RetrogeneDB ID:

retro_opri_579

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_181:344048..344565(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM192A
Ensembl ID:ENSOPRG00000006909
Aliases:None
Description:family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]


Retrocopy-Parental alignment summary:






>retro_opri_579
GATGGAGGAGATGCTGGCAATCTTGTTATCAAAAAGAGTTTTGTGTCAGAGGCAGGACTAGACTAACGGCGCAAAAGGAC
GCAAGAAGAATGGGAGAAAATTCAAAGACAGGAAGATCTAGAGGAATGTCAGGGAGAAGCTTATGACCCCCGGTCTTTAT
GAAAGACTACAGGAGCAGAAAGACAGGAAGCAGCCGGAGTAGGAGGAGCAGTTCAAGTTTAAAACCATGGTAAGAGGCTT
AGATGAAGATGAGACCAACTTCCTTGATAAGGTTTCTCGGCAGCAAGAACTGATAGAAAAGCAGTGAAAAGAGGAAGAGC
TGAAAGAACTGAAGGAGTACAGAAGTAACCTCAGTAAGGCTGGACTGGCTTCAGAAAACAAGGAGGAAGTGGAGAAGAAG
CGGACTGTGAAACCCATACAAAGCAAGAACACGTTCTCCCAAGCGAAGCTGTTGGCAGGAGCTGTGAAGCCTGAGCTCAG
ACAGCGGCCACTGTGAAAACTGAAACCAGACCCAGAT

ORF - retro_opri_579 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 68.9 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDGGDDGNLVIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECP-EEAYDPRSLYERLQEQKDRKQQEYE
DGGD.GNLVIKK.FVSEA.LD.RRKR.QEEWEK....ED.EEC..E....P..LYERLQEQKDRKQ.E.E
RetrocopyDGGDAGNLVIKKSFVSEAGLD*RRKRTQEEWEKIQRQEDLEECQ>EKLMTP-GLYERLQEQKDRKQPE*E
ParentalEQFKFKNMVRGLDEDETNFLDEVSRQQELLEKQRREEELKELKEYRSNLSKVGISSENKKEVEKKLTVKP
EQFKFK.MVRGLDEDETNFLD.VSRQQEL.EKQ..EEELKELKEYRSNLSK.G..SENK.EVEKK.TVKP
RetrocopyEQFKFKTMVRGLDEDETNFLDKVSRQQELIEKQ*KEEELKELKEYRSNLSKAGLASENKEEVEKKRTVKP
ParentalIETKNKFSQAKLLAGAVKPKSSESGNSVKRLKPDPD
I..KN.FSQAKLLAGAVKP...........LKPDPD
RetrocopyIQSKNTFSQAKLLAGAVKPELRQ--RPL*KLKPDPD

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_579 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 15 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000022421 retrocopy
Cavia porcellus ENSCPOG000000013921 retrocopy
Equus caballus ENSECAG000000093241 retrocopy
Echinops telfairi ENSETEG000000143791 retrocopy
Homo sapiens ENSG000001727751 retrocopy
Gorilla gorilla ENSGGOG000000039381 retrocopy
Macaca mulatta ENSMMUG000000134921 retrocopy
Mus musculus ENSMUSG000000317741 retrocopy
Nomascus leucogenys ENSNLEG000000027161 retrocopy
Ochotona princeps ENSOPRG00000006909 2 retrocopies
retro_opri_175, retro_opri_579 ,
Pongo abelii ENSPPYG000000073821 retrocopy
Pan troglodytes ENSPTRG000000081481 retrocopy
Tarsius syrichta ENSTSYG000000133001 retrocopy
Tursiops truncatus ENSTTRG000000127911 retrocopy
Vicugna pacos ENSVPAG000000059731 retrocopy



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