RetrogeneDB ID:

retro_opri_987

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_5297:73398..73674(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSOPRG00000007092
Aliases:None
Description:ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]


Retrocopy-Parental alignment summary:






>retro_opri_987
CAGCAGATTAGGAATCTGATTAAGGATGGGCTGATTATCCACAAACCAGTGACCGTCCACTCCCGGGCTCAGTGCCAGAA
GAACACCCTGACCCGCAGAAAAGGCAGGCACATGGGCATAGAGAAGCATAAGGCTACAGCCAAAGCGCGCATGCTGGAAA
AGGTGACCTGGATGAGGAGGATGCGGATCCTGCGCCGCCTGCTCAGGAGATACCAGGAGTCCAAGAAGATTGACCGCCAC
AGGTACCAGAAGGTGAAGGGAAGCATGTTCAAAAAT

ORF - retro_opri_987 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.21 %
Parental protein coverage: 60.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRR
QQIR.LIKDGLII.KPVTVHSRA.C.KNTL.RRKGRHMGI.K.K.TA.ARM.EKVTWMRRMRILRRLLRR
RetrocopyQQIRNLIKDGLIIHKPVTVHSRAQCQKNTLTRRKGRHMGIEKHKATAKARMLEKVTWMRRMRILRRLLRR
ParentalYRESKKIDRHMYHSLYLKVKGNVFKN
Y.ESKKIDRH.Y.....KVKG..FKN
RetrocopyYQESKKIDRHRYQ----KVKGSMFKN

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_987 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 11 parental genes, and 136 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000020605 retrocopies
Callithrix jacchus ENSCJAG000000085204 retrocopies
Microcebus murinus ENSMICG000000026635 retrocopies
Macaca mulatta ENSMMUG000000042352 retrocopies
Nomascus leucogenys ENSNLEG0000000074819 retrocopies
Ochotona princeps ENSOPRG00000007092 2 retrocopies
retro_opri_1220, retro_opri_987 ,
Procavia capensis ENSPCAG000000152281 retrocopy
Pongo abelii ENSPPYG0000000849220 retrocopies
Rattus norvegicus ENSRNOG0000000474137 retrocopies
Tupaia belangeri ENSTBEG0000000807731 retrocopies
Tarsius syrichta ENSTSYG0000000869810 retrocopies



Copyright © RetrogeneDB 2014-2017