RetrogeneDB ID:

retro_tcac_8

Retrocopy
location
Organism:Cacao (Theobroma cacao)
Coordinates:5:4533332..4534007(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:TCM_022426
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:TCM_028816
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_tcac_8
ATGGCAGCTTCCTTAACAGTCTCAAGGTTTCTCTCGCCAACCGTCCTCTCTTTTTCCGCTACCACCACCAAACTTTACCC
TAAATCCTTTTCGTCGAAACTCTCCTTTTCTCCCCGTTCCCTCAACCTCCACCGCCGCCCTTCAAAACCCATTTCCTTTT
CCACCAAAACAACCCAAATCTCCGCCTCAATCTCCGTCGGAGACAAGCTTCCCGACGCAACCCTCTCCTACTTCGACGCC
GACGGAGAACTCCAAACCACCTCAGTCTCCTCCCTAACCGCTGGCAAAAAAGTCGTCCTCTTCGCCGTTCCGGGCGCTTT
CACTCCCACCTGTTCCCAAAAGCACCTCCCGGGCTTCGTCGAAAAATCGGGGGAGCTCAAAGCCAAAGGGGTCGATACCA
TTGCCTGCGTGTCGGTGAACGACTCGTTTGTGATGCGTGCGTGGAAGGAGAATCTGGGGATTAACGACGAGGTTCTGTTG
TTATCTGATGGGAATGGGGAGTTCACGAAGAAAATTGGGTGTGAATTGGATTTGAGTGATAAGCCCGTTGGGCTCGGAGT
CCGCTCCCGAAGATACGCGCTTTTGGCTGAAAATGGAGTCGTTAAGGTTCTTAATTTGGAGGAAGGTGGTGCTTTTACTT
TCAGCGGGGCTGAAGACATTCTCAAAGTGCTCTGA

ORF - retro_tcac_8 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.5 %
Parental protein coverage: 97.53 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAVGDTIPDGTLSYADEDDQILNVSVHSLAACKQVILVGVPGAFTPTCSLKHVPGFIEKAEELKSKGISEI
.VGD..PD.TLSY.D.D......SV.SL.A.K.V.L..VPGAFTPTCS.KH.PGF.EK..ELK.KG...I
RetrocopySVGDKLPDATLSYFDADGELQTTSVSSLTAGKKVVLFAVPGAFTPTCSQKHLPGFVEKSGELKAKGVDTI
ParentalFLISVNDPYVMKAWAKSYPENKHVKFFSDSSAAYIKTLGLDLDVSDR--GFGVRSQRFALLIDDLKVKVV
...SVND..VM.AW......N..V...SD......K..G..LD.SD...G.GVRS.R.ALL.....VKV.
RetrocopyACVSVNDSFVMRAWKENLGINDEVLLLSDGNGEFTKKIGCELDLSDKPVGLGVRSRRYALLAENGVVKVL
ParentalNVESGGQFKVSSAEDMLKSL
N.E.GG.F..S.AED.LK.L
RetrocopyNLEEGGAFTFSGAEDILKVL

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_8 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 10 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Arabidopsis thaliana AT1G659801 retrocopy
Arabidopsis lyrata fgenesh2_kg.2__836__AT1G65980.11 retrocopy
Glycine max GLYMA07G092401 retrocopy
Hordeum vulgare MLOC_129541 retrocopy
Populus trichocarpa POPTR_0018s090301 retrocopy
Prunus persica PRUPE_ppa012586mg1 retrocopy
Sorghum bicolor Sb03g0309501 retrocopy
Selaginella moellendorffii SELMODRAFT_1592251 retrocopy
Solanum lycopersicum Solyc07g020860.21 retrocopy
Theobroma cacao TCM_028816 1 retrocopy
retro_tcac_8 ,



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