RetrogeneDB ID: retro_tcac_20

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 8:889080..890853(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_033966
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_025075
• Aliases: None
• Description: None

Sequence

>retro_tcac_20
ATGTCGGGTTCTGAGGACGACAACAACCTTGGCAACGACGATGGCGATTATTACTTCTGTAACGCGGAAGATACAGAGGA
TGATGACGAGGGGATTGCTCTACAAGAAGATGAAACCGATAATCTCCCTAGGTCGCACCAGAATTATACTGTTCTGAAAG
AAGCGGATATACGTCACCGTATGGAGGATAGTATCGGTGAAGTCTCCGGTGTGCTTTCCATCTCGAAAGTCGAGGCAAGT
ATCTTACTCCTTCACTATAATTGGAGTGTGGGTAAAGTACATGATTCATGGTTTACTGATGAAGGTGAAGCCCGTAAAAA
GGCTGGCTTGGTTGTGAAACCATTGATCGAATTGCCCGATCATGGCGATATTCTTTGTAGAATCTGCTTTGAATCTTACT
CTCGAGATGGGATTAAGTCCACAGTGTGTGGGCATCCTTATTGCAGTGATTGTTGGAGTTCTTATATTAAAACGGCCATT
GCTGATGGCCCTGGAAGTTTATTGCTCAAGTGTCCCGAGCCATCTTGTCGTGCTGCTGTGGGTGAAGACATGATTGGTGT
ATTTGCATCTGAGGAAGAGAAAAAGAAGTATTCTGGTTACTTTGTTATGTCATATATCGAAGATAGCAAGATGATCAAGT
GGTGTCCTGGTCCAGGCTGTGAAAACGCTATTAATTTTGATGCTGGGAGTACAAATTTCGATGTTTCTTGTGCTTGCTCT
CATTTGTTTTGCTGGAATTGTAGTGAAGAAGCTCATCGTCCTGTGGACTGCGAAACTGTGAGAAAATGGATAATGAAGAA
CAGCTCGGAGGCTGAGAATGTGAATTACATTCTAGCTTTTACCAAGCCTTGTCCCAAATGCAGAAGACCAATCGAGAAAA
ACATGGGTTGTTCCCACATGTCATGTATGGCACCTTGCTATTATCAATTTTGCTGGCTATGCCTTAAAGATTGGAGCAAT
CATGGTGCTTGTAATCGTTATAATCAGGATCCCGAAGAGGAAAGAAGAGAGAAGGCAAAGAAATATATGATGAGATACTC
TCACTACTTTGAACGTTGGGCGACCAATCAAAAGTCAATGAAAAAGGCTGCTGCCGATATGGAAAATGTGCAAAGCAATC
AGTTAGAGATTCTTGCTCGCATTCAACTCCTACCTGAGACTCAATTCAGTTTTCTAACAGAGGCTTGGCAACAGATAGTT
GAATGTAGAAGGGTGCTTGCATGGACATATGCCTATGGGTACTACTTGCCTGATCAAGACCCGGCTAAAAGGAACCTGTT
TGAGTACTTGCAAGGTCAGGCTGAGTCTGGCTTGGAAAGGCTTCATGATTGCGCAGAGAAGGAGCTTCGACCATTCCTGA
AAGATCAGCACCCGGAAAATGAATTCATCGACTTCCGTAAAAGGCTTTCTGTGCTCACCACGGTGACTAGGAATTACTTT
GATAACTTGGTCACAGCTTTAGAGAATGGACTATCTGATGTAAAATCCCAGAATTCTTCAAGTGTCTCAAAGAAACCCAG
AAGGGAATCGACAATGAATACTGCTGATGCTGCTGATGTTGTTGCTGGAGCTCAAATCTTGACTACACGCATAAAGGCTT
CCTTTTCCGAGGGACCATGGGTTTGTCCCTATTGTAGCTATAGAAACAATGGTTCTGCCACGTCTTGTGGAATGTGTGCA
AGACGAGGTACTTGGGCTTGTGACCACTGCACCTTCGCCAATACGAGGACCGCCACAACATGTTTCATGTGTCTCGAACC
CCGGCAACCTTAG

Alignment

ORF - retro_tcac_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.31 %
• Parental protein coverage: 54.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGEDDFYSGGDDDAGAMAAYDDSDADVADYEFIDNDSDDSDDLVSHRYQQNYTVLSEVDICQRQEDDIMR
          SG..D....G.DD............D..D.E.I....D..D.L...R..QNYTVL.E.DI..R.ED.I..
Retrocopy SGSEDDNNLGNDDGDYYFCNAEDTED--DDEGIALQEDETDNLP--RSHQNYTVLKEADIRHRMEDSIGE

Parental  VSTVLSISKVEAGILLRYYNWSVSKVHDEWFADEEKVRRSVGLLEKPVVPFPDGREMTCGICFETYPYDR
          VS.VLSISKVEA.ILL..YNWSV.KVHD.WF.DE...R...GL..KP....PD.....C.ICFE.Y..D.
Retrocopy VSGVLSISKVEASILLLHYNWSVGKVHDSWFTDEGEARKKAGLVVKPLIELPDHGDILCRICFESYSRDG

Parental  LHTAACGHPFCNSCWAGYISTSINDGPGCLMLRCPDPSCAAAVGQDMINVLASDEDKEKYFRYFIRSYVE
          .....CGHP.C..CW..YI.T.I.DGPG.L.L.CP.PSC.AAVG.DMI.V.AS.E.K.KY..YF..SY.E
Retrocopy IKSTVCGHPYCSDCWSSYIKTAIADGPGSLLLKCPEPSCRAAVGEDMIGVFASEEEKKKYSGYFVMSYIE

Parental  DNRKTKWCPAPGCDYAVDFILGSGSYDVTCRCSYSFCWNCTEEAHRPVDCGTVAKWILKNSAESENMNWI
          D....KWCP.PGC..A..F..GS...DV.C.CS..FCWNC.EEAHRPVDC.TV.KWI.KNS.E.EN.N.I
Retrocopy DSKMIKWCPGPGCENAINFDAGSTNFDVSCACSHLFCWNCSEEAHRPVDCETVRKWIMKNSSEAENVNYI

Parental  LANSKPCPKCKRPIEKNQGCMHITCTPPCKFEFCWLCLGAWSDHG
          LA..KPCPKC.RPIEKN.GC.H..C..PC...FCWLCL..WS.HG
Retrocopy LAFTKPCPKCRRPIEKNMGCSHMSCMAPCYYQFCWLCLKDWSNHG

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_20 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_025075	1 retrocopy	retro_tcac_20 ,