RetrogeneDB ID: retro_tcac_7

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:2381313..2383689(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_030989
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_007148
• Aliases: None
• Description: None

Sequence

>retro_tcac_7
ATGGCGTTTAATAATTTAAGCTCGCCCACCACCGGAATGGAAGGTCAAGTCAGAGTGGAGGAAGTCTGTCTTAAATTTCC
TCCCAAAGTCAGCTCCCCAGGCTTGGCTGCATTGATCTTGAGCAACGAACAAAAAGAAACATTCATGGACTTTGCTGGGC
CAAGACTTCATTTCCAGATGATTCTCATTTTTGTTTTCACTCAAGTTATTCATAATATGCTCAAACACCTGGGATTGCCA
ATGTTCATCTCCCAGATTCTTGTAGGAATGATACTCGGTCCTATGGTTTTCAAGGGTCACGATTCATTGGTTACAATGTC
AGAGGATAGTGTTCAGGTTCTTGGTACGGTGGCATCCTTCGGCTATATATTCTTTTTGTTTTTAAGTGGGGTGAAGATGG
ACCTGAGCATGACATACAAGGCTGGAAGGATGGCCGTATGCATTGGTTTACTAGCAGTGGTGGTGCCTCTGACATTTTGT
TTGATAACGGTTAAGGCCCTTAGCACAGACGGCGAATTGTTTGAAAACAACAGTTTATTTCTTGCAGTAACAAATTCCGG
AACTTCATTTCCGGTCATACATTGCCTTCTCGATGAGCTGAAAATCCTGAATTCAGAACTTGGCAGGCTAGGACTATCAG
CAGCACTTGTCAGTGACATTGCGTCATTAGTTCTTATGAATCTCAGCCAATGGGTGAAGGTAGCGCAAGAAATATCAGCA
ACGCTGGTTCTCAAGGATTTTGGACTGGCTATAGCCTTTGTTTTAGTAGTGGTGTTTGTGTTGCGACCGGGGATGAAATG
GATGGTGAGACGCACGCCTGAGGGTGGCCAGATAAAAGATGTATTCCTTTATGCCGTTATTTTGGGGTTCATGTCGTCTC
CTAGGATAAACGAATTCTTTAATATATTTCTTCTCTTTGGCCCATTTATTTTGGGATTGGCTGTCCCAGATGGACCCCCA
TTGGGATCTGCTCTGGTCGAAAAGTTGGACCCAGTTGTTTCAGGGTTGTTTTTGCCTTTGTTTGCATCAACATGCGGCAT
GAGGATTGATCTGTCTTACCTCAAAAAGAGTACGGAATATGCACAAAACCAAGCCATTGCAGCTGTTGTAGCAGTTATTT
TCAAATTTGGGGTCTCTCTGGCGCTGCCATTATTATGCAAGATGCCCCTGAGGGATTCTTTGGCACTTGCTTTTATAATG
ATAACCAAAGGTATCGTTGAGATGGGTTCGTATAGCTTCTTATTTGACAACATGGTTATATCTCAAGATCTATTCGCTTT
CATGTCTATTATCATCATTTTGTTAGCAAGCATTGTGCCAATACTTGTGAAAAGACTCTATGATCCTTCAAGGAAGTATA
TAGGTTACCAAAAACGGAGCATCATGCATTCCAAGCTCAAAGAGGAGTTGCGAATGATTGGTTGCATTCACGTACCGGGT
AATGTCAATTCTATCATTAACATTTTGAATGCCTCCTGTCCAAACAGAGAAAACCCTATTGCTCTTGATGTCCTTCACCT
TGTTAAGCTCAGTGGGCGTGCCACACCCCTTTTCATTGCGCATCAAAAGCACAGGAAAACCCAGTCTAACAAATCTTACT
CTGAGAACGTTGTCCTAGCTTTTAATCAGTTTGAACGAGACAACTGGGAAGCTGTATCAGTGAATGTTTTCACTGCAGTC
TCTCCACCAAATTTGATGTACGAGGATATATGCAATCTCGCCCTAGACAAGCTCACATCCTTTATACTACTTCCATTTCA
TCGCAGATGGTACATTGACGGGAGCATTGAATCAGAAGACCAAGCCATCAGAAGCTTGAATTGTAGCATCCTGGAAAGGG
CACCTTGCTCAGTAGGGATCCTTGTTGAAGGCCGTCGCCCTCTAAAACGCTCCAATTCTAGAGACAAATTATCATCAGAG
TCATCATCATACAGCATCGCTGTGATTTTCTTGGGGGGTAAAGATGATAGGGAGGCGCTAGCGTTAGCCAAACGCATTTC
CCAAGATCAAAGGGTTAGCCTTACTGTAATTCATCTCAAAGGTACCAACAATTTAGGCGCCATCCTAGCTGATCTGGATA
GAATGCTTGATGATGAGATGTTGAGGGGTGTTAAGGAAGGTGGATACATAAGATACGTCGATAAGCAGGTAAATGATGGG
CCTGAAACCTCATCGTTTCTTCGATCTATTGTAGATGACCACCAGCTTATCATTGTTGGGAGACGATACAACACAGAAGA
TCCACGGACTTTTGGTCTTGAGGAATGGAGTGAATTTCAGGAGATTGGAATCATTGGAGACCTGCTTTCATCTGCAGATT
TTGGTGGCAATTATTCTGTGTTGATTGTGCAACAACAACAACTAAGGATTGCATAA

Alignment

ORF - retro_tcac_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFSNLSSSTTGMEGQGIVEEICLKFPPKVSSPGLAAYILSNEQNEKFTDFAAPRLHFQMIVIFALTQII
          MAF.NLSS.TTGMEGQ..VEE.CLKFPPKVSSPGLAA.ILSNEQ.E.F.DFA.PRLHFQMI.IF..TQ.I
Retrocopy MAFNNLSSPTTGMEGQVRVEEVCLKFPPKVSSPGLAALILSNEQKETFMDFAGPRLHFQMILIFVFTQVI

Parental  HYLLKHLGLPIFISQILAGILLGPMVFKGHNSLVTMSEDSVQVLGTVASLGYIFFLFLSGVKMDLSMTYK
          H..LKHLGLP.FISQIL.G..LGPMVFKGH.SLVTMSEDSVQVLGTVAS.GYIFFLFLSGVKMDLSMTYK
Retrocopy HNMLKHLGLPMFISQILVGMILGPMVFKGHDSLVTMSEDSVQVLGTVASFGYIFFLFLSGVKMDLSMTYK

Parental  AGRKAVCIGLLTVVVPLTFSLITVKALSTD-ELFKNNSFFLAVTYSGTSFPVIHCLLSELKILNSELGRL
          AGR.AVCIGLL.VVVPLTF.LITVKALSTD.ELF.NNS.FLAVT.SGTSFPVIHCLL.ELKILNSELGRL
Retrocopy AGRMAVCIGLLAVVVPLTFCLITVKALSTDGELFENNSLFLAVTNSGTSFPVIHCLLDELKILNSELGRL

Parental  GLSAALVSDMASLVLMNLSQWVKVAQEKSATLVLKDFGLAIAFFLVVAFVLRPGMKWMVKRTPEGGQIKD
          GLSAALVSD.ASLVLMNLSQWVKVAQE.SATLVLKDFGLAIAF.LVV.FVLRPGMKWMV.RTPEGGQIKD
Retrocopy GLSAALVSDIASLVLMNLSQWVKVAQEISATLVLKDFGLAIAFVLVVVFVLRPGMKWMVRRTPEGGQIKD

Parental  VFLYAVILGFMSSPRITGIFNIFLLFGPFILGLAVPDGPPLGSALVEKLDPVVSGLFLPLFASTCGMRID
          VFLYAVILGFMSSPRI...FNIFLLFGPFILGLAVPDGPPLGSALVEKLDPVVSGLFLPLFASTCGMRID
Retrocopy VFLYAVILGFMSSPRINEFFNIFLLFGPFILGLAVPDGPPLGSALVEKLDPVVSGLFLPLFASTCGMRID

Parental  LSYLKESKEYAQHQAIAAVVALIVKFGVSLALPLLCKMPMRDSLALACIMMSKGIVEMASYSFLNDNMVI
          LSYLK.S.EYAQ.QAIAAVVA.I.KFGVSLALPLLCKMP.RDSLALA.IM..KGIVEM.SYSFL.DNMVI
Retrocopy LSYLKKSTEYAQNQAIAAVVAVIFKFGVSLALPLLCKMPLRDSLALAFIMITKGIVEMGSYSFLFDNMVI

Parental  SQDVFAFMSIIIVLLASIVPLLVKRLYDPSRKYIGYQKRSIIHSKLNEELRMIGCIHVPGNVNSIINILN
          SQD.FAFMSIII.LLASIVP.LVKRLYDPSRKYIGYQKRSI.HSKL.EELRMIGCIHVPGNVNSIINILN
Retrocopy SQDLFAFMSIIIILLASIVPILVKRLYDPSRKYIGYQKRSIMHSKLKEELRMIGCIHVPGNVNSIINILN

Parental  ASCPNRENPIALDVLHLVKLSGRATPLFIAHQKHKNTLSNKSYSENVVLAFNQFERDNWEAVSVNVFTAV
          ASCPNRENPIALDVLHLVKLSGRATPLFIAHQKH..T.SNKSYSENVVLAFNQFERDNWEAVSVNVFTAV
Retrocopy ASCPNRENPIALDVLHLVKLSGRATPLFIAHQKHRKTQSNKSYSENVVLAFNQFERDNWEAVSVNVFTAV

Parental  SPPNLMYEDICNLALDKLTSFILLPFHRRWYIDGSIESEGQAIRSLNCSILERAPCSVGILVEGRRHLKR
          SPPNLMYEDICNLALDKLTSFILLPFHRRWYIDGSIESE.QAIRSLNCSILERAPCSVGILVEGRR.LKR
Retrocopy SPPNLMYEDICNLALDKLTSFILLPFHRRWYIDGSIESEDQAIRSLNCSILERAPCSVGILVEGRRPLKR

Parental  SNSRDILSSESSSYSIAVIFLGGKDDREALALAKRISQGQRVNLTVIHLKATNGLGAVLSDSDRLLDDEM
          SNSRD.LSSESSSYSIAVIFLGGKDDREALALAKRISQ.QRV.LTVIHLK.TN.LGA.L.D.DR.LDDEM
Retrocopy SNSRDKLSSESSSYSIAVIFLGGKDDREALALAKRISQDQRVSLTVIHLKGTNNLGAILADLDRMLDDEM

Parental  LRGVKESGYIRYVDEQVNDGPETSSFLRSIADNYQLIIVGRRYNTEDPRTLGLEEWSEFQEIGIIGDLLS
          LRGVKE.GYIRYVD.QVNDGPETSSFLRSI.D..QLIIVGRRYNTEDPRT.GLEEWSEFQEIGIIGDLLS
Retrocopy LRGVKEGGYIRYVDKQVNDGPETSSFLRSIVDDHQLIIVGRRYNTEDPRTFGLEEWSEFQEIGIIGDLLS

Parental  SADFGGNYSVLIVQQQQLRAA
          SADFGGNYSVLIVQQQQLR.A
Retrocopy SADFGGNYSVLIVQQQQLRIA

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_7 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_007148	1 retrocopy	retro_tcac_7 ,