGGACCCTTGTGCCGCTCAGGC
AGATAACTCAGGCCTCTCCATCATTCCAATCTATGGCAAATGTTCACCATTCAACCCACCAAAACCTGACTCATGGGTCA
ACACAGTCATTAACATGGCCGCAAAAGACCCAGCGAGGGTCAAGTACTTGTCCAGCCTGGCGGCCCAGAAAACCACGGCT
GTTCCAATTGCTTCAGGCCAACAAGTTCTAAACATTGGCAACTATGTTGTAAGGGTCAAGCTCGGCACTCCAGGTCAGCT
CATGTTCATGGTACTTGATACTAGTAATGATGCTGCTTGGGTCCCATGCTCCGGATGCATTGGCTGCTCAGCTACCACTT
TCTCACCCAACACTTCTTCCAGTTACGGGTCACTGGATTGCTCCTTGCCCCAGTGCTCCCAGGTCCGCGGACTCTCGTGC
CCGGCAACTGGGGCTGCTGCATGCTCTTTTAACCAATCCTACGGTGGAGATTCATCGTTCTCTGCCACCTTGGTACAAGA
TTCCTTGGGATTAGCCAATGACATTCTCCCAAATTTTGCTTTTGGATGTATTAACTCTATCTCTGGTGGGTCAGTCCCAC
CCCAAGGGCTTTTGGGTCTGGGGCGGGGCCCCATGTCACTTCTTTCACAATCCGGGTCACTCTACTCCAGCGTGTTTTCC
TATTGTTTACCCAGTTTCAAGTCCTACTACTTCTCGGGTTCCCTCAAACTCGGGCCAGTAGGTCAGCCCAAAAATATTCG
GACCACCCCGCTCCTAAAAAACCCCCACCGGCCCTCACTTTACTACGTTAACCTAACAGGGGTCAGCGTAGGCAGGGTTC
GGGTCCCCATCGCCCCAGAATATATAGCATTTAACCCCAACACCGGGGCGGGGACCATAATCGACTCGGGTACGGTTGTA
ACCCGGTTTGTCCAACCCGTTTATGAGGCAATCCGGAATGAGTTTGTCAAGCACTTGAAAGGGCCATTCTCAACAATAGG
GGTATTTGACACATGCTTCGACGCTGCAGCAGAATCTGAGGCACCTTTAATAACGTTACATCTTGAAGGCTTGTCCATGA
CATTGCCAATGGAAAACAGCTTCCTACATTCCAGTGCAGGGTCACGCGCTTGCTTGGCCATGGCACCAGTTCCAAATAAC
GTGAACGCCGCCTTGAATGTGATAGCCAATTTGCAGCAGCAGAATCACAGGATTCTGTTTGATGTGGCCAATTCTCGCTT
GGGAATTGCTCGTGAAGTTTGTAACTAA

Alignment

ORF - retro_tcac_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.06 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFFSLAEGLHPKCDTQDHGSNLQVFHIYSPCSPFKPSKPLSWEEDLLQTQAKDQARLQYLSSLVAKKSV-
          L..S....L.P.C..Q...S.L....IY..CSPF.P.KP.SW........AKD.AR..YLSSL.A.K...
Retrocopy LLISSTKALDP-CAAQADNSGLSIIPIYGKCSPFNPPKPDSWVNTVINMAAKDPARVKYLSSLAAQKTTA

Parental  VPIASGRQIVQSPTYIVRAKIGTPPQTMLMAMDTSNDAAWLPCSGCLGCSSSVFDNAKSTTFKALGCQAG
          VPIASG.Q......Y.VR.K.GTP.Q.M.M..DTSNDAAW.PCSGC.GCS...F....S.....L.C...
Retrocopy VPIASGQQVLNIGNYVVRVKLGTPGQLMFMVLDTSNDAAWVPCSGCIGCSATTFSPNTSSSYGSLDCSLP

Parental  QCKQVPNPTCDGS---ACIFNMTYGG-SSIAANLSQDTITLATDPVPSYTFGCLQKTTGNSVPPQGLLGL
          QC.QV....C......AC.FN..YGG.SS..A.L.QD...LA.D..P...FGC.....G.SVPPQGLLGL
Retrocopy QCSQVRGLSCPATGAAACSFNQSYGGDSSFSATLVQDSLGLANDILPNFAFGCINSISGGSVPPQGLLGL

Parental  GRGPLSLLSQTQNWYQSTFSYCLPSFRSLNFSGSLRLGPVGQPLRIKYTPLLKNPRRPSLYFVNLIGIRV
          GRGP.SLLSQ....Y.S.FSYCLPSF.S..FSGSL.LGPVGQP..I..TPLLKNP.RPSLY.VNL.G..V
Retrocopy GRGPMSLLSQSGSLYSSVFSYCLPSFKSYYFSGSLKLGPVGQPKNIRTTPLLKNPHRPSLYYVNLTGVSV

Parental  GRKIVDIPPSDLAFNPTTGSGTIIDSGTVFTRLVATAYVAVRDEFRRRVRVTNVTSLGGFDTCY--TGPI
          GR..V.I.P...AFNP.TG.GTIIDSGTV.TR.V...Y.A.R.EF............G.FDTC.......
Retrocopy GRVRVPIAPEYIAFNPNTGAGTIIDSGTVVTRFVQPVYEAIRNEFVKHLK-GPFSTIGVFDTCFDAAAES

Parental  VAPTITFMFAGMNVTLPQDNLLIHSTAGSITCLAMASAPENMNSVLNVIANMQQQNHRVLFDVPNSRLGV
          .AP.IT....G...TLP..N...HS.AGS..CLAMA..P.N.N..LNVIAN.QQQNHR.LFDV.NSRLG.
Retrocopy EAPLITLHLEGLSMTLPMENSFLHSSAGSRACLAMAPVPNNVNAALNVIANLQQQNHRILFDVANSRLGI

Parental  ARELC
          ARE.C
Retrocopy AREVC

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_5 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
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10,
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5 ,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,