RetrogeneDB ID:

retro_opri_152

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2937:274049..274417(-)
Located in intron of:ENSOPRG00000001263
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL31
Ensembl ID:ENSOPRG00000001204
Aliases:None
Description:ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]


Retrocopy-Parental alignment summary:






>retro_opri_152
ATGGCTCCCGCAAAGAAAGGCAGCAACAAGAAGCGCCGTTCTGCCATCAACGAGGTGGTGACGCGGAAGTACACCATCAA
CATCCACAAGCACATCCATGGAGTGGGCTTCAAGCCAGCTCCCCAGGCGCTGAAGGAGATCCGGAAGTTTGCCGTGAAAG
AAATGGGTACGCCAGATGTGCGCATTGATACGAGGCTCAACAAAGCTGTGTGGGCCAAAGGAATAAGGAACGTCCCGTCC
GCATCCGTGTGAGGTTGTCCAGGAAACCTAACAAGGATGAAGATTCGCCCAACAAGCTCTATACTCTGGTTACCTAAATG
CCTGTCACCACTTTCAAAAATCTACAAACTGTCAATGTGGATGAGAAC

ORF - retro_opri_152 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
MAPAKKG..KK..RSAINEVVTR.YTINIHK.IHGVGFK..AP.ALKEIRKFA.KEMGTPDVRIDTRLNK
RetrocopyMAPAKKGSNKKR-RSAINEVVTRKYTINIHKHIHGVGFKP-APQALKEIRKFAVKEMGTPDVRIDTRLNK
ParentalAVWAKGIRNVP-YRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN
AVWAKGIRNVP..RIRVRLSRK.N.DEDSPNKLYTLVT..PVTTFKNLQTVNVDEN
RetrocopyAVWAKGIRNVP<VRIRVRLSRKPNKDEDSPNKLYTLVT*MPVTTFKNLQTVNVDEN

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






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.