RetrogeneDB ID: retro_tcac_13

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 5:31993819..31995904(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: TCM_025336
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_025338
• Aliases: None
• Description: None

Sequence

>retro_tcac_13
ATGAGAGCTGGATATCATGAGGATGTTGCTTCAGGGAGCAATGGAGTATTAGCGGTCAACCACACGGTGGTCTGTGACAA
TCCTCAACCCCTAACAATACTGCCTATCACGGCGCAAGATCCTCTTATGGCACGAAAAGAAGAAGAAGTAGCAGTCCAAG
CTCCAATTATTTCTCAATACAATGACCAAATCCGACCTCTGCTTGATGCCATTGACAGGCTCAGGCTTCTTATGGTCATG
AAAGAAGGCATACAACTCCCCACAATTGTTGTAGTTGGAGACCAATCATCAGGGAAGTCCAGTGTTCTTGAATCACTTGC
TGGCATTAGTCTTCCTCGAAGCCAGGGTATTTGTACCAGAGTACCCCTCATAATGAGGCTGCAAAGTCATCAAAGTCCAG
CGCCAGAGCTTCACTTGGAGTACAATGGCAAGATAGTCCCTGTAGAGGAATCCGATATCACAACTGCCATAAATCTTGCA
ACTGATGAGATTGCAGGTCATGGAAAGGGCATATCTAACACACCGCTTACTTTGGTGGTGAAAAAGGATGGTGTTCCTGA
TCTTACTATGGTTGATCTTCCTGGTATTACTAGAGTGCCTGTTCAAGGTCAGCCTGAGAATATCTATGAGCAGATCAGAG
ATATTATCATGGAGTATATAACACCCGAGGAAAGCATCATCCTCAATGTTTTGTCTGCCACTGTTGATTTTTCTACCTGT
GAATCCATTAGGATGTCACAGAAAGTCGACAAGACGGGTGAAAGAACTCTTGCCGTGGTTACCAAGGCTGATAGGGCCCC
TGAAGACCTATTTGAGAAGGTTACTGCTGATGATGTGAATATAGGACTTGGTTATGTCTGTGTCAGAAATCGTATTGGTG
ATGAGTCCTATGAAGAAGCAAGGAGGGAAGAGGCCAGATTGTTCCAAACTCATCCACATCTGTCAAGGATTGATAAATCA
ATTGTGGGTGTCCCAGTGTTGGCCCAGAAACTTGTTCATATACAGGCAAATATTATTGCGAGGTGCTTACCGGTGATCGT
GAAGAACATTAATGAAAAGCTGAATGCAAATGCTTCAGAGCTGGAAAGAATGCCCAAGGCTTTGACTTCTGTTGCAGATG
CCATGGCAGCTTTTATGAGGATCATTGGAGCAGCTAAAGAATCCCTCAGGAAACTTCTTCTGAGAGGGGAATTTGATGAA
TACCCTGATGATAGTAGCAAGCATGGCACTGCTCGTTTGGTTGAAATGCTCAATCAATTCTCTGATGAGCTTCACGAGTC
TGAGGATAATGATCCCACAAAAGACTTTTTAATTGAGGAGATTAAGGTTTTGGAAGATGCTCAAGGAATTGGACTGCCAA
ATTTCCTTCCTCGCAGCGCATTCCTTCGCATCTTGCAGACAAAAGTTGATAGGATTTCCAATATGCCAATTGAATTTGCT
GAAAAGGTTTGGGACTGCATAGATGGGATGGTGACTTCTGTTTTGACGCGCCACTCGGAAATATATTACCAGCTTAAGGT
ATCTACGAAGAAAGCAGCTCATAATCTCGTCGAAAGGATGAGGGAGCAGTCGATGAATAGGGTGAAGGAGATTGTGCAGA
TGGAGAAGCTGACAGATTATACCTGCAATCCTGATTACATGGTGAAGTGGACTAAGCTCATGACTCAACAAGAAAGTTTC
CACAAGAAAGTAAATGATGCAGTAATGTACGGGCATTCCAGGGTGAGTCTGGAAGGTTTTGGGGATATTGAAGTTGAACA
TCTGAGGCGGCATCGTAATGTTCTGCATCAAGCTTTCGACCTGAAGGTGAGAATGACTGCCTACTGGAAGATAGTTCTGC
GAAGGTTGGTCGATTCCATGGCATTGCATTTGCAGTATAGTGTTCATAATCTTGTGAACAATGACATGGAGGAGATTGTG
AATGAGTTGATGGGGCCAGACGGGCGTGGAATTGAAAGGATGCTGGTGGAATCCCCTGCAATTGCTGGAAAGAGAGAGAA
GCTGAAAAGGAGCATCAAGCTGTTGAAGGAGTCCAAGGATGTCGTGGCCAAGATCATGGACAGGATTGCAGGTTATGATG
ATTAG

Alignment

ORF - retro_tcac_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 98.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDEDVASTSNGALVVSGMVVYDDSQLLTILPIKAEDPLMARGEE-VAVQAPIVSQYNDQIRPLLDAIDRL
          Y.EDVAS.SNG.L.V...VV.D..Q.LTILPI.A.DPLMAR.EE.VAVQAPI.SQYNDQIRPLLDAIDRL
Retrocopy YHEDVASGSNGVLAVNHTVVCDNPQPLTILPITAQDPLMARKEEEVAVQAPIISQYNDQIRPLLDAIDRL

Parental  KLLMVMKEGIQLPTIVVVGDQSSGKSSVLESLAGISLPRSQGICTKVPLIMRLQSHQSPTPELHLEYNGK
          .LLMVMKEGIQLPTIVVVGDQSSGKSSVLESLAGISLPRSQGICT.VPLIMRLQSHQSP.PELHLEYNGK
Retrocopy RLLMVMKEGIQLPTIVVVGDQSSGKSSVLESLAGISLPRSQGICTRVPLIMRLQSHQSPAPELHLEYNGK

Parental  TVSVEESHITTAINLATDEITGHVRDDSEIQKEL--QEDGVPDLTMVDLPGITRVPVQGQPENIYEQIRD
          .V.VEES.ITTAINLATDEI.GH....S.....L....DGVPDLTMVDLPGITRVPVQGQPENIYEQIRD
Retrocopy IVPVEESDITTAINLATDEIAGHGKGISNTPLTLVVKKDGVPDLTMVDLPGITRVPVQGQPENIYEQIRD

Parental  IIMEYIIPEESIILNVLSATVDFSTCESIRMSQKVDKTGERTRAVVTKADRAPEDLFEKVTADDVNIGLG
          IIMEYI.PEESIILNVLSATVDFSTCESIRMSQKVDKTGERT.AVVTKADRAPEDLFEKVTADDVNIGLG
Retrocopy IIMEYITPEESIILNVLSATVDFSTCESIRMSQKVDKTGERTLAVVTKADRAPEDLFEKVTADDVNIGLG

Parental  YVCVRNRIGDESYEEARREEARLFQTHPHLSMIDKSIVGVPVLAQKLVQIQANIIARCLPVIVKNISEKL
          YVCVRNRIGDESYEEARREEARLFQTHPHLS.IDKSIVGVPVLAQKLV.IQANIIARCLPVIVKNI.EKL
Retrocopy YVCVRNRIGDESYEEARREEARLFQTHPHLSRIDKSIVGVPVLAQKLVHIQANIIARCLPVIVKNINEKL

Parental  NANVSELERMPKALTSVADAMTAFMRIIEAAKESLRKLLLRGEFDEYPDDTSKHGTARFVEMLNHFSDEL
          NAN.SELERMPKALTSVADAM.AFMRII.AAKESLRKLLLRGEFDEYPDD.SKHGTAR.VEMLN.FSDEL
Retrocopy NANASELERMPKALTSVADAMAAFMRIIGAAKESLRKLLLRGEFDEYPDDSSKHGTARLVEMLNQFSDEL

Parental  RKSKESDSTKDFLIEEIKVLEDAKGIGLPNFLPRNAFLRILQRKVDRISIMPIEFAEKIWDYIDGMVTSV
          ..S...D.TKDFLIEEIKVLEDA.GIGLPNFLPR.AFLRILQ.KVDRIS.MPIEFAEK.WD.IDGMVTSV
Retrocopy HESEDNDPTKDFLIEEIKVLEDAQGIGLPNFLPRSAFLRILQTKVDRISNMPIEFAEKVWDCIDGMVTSV

Parental  MIRHSEIYYQLKGSTKRAAHNLIGKMREQSMNRMKEIVQMEKLTDYTCNPDYMVECTKLMAQQENFVRNV
          ..RHSEIYYQLK.STK.AAHNL...MREQSMNR.KEIVQMEKLTDYTCNPDYMV..TKLM.QQE.F...V
Retrocopy LTRHSEIYYQLKVSTKKAAHNLVERMREQSMNRVKEIVQMEKLTDYTCNPDYMVKWTKLMTQQESFHKKV

Parental  NAALKKTYGPYRVSLEGFGDIEVEHLRQHCNFVHQAFDLKMRMTAYWKIVLQRLVDSMALHLQYSVHSLV
          N.A....YG..RVSLEGFGDIEVEHLR.H.N..HQAFDLK.RMTAYWKIVL.RLVDSMALHLQYSVH.LV
Retrocopy NDAV--MYGHSRVSLEGFGDIEVEHLRRHRNVLHQAFDLKVRMTAYWKIVLRRLVDSMALHLQYSVHNLV

Parental  NNDMEEIVHELMGPDGRGIERMLVESPAIAKKREKLKKSIKLMKESKDVVAKIMDRIAGYDD
          NNDMEEIV.ELMGPDGRGIERMLVESPAIA.KREKLK.SIKL.KESKDVVAKIMDRIAGYDD
Retrocopy NNDMEEIVNELMGPDGRGIERMLVESPAIAGKREKLKRSIKLLKESKDVVAKIMDRIAGYDD

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_13 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Theobroma cacao	TCM_025338	1 retrocopy	retro_tcac_13 ,