RetrogeneDB ID:

retro_atri_48

Retrocopy
location
Organism:Amborella (Amborella trichopoda)
Coordinates:AmTr_v1.0_scaffold00157:211232..211490(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:AMTR_s00104p00132470
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_atri_48
CAACATAATGAAGTGGAGTTGTCAGCCCTAGGGATGGCTATTGCTATTGTGGTCACAATTGATGGGATTCTAAAGAACAA
TGGACTGACCATTGAGAAGAAGATCATGAATTCAACTATTGATATGAAAGTTGAATCGAGAGGGTGATCTATTTAGGAAG
AAAAGATCAAAATTTTGCTTGGGAAAACTGCAAATTTCGAGGAACTGATGGCCGCTATAGCTGACAAGAAAGAAATTGCA
TAAGTAAAGGAGCAAAGC

ORF - retro_atri_48 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.58 %
Parental protein coverage: 65.15 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQHNEVELSALGMAIATVVTIAEILKNNGLAIEKKIMTSTVDMKDESRGRPIQKAKIEILLGKTANFDELM
QHNEVELSALGMAIA.VVTI..ILKNNGL.IEKKIM.ST.DMK.ESRG..I...KI.ILLGKTANF.ELM
RetrocopyQHNEVELSALGMAIAIVVTIDGILKNNGLTIEKKIMNSTIDMKVESRG*SI*EEKIKILLGKTANFEELM
ParentalAAAAEEREIAEGEEQS
AA.A...EIA...EQS
RetrocopyAAIADKKEIA*VKEQS

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






Amborella trichopoda was not studied using RNA-Seq expression data.
Amborella trichopoda was not studied using ChIP-Seq data.
Amborella trichopoda was not studied using EST data.
Amborella trichopoda was not studied using FANTOM5 data.
retro_atri_48 was not experimentally validated.

Retrocopy orthology:
Amborella trichopoda 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 2 retrocopies.

Species Parental gene accession Retrocopies number
Amborella trichopoda AMTR_s00104p00132470 2 retrocopies
retro_atri_18, retro_atri_48 ,



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