RetrogeneDB ID:

retro_opri_335

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_5354:471231..471780(+)
Located in intron of:ENSOPRG00000001219
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOPRG00000001234
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opri_335
GACGCGGAGGACGCGGTGCACGAGCGAGACGGCTACGATTACGACGGGTACCGTCTCCGGGTCGAGTTTCCACGGAGCGG
CCGCGGGCCGGGCCGAGGCGGAGGTGCAGGTGGATGGGGCGGAGCGCCCCGCGGCCGCTATGGCCCCCCATCCCGGCGGT
CCGACCACCGCGTGGTGGTCTCCGGACTGCCTCCGAGTGGAAGCTGGCAGGATTTGAAGGATCACATGCGCGAGGCGGGC
GATATATGTTACGCTGATGTCCACCGAGATGGCACCGGTGTCGTGGAGTTTGTACGGAAAGAAGATATGACCTATGCAGT
TCGAAAACTGGACAACACTAAGTTTAGATCTCACGTGGGAGAAACCGCCTACATCCGGGTGAAGGCTGATGGGCCCAGAA
GTCCCAGTTCTGGAAGATCTCCATCTCGAAGCCGCCGTCGCAGCCGAAGCCGTAGCAGAAGCAACAGCAGGAGTCGCAGT
TACTCCCCAAGGAGAAGCAGAGGATCACCACGCTATTCTCCCCGTCATAGCAGATCTCGCTCTCGTACA

ORF - retro_opri_335 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.35 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQ
DAEDAV..RDGYDYDGYRLRVEFPRSGRG.GRGGG.GG.GGAPRGRYGPPSRRS..RVVVSGLPPSGSWQ
RetrocopyDAEDAVHERDGYDYDGYRLRVEFPRSGRGPGRGGGAGGWGGAPRGRYGPPSRRSDHRVVVSGLPPSGSWQ
ParentalDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRS
DLKDHMREAGD.CYADV.RDGTGVVEFVRKEDMTYAVRKLDNTKFRSH.GETAYIRVK.DGPRSPS.GRS
RetrocopyDLKDHMREAGDICYADVHRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHVGETAYIRVKADGPRSPSSGRS
ParentalRSRSRSRSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT
.SRSR.RSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT
RetrocopyPSRSRRRSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT

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






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_335 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps 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 6 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000092551 retrocopy
Myotis lucifugus ENSMLUG000000110401 retrocopy
Otolemur garnettii ENSOGAG000000259501 retrocopy
Ochotona princeps ENSOPRG00000001234 2 retrocopies
retro_opri_335 , retro_opri_625,
Ochotona princeps ENSOPRG000000042341 retrocopy
Ochotona princeps ENSOPRG000000060063 retrocopies



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