RetrogeneDB ID:

retro_opri_872

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_39353:10026..10385(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IFT20
Ensembl ID:ENSOPRG00000005826
Aliases:None
Description:intraflagellar transport 20 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:30989]


Retrocopy-Parental alignment summary:






>retro_opri_872
CTGCATTTTGATATGCCAAGTAAGCCGCAAATATTGGACCCAGAGGTTCCCCAGCAGCCAATGGATCTCAGAGAAGGATG
GCAGGTACACTGCAAACAAGATTGTTCAGCTTCAGAAGATAGCTGGTGGTCTAAATGAACTTACTGGTCATCTTGTAAAA
GAAGCTGAAAATGAGAAAATGAAAGCCATTGCCACTGAGAACTTGCTCAAATCTCTAGTCCAGTGGAGAGCAGACAACAA
CAACAACTTCAAACACTTGTAAACGGAAAGAAAATGCAGTTAGAAAGCTACCAGTCTAAATATAAGCTTTGTGTGAAGTA
GAAGTACAGTAAAATAAATTTGTTGACCAATTTGCTTTC

ORF - retro_opri_872 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.1 %
Parental protein coverage: 76.92 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLHFDELNKLRVLDPEVMQQTTELKE-ECKDFVGKIGQFQKIVGGLIELVDQLAKEAENEKMKAIGSRNLL
LHFD...K...LDPEV.QQ...L.E........KI.Q.QKI.GGL.EL...L.KEAENEKMKAI...NLL
RetrocopyLHFDMPSKPQILDPEVPQQPMDLRE>DGRYTANKIVQLQKIAGGLNELTGHLVKEAENEKMKAIATENLL
ParentalKSIAKQR-EAQQQQLQALIAEKKMQLERYRVEYE-ALCKVEAEQNEFIDQFIF
KS....R...QQQQLQ.L...KKMQLE.Y...Y..ALC.VE...N.F.DQF.F
RetrocopyKSLVQWR<SRQQQQLQTLVNGKKMQLESYQSKYK<ALCEVEVQ*NKFVDQFAF

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_872 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 22 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000051112 retrocopies
Bos taurus ENSBTAG000000081101 retrocopy
Callithrix jacchus ENSCJAG000000125342 retrocopies
Cavia porcellus ENSCPOG000000031531 retrocopy
Echinops telfairi ENSETEG000000188432 retrocopies
Homo sapiens ENSG000001090831 retrocopy
Gorilla gorilla ENSGGOG000000045682 retrocopies
Microcebus murinus ENSMICG000000050741 retrocopy
Myotis lucifugus ENSMLUG000000087092 retrocopies
Macaca mulatta ENSMMUG000000191432 retrocopies
Monodelphis domestica ENSMODG000000192331 retrocopy
Mustela putorius furoENSMPUG000000143531 retrocopy
Mus musculus ENSMUSG000000011051 retrocopy
Nomascus leucogenys ENSNLEG000000018832 retrocopies
Oryctolagus cuniculus ENSOCUG000000077731 retrocopy
Otolemur garnettii ENSOGAG000000033332 retrocopies
Ochotona princeps ENSOPRG00000005826 6 retrocopies
Pongo abelii ENSPPYG000000080872 retrocopies
Pan troglodytes ENSPTRG000000089111 retrocopy
Sus scrofa ENSSSCG000000237191 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000075541 retrocopy
Tupaia belangeri ENSTBEG000000055572 retrocopies



Copyright © RetrogeneDB 2014-2017