RetrogeneDB ID:

retro_opri_862

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_38643:1550..1975(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOPRG00000012290
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opri_862
CTGAATATCTCCTTCTCAGCTCCTGGCTGCCAAAAACTCATTGCAATGGATGATGAACATAAACTTTGTACTTGTGAGGA
GAAGCGTACGGTCACAGAAGTTGCTGCTGATGCTCTGGGTGAAGAGTGGAAGGGTTATGCCATCTGGCTCCGTGATGGAA
ATGACAAGCAAGGCTTTCCCGTGAACCAGGGTTTCTTGATCCATGACTGAGTCCACCTATTGCTGAGTGAGGAGGCTTCC
TATTACAGACCAAGAAGAACTGGAGAAAGAAAGCACAAATCTGTTTGGGGCAGCGTTGTCAATGTCAACTTGAATGTTTT
CAACATGGTTATTGTAAAGAAGAAATGAGATAAAAATAGTCCCGAATGACTGATATTGGGATGCCTCATCACGTGGGTCC
TAAAAGAGCCAGTAGAATCTGCAAA

ORF - retro_opri_862 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGR
LNISF.A.GCQKLI..DDE.KL.T..EKR..TEVAADALGEEWKGY......GNDKQGFP..QG.L.H..
RetrocopyLNISFSAPGCQKLIAMDDEHKLCTCEEKRTVTEVAADALGEEWKGYAIWLRDGNDKQGFPVNQGFLIHD*
ParentalVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKG-EKDIP-GLTDTTVPRRLGPKRASR
V.LLLS...S.YRPRRTGERK.KSV.G..V..NL.V.N.VIVKK...K..P...TD...P...GPKRASR
RetrocopyVHLLLSEEASYYRPRRTGERKHKSVWGSVVNVNLNVFNMVIVKKK*DKNSP<RMTDIGMPHHVGPKRASR
ParentalIRK
I.K
RetrocopyICK

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_862 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 35 parental genes, and 412 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000176341 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000292514 retrocopies
Canis familiaris ENSCAFG000000016154 retrocopies
Choloepus hoffmanni ENSCHOG0000000462215 retrocopies
Callithrix jacchus ENSCJAG000000206126 retrocopies
Cavia porcellus ENSCPOG000000037504 retrocopies
Dasypus novemcinctus ENSDNOG000000072411 retrocopy
Dipodomys ordii ENSDORG000000120572 retrocopies
Equus caballus ENSECAG000000161905 retrocopies
Echinops telfairi ENSETEG0000000158418 retrocopies
Ficedula albicollis ENSFALG000000030781 retrocopy
Felis catus ENSFCAG0000000254126 retrocopies
Homo sapiens ENSG0000013715416 retrocopies
Gorilla gorilla ENSGGOG0000000265213 retrocopies
Loxodonta africana ENSLAFG000000107664 retrocopies
Microcebus murinus ENSMICG0000000726224 retrocopies
Myotis lucifugus ENSMLUG0000000758827 retrocopies
Macaca mulatta ENSMMUG000000034121 retrocopy
Monodelphis domestica ENSMODG000000040951 retrocopy
Mus musculus ENSMUSG0000002849545 retrocopies
Nomascus leucogenys ENSNLEG0000001753214 retrocopies
Otolemur garnettii ENSOGAG0000001625421 retrocopies
Ochotona princeps ENSOPRG000000007516 retrocopies
Ochotona princeps ENSOPRG00000012290 5 retrocopies
Pongo abelii ENSPPYG0000001919315 retrocopies
Pan troglodytes ENSPTRG0000003915319 retrocopies
Rattus norvegicus ENSRNOG0000000766321 retrocopies
Rattus norvegicus ENSRNOG000000490258 retrocopies
Sorex araneus ENSSARG000000065496 retrocopies
Sarcophilus harrisii ENSSHAG000000054861 retrocopy
Sus scrofa ENSSSCG000000051696 retrocopies
Tupaia belangeri ENSTBEG0000000347433 retrocopies
Tarsius syrichta ENSTSYG000000085698 retrocopies
Tursiops truncatus ENSTTRG0000000178711 retrocopies
Vicugna pacos ENSVPAG0000000603010 retrocopies



Copyright © RetrogeneDB 2014-2017