RetrogeneDB ID:

retro_opri_663

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_22613:44578..45027(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLMO2
Ensembl ID:ENSOPRG00000002550
Aliases:None
Description:slowmo homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:15892]


Retrocopy-Parental alignment summary:






>retro_opri_663
ATGAAGAGCTGGACCTCAGAACACGTCTTTGATCACTCGTGGGAAGCCATTGCAACAGCTGCAAGGCAGAAACACCTCAA
TCCAGTGAACCCGAGTGTGGTTGGCGTGGACGTGCCAGACAGACACGTGGAACCCTCGTGAAAGCTAAAAAGTCACAGAC
TTCTCAGTACCCGGTGGGGGCTGCCTCCCGTTGTGCAGCCTCTTATCGGTGCAGCAAGAACCAAAATGTGAGTGCACAAG
CATTGTGTGGTTGACCCTGGAGAAAGAACCATCAATAGTTCATTTAAAAATATGGTTTCAGTTAGTGAAACACTTGTATA
CAAACCACATCCTCAGGACCTAGAAAAACTGTTCTAACTCAAGAAACCAGAATCACTGTGAAAGGCGCTGCCCTTAGCAG
TTACCTGGAAAGACTGATGGCAAGTACGATATCTTAAAATGACAGTAAG

ORF - retro_opri_663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.46 %
Parental protein coverage: 79.79 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMKIWTSKHVFHRPCATVKTAAMQKYPNLMNPSVVGVDVLDRHVDPAGKL-HHRLLSTEWGLPSIVKSLIG
MK.WTS.HVF........TAA.QK..N..NPSVVGVDV.DRHV.P..KL..HRLLST.WGLP..V..LIG
RetrocopyMKSWTSEHVFDHSWEAIATAARQKHLNPVNPSVVGVDVPDRHVEPS*KLKSHRLLSTRWGLPPVVQPLIG
ParentalAARTKTYVQEHSVVDPAERVMELNSTNISFTNMVSVDERLLYKPHPQD-PGRTVLTQEAIITVKGVSLSS
AARTK..V..H.VVDP.ER....NS....F.NMVSV.E.L.YKPHPQD.P..TVLTQE..ITVKG..LSS
RetrocopyAARTKM*VHKHCVVDPGERT--INSS---FKNMVSVSETLVYKPHPQD<PRKTVLTQETRITVKGAALSS
ParentalYLEGLMATSISSNANK
YLE.LMA..IS.N..K
RetrocopyYLERLMASTIS*NDSK

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_663 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 12 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000189054 retrocopies
Dasypus novemcinctus ENSDNOG000000145483 retrocopies
Echinops telfairi ENSETEG000000096513 retrocopies
Loxodonta africana ENSLAFG000000003001 retrocopy
Myotis lucifugus ENSMLUG000000149072 retrocopies
Macaca mulatta ENSMMUG000000075604 retrocopies
Monodelphis domestica ENSMODG000000166085 retrocopies
Mus musculus ENSMUSG000000162572 retrocopies
Oryctolagus cuniculus ENSOCUG000000056218 retrocopies
Ochotona princeps ENSOPRG00000002550 8 retrocopies
Rattus norvegicus ENSRNOG000000466442 retrocopies
Sorex araneus ENSSARG000000046712 retrocopies



Copyright © RetrogeneDB 2014-2017