RetrogeneDB ID:

retro_opri_847

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_3655:133742..134199(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PPA2
Ensembl ID:ENSOPRG00000007086
Aliases:None
Description:pyrophosphatase (inorganic) 2 [Source:HGNC Symbol;Acc:28883]


Retrocopy-Parental alignment summary:






>retro_opri_847
CCTCAGACTCGGGAAGACCCGGGACACAATGATAAACATACGGCTGTTGTGGCGGCAATGACCCAATTCATGTGTGTGAA
ACTGGAAGTAAGGAGTGTGCAAGAGGTGAAATGATCAAGGTGAAAGTTCTGGACATATTGGCTATGATTGACGAAGGGGA
AAGCGACCGGAAAGTCATTGCTATTAATGAGGACGATCCTGATGTGACCAATTACAATGATATTAATGATGTCAAACGGC
AGACACCTGGCTACCTAGAAGCTACTGTGGACTGGTTTAGAAGGTACAAGGTTCCTGATGGAAAACCAGAAAATGAATTT
GCTTTCAATGCGGAATCTAAAGATAAGGACTTTGCAGTTAGTATTATTAAAAGCACTCGTGGCTGTTGGAAAGTTGTAGT
ACTAAGAAGATGGGTGGAGAGGGAATCAGCTGCACGAATACGACAGTGGCGGAAAGC

ORF - retro_opri_847 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.65 %
Parental protein coverage: 51.69 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPQTWEDPGQTDEST-NCCGDNDPIDVCEIGSKVLTRGEVIPVKILGILALIDESETDWKLIAINANDPDA
PQT.EDPG..D..T..CCG.NDPI.VCE.GSK...RGE.I.VK.L.ILA.IDE.E.D.K.IAIN..DPD.
RetrocopyPQTREDPGHNDKHT<GCCGGNDPIHVCETGSKECARGEMIKVKVLDILAMIDEGESDRKVIAINEDDPDV
ParentalSKFDDIDDVKKFKPGYLEATLNWFRYYKVPDGKPENQFAFNGEFRNKAFALEIIKSTHDHWKALLM-KKC
....DI.DVK...PGYLEAT..WFR.YKVPDGKPEN.FAFN.E...K.FA..IIKST...WK.....KK.
RetrocopyTNYNDINDVKRQTPGYLEATVDWFRRYKVPDGKPENEFAFNAESKDKDFAVSIIKSTRGCWKVVVL<KKM
ParentalDGGAINCTNVQVCDS
.G..I.CTN..V..S
RetrocopyGGEGISCTNTTVAES

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_847 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 9 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000108871 retrocopy
Choloepus hoffmanni ENSCHOG000000087313 retrocopies
Echinops telfairi ENSETEG000000148161 retrocopy
Macaca mulatta ENSMMUG000000170041 retrocopy
Monodelphis domestica ENSMODG000000206355 retrocopies
Oryctolagus cuniculus ENSOCUG000000059412 retrocopies
Ochotona princeps ENSOPRG00000007086 1 retrocopy
retro_opri_847 ,
Sus scrofa ENSSSCG000000223651 retrocopy
Tursiops truncatus ENSTTRG000000031412 retrocopies



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