RetrogeneDB ID:

retro_tcac_3

Retrocopy
location
Organism:Cacao (Theobroma cacao)
Coordinates:3:31840587..31841529(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:TCM_016205
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:TCM_032188
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_tcac_3
ATGGTTAAACGGCTTCTTCCTGGCCATTTGAGATTTTCTCGGCGACCTCTCTATGGGTTCTTTCCCCATCTGCAAAGGGT
CTCCGGAAGGGTTGAAAAGAAAAAGTCGGACAGGGCAATTTTAAAGCTCTGTTCAAGACAAAGACCTGAATTGGAGGCAA
CAGGTAAAGGGATTAACGCAGTTGAAGCAAAGGACAAGACATTAGAGTTGGTGAATAAGGGAAGAAATCAGTTGGTGAGG
AACGAAACGATATCTGAGGTCGCAGCATTTGAGCTCCCTGGTATTCCCTTGGCACATTCAGAACCAGACAGAAAATCCGG
AGTAACCTTTGTTCTCGAGCAAGCCTCATTGGTTTGTGCTAAGGTTGGAAGGAGATACCCGATTTTAAACTCCAATGAAC
ATGCGGCCTTCTTGCGGAAAAAGAATAAGAATCCTTATAAATACAGACCTGACATCATTCATGAGGTGCTAAGTAGAATT
ATAGATAGCCGACTCTGCAAGTCGGGTAGGATACAAGCTATATATGTGAAGACTGACGAAGGGGTCTTGATTAAAGTTGA
ACCAAATACTCACATACCAAGGACACCACGACGTTTTAGGAATATGATGGCTGAGTTATTGCAAAAGTTGAGTGTCAAAG
CTGCGAATAAACATGGGAAGCTTTTACGCTTGGTTCAGAATCCTGTGACTCAACACCTTCCAGCCAACTCGCGTAAAATA
GGTCTTTCTTATAGCTCAAACCAATTGGTTCGCCTAAAGGACTACGTTGGTGGTATTAGTGACAACGAGAACCTTGTTTT
TGTGGTTGGTGCAATGGCTCACGGGAAAATTGATGCTGACTACGTAGATGATCTCATATCAATTTATGGAGGTCGGATGA
GTGCTAGAATGTGTTTGGAAGAAATATTCGAAGCTGTGGAGAGTAAATGGAAGATCTTATGA

ORF - retro_tcac_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.51 %
Parental protein coverage: 71.91 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEEEKESGAHELVGIPIAPSDQNTKKAGVIFVLEKASLEVAKVGKSFQLLNSDDHANFLRKNKKNPADYRP
E...E..A.EL.GIP.A.S.....K.GV.FVLE.ASL..AKVG.....LNS..HA.FLRK..KNP..YRP
RetrocopyETISEVAAFELPGIPLAHSEPD-RKSGVTFVLEQASLVCAKVGRRYPILNSNEHAAFLRKKNKNPYKYRP
ParentalDIAHQALLAILDSPINKAGRLQAVYVKTEKGVLFEVKPHVRIPRTYKRFSGIILQLLQQHKITAVGKRES
DI.H..L..I.DS...K.GR.QA.YVKT..GVL..V.P...IPRT..RF......LLQ.....A..K...
RetrocopyDIIHEVLSRIIDSRLCKSGRIQAIYVKTDEGVLIKVEPNTHIPRTPRRFRNMMAELLQKLSVKAANKHGK
ParentalLLRLIKNPVTQYFPVNSRKIGFSYSSEKLVKMSKYVDAVGDDVNLVFMVGAMAHGKIETEYVDDFIAISG
LLRL..NPVTQ..P.NSRKIG.SYSS..LV....YV....D..NLVF.VGAMAHGKI...YVDD.I.I.G
RetrocopyLLRLVQNPVTQHLPANSRKIGLSYSSNQLVRLKDYVGGISDNENLVFVVGAMAHGKIDADYVDDLISIYG
ParentalYPLSAAMCIARITEALAEKWNIL
...SA.MC...I.EA...KW.IL
RetrocopyGRMSARMCLEEIFEAVESKWKIL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Theobroma cacao was not studied using RNA-Seq expression data.
Theobroma cacao was not studied using ChIP-Seq data.
Theobroma cacao was not studied using EST data.
Theobroma cacao was not studied using FANTOM5 data.
retro_tcac_3 was not experimentally validated.

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_032188 1 retrocopy
retro_tcac_3 ,



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