RetrogeneDB ID:

retro_opri_84

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2097:248546..248942(+)
Located in intron of:ENSOPRG00000015647
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM96A
Ensembl ID:ENSOPRG00000015229
Aliases:None
Description:family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235]


Retrocopy-Parental alignment summary:






>retro_opri_84
CAGCCCCGGATCATGGAAGAGAAAGTGCTAGAGGTTTATGATTTGATTCGAACTATCCGGGACCCAGAAAAACCCAATAC
TTTGGAAGAACTGGAAGTGGTGACGGAAAGCTGCGTGGAGGTTCAGGAGATAAATGAAGACGACTACTTGGTTGTCATCA
GGTTCACACCAACAGTACCTCATTGCTCTTTGGCAACTCTTATTGGGCTATGCTTAAGAGTAAAACTTCAGAGATGTTTA
CCATTTAACCATAAGTTGGAGATCTACATTTCTGAAGGAACTCACTCAACAGAAGAAGACATCAACAAGCAGATCAATGA
CAAAGAGCGGGTGGCCGCTGCAATGGAGAACCCCAACCTACGGGAGATAGTGGAACAGTGTGTCCCGGAGCTTGAC

ORF - retro_opri_84 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.85 %
Parental protein coverage: 82.5 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVTESCVEVQEINEDDYLVVIRFTPTVPHCSLATLIGL
QPRIMEEK.LEVYDLIRTIRDPEKPNTLEELEVVTESCVEVQEINEDDYLVVIRFTPTVPHCSLATLIGL
RetrocopyQPRIMEEKVLEVYDLIRTIRDPEKPNTLEELEVVTESCVEVQEINEDDYLVVIRFTPTVPHCSLATLIGL
ParentalCLRVKLQRCLPFKHKXXXXXXXXXXXXXXXXNKQINDKERVAAAMENPNLREIVEQCVLEPD
CLRVKLQRCLPF.HK................NKQINDKERVAAAMENPNLREIVEQCV.E.D
RetrocopyCLRVKLQRCLPFNHKLEIYISEGTHSTEEDINKQINDKERVAAAMENPNLREIVEQCVPELD

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_84 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 21 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024481 retrocopy
Bos taurus ENSBTAG000000020122 retrocopies
Canis familiaris ENSCAFG000000170352 retrocopies
Callithrix jacchus ENSCJAG000000048341 retrocopy
Equus caballus ENSECAG000000103031 retrocopy
Erinaceus europaeus ENSEEUG000000008541 retrocopy
Felis catus ENSFCAG000000041781 retrocopy
Homo sapiens ENSG000001667972 retrocopies
Gorilla gorilla ENSGGOG000000165502 retrocopies
Loxodonta africana ENSLAFG000000111141 retrocopy
Macropus eugenii ENSMEUG000000059792 retrocopies
Microcebus murinus ENSMICG000000110721 retrocopy
Myotis lucifugus ENSMLUG000000282332 retrocopies
Mustela putorius furoENSMPUG000000006051 retrocopy
Mus musculus ENSMUSG000000323811 retrocopy
Nomascus leucogenys ENSNLEG000000269323 retrocopies
Ochotona princeps ENSOPRG00000015229 5 retrocopies
Pongo abelii ENSPPYG000000065441 retrocopy
Pan troglodytes ENSPTRG000000071532 retrocopies
Sorex araneus ENSSARG000000020683 retrocopies
Tarsius syrichta ENSTSYG000000041862 retrocopies



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