RetrogeneDB ID:

retro_opri_981

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_524:85323..85717(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSOPRG00000012620
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_opri_981
GCACTGAAGCCAAGAAGCGCACTGAGAGGTGGTGTTCACAGCCACGAGAGAAAGAGAATGCACCCACATTCTGGAGGCCC
AAGACCGTTTGTCTCTGCTGGCACCCCACACATCCTTGGAAGAGCGGCCCCAGGAGGACTGAGCTTGACCACTCTGCCAT
CACCAAGTTTCCTTTGACCATGGAGTCTGCTGTGAAAAAGACAGACAACACACTCATGTTCATTATAGATGTCAAGGCCA
ACAAGACTCGATCACACAAGCTGTGAAGAAACTCTATGAAACTAATATGGCCAGAGTCAATACTTAGATCAGACCTGACT
GAGAAAAACAGGCAGACGTGTTGCTGGCTCCTGATTATGATGCTTCGGATGTTGCCAACAAAACCGGGATCATC

ORF - retro_opri_981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.87 %
Parental protein coverage: 92.52 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalALKAKKAVLKGVHSHKKKKIR-TSPTFRRPKTQRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKK
ALK...A...GV..H.....R...PTF.RPKT..L...P..P.KS.PRR..LDH.AI.KFPLT.ESA.KK
RetrocopyALKPRSALRGGV--HSHERKR<NAPTFWRPKTVCLCWHPTHPWKSGPRRTELDHSAITKFPLTMESAVKK
ParentalIEDNNTLVFIVDVKANKHQ-IKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII
....NTL.FI.DVKANK...I.QAVKKLY....A.VNT.IRPD.EK.A.V.LAPDYDA.DVANK.GII
RetrocopyTD--NTLMFIIDVKANKTR<ITQAVKKLYETNMARVNT*IRPD*EKQADVLLAPDYDASDVANKTGII

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.