RetrogeneDB ID: retro_tcac_50

Retrocopy location

• Organism: Cacao (Theobroma cacao)
• Coordinates: 7:15240424..15241151(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TCM_026940
• Aliases: None
• Description: None

Sequence

>retro_tcac_50
CTCTACCCTACCCTCATAAAGCATTCAATTCTTGCTGAGAACTTTCCCATCATACCATTGAGCCTAATGATGCCCGAGTT
AATGTCTTGGATGAGTGCTTTGGAGGGTTGTGCCAATTGTACAAGCCCAAAAATGAGGTTTCAATTTTCTTAGAAATTCA
TCATATAATTTGACTAGTTAGAGGTGCCCATCAAAGGCAAGGATTGGGCATTAGCTTCTTGTCTCACATCTATGTAATTG
ATGGCAGTTTTCATGTTTTACATGCATTTGAAGATTCAGACATCATCCATGTTGATGATTTTGTGGGTCTTGTAAGGAAT
TTAGAGATTATTAGTGTAAAATTACGGTTAAAGGACATTAAATTTATTGTAAAAAAGATAGAGCATATTGAAAAGAGCAT
GAAGAAGAGTAATGATAAGCAATTAAAAATAAAGCTTGAATTTTGTCAAAAGGTCATGGCATGAGCTTAAGATGGAATAG
ATGTTTGTCCAAGGGATTGGAAAGCGATTGATAGTAAGATATTAAATACTTTTCAATTGCTTAGTGTCAAGCCTGTTCTT
TATTTGGTTAACATGACTAACAAAGTTTACATCAAGTTCTTTCCAAAGATTCACGCTTTATGCAAAAACATGGTGGTGAA
CCAATCATTCCATTTAGTGGCATGTTTAAGAGAAACCTTGTTGATGTGGAACTTGAAAGAGCAAAAAAGTGTTGTGACGA
AAACAAG

Alignment

ORF - retro_tcac_50 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 62.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFNTLTKLSIPAENFPFC-TIEPNEARVNVPDGRFDWLCQLYKPKNEVSAFLEIHDIAGLVRGAHQGQGL
          L..TL.K.SI.AENFP...TIEPN.ARVNV.D..F..LCQLYKPKNEVS.FLEIH.I..LVRGAHQ.QGL
Retrocopy LYPTLIKHSILAENFPII<TIEPNDARVNVLDECFGGLCQLYKPKNEVSIFLEIHHII*LVRGAHQRQGL

Parental  GNSFLSHIRAVDGIFHVLRAFEDSDIIHVDDSVDPVRDLETISAELRLKDVEFIEKKVEDLEKSMKRSND
          G.SFLSHI...DG.FHVL.AFEDSDIIHVDD.V..VR.LE.IS..LRLKD..FI.KK.E..EKSMK.SND
Retrocopy GISFLSHIYVIDGSFHVLHAFEDSDIIHVDDFVGLVRNLEIISVKLRLKDIKFIVKKIEHIEKSMKKSND

Parental  KQLKIELELCQKVKSWLEDGKDIRLGDWKAADIEILNTFQLLSAKPVVYLVNMTEKDYQRKKNKFLPKIH
          KQLKI.LE.CQKV.....DG.D....DWKA.D..ILNTFQLLS.KPV.YLVNMT.K.Y......F.PKIH
Retrocopy KQLKIKLEFCQKVMA*A*DGIDVCPRDWKAIDSKILNTFQLLSVKPVLYLVNMTNKVYIK----FFPKIH

Parental  A-WVQEHGGEPIIPFSGVFERNLVDMESEEAAKYCEENK
          A...Q.HGGEPIIPFSG.F.RNLVD.E.E.A.K.C.ENK
Retrocopy A<FMQKHGGEPIIPFSGMFKRNLVDVELERAKKCCDENK

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_50 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_026940	1 retrocopy	retro_tcac_50 ,