RetrogeneDB ID:

retro_opri_460

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_1268:186505..186947(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOPRG00000017118
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1A
Ensembl ID:ENSOPRG00000003999
Aliases:None
Description:RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]


Retrocopy-Parental alignment summary:






>retro_opri_460
ACCGTGCAGTTCGTGACGGGCTCCTTCATTCGAGAAGTACGACCCGACCATCGAGGACTTCTACCGTAAGGAGATCGACG
GTGGACTCGTCGCCGTCGGTGCTGGAGATCCTGGACACGGGCGGGCACCGAGCAGTTCGCCTCCATGCGGGACCTGTACA
TCAAGAACGGGCCAGGGCTTCATCCTCGTCTACAGCCTCGTCAACCAGCAGAGCTTCCAGGACATCAAGCCCATGCGGGA
CCAGATCATCCGCGTGAAGCGGTACGAGCGCGTGCCCATGATCCTGGTGGGCAATAAGGTGGACCTGGAGGGCGAGCGCG
AGGTCTCGTACGGCGAGGGCAAGGCCCTGGCCGAGGAGTGGAGCTGCCCCTTCATGGAGACGTCGGCCAAAAACAAAGCC
TCGGTGGACGAGCTGTTCGCCGAGATTGTACGGCAGATGAAC

ORF - retro_opri_460 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.26 %
Parental protein coverage: 89.09 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalTVQFVQGIFV-EKYDPTIEDSYRKQVE-VDCQQCMLEILDT-AGTEQFTAMRDLYMKNGPG-FALVYSIT
TVQFV.G.F..EKYDPTIED.YRK....VD.....LEILDT.AGTEQF..MRDLY.KNGPG.F.LVYS..
RetrocopyTVQFVTGSFI>EKYDPTIEDFYRKEID>VDSSPSVLEILDT>AGTEQFASMRDLYIKNGPG>FILVYSLV
ParentalAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVN
.Q..F.D....R.QI.RVK..E.VPMILVGNK.DLE.ER.V....G..LA..W..C.F.E.SAK.K..V.
RetrocopyNQQSFQDIKPMRDQIIRVKRYERVPMILVGNKVDLEGEREVSYGEGKALAEEW-SCPFMETSAKNKASVD
ParentalEIFYDLVRQIN
E.F...VRQ.N
RetrocopyELFAEIVRQMN

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_460 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 19 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000053841 retrocopy
Canis familiaris ENSCAFG000000136861 retrocopy
Callithrix jacchus ENSCJAG000000133927 retrocopies
Dasypus novemcinctus ENSDNOG000000078095 retrocopies
Equus caballus ENSECAG000000164341 retrocopy
Erinaceus europaeus ENSEEUG000000104462 retrocopies
Echinops telfairi ENSETEG000000168932 retrocopies
Homo sapiens ENSG000001164731 retrocopy
Myotis lucifugus ENSMLUG000000105713 retrocopies
Monodelphis domestica ENSMODG000000013233 retrocopies
Mus musculus ENSMUSG000000687982 retrocopies
Nomascus leucogenys ENSNLEG000000040181 retrocopy
Ochotona princeps ENSOPRG00000003999 3 retrocopies
retro_opri_321, retro_opri_460 , retro_opri_875,
Pongo abelii ENSPPYG000000010281 retrocopy
Pan troglodytes ENSPTRG000000011021 retrocopy
Rattus norvegicus ENSRNOG000000324633 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278471 retrocopy
Tarsius syrichta ENSTSYG000000045213 retrocopies
Vicugna pacos ENSVPAG000000100331 retrocopy



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