RetrogeneDB ID:

retro_opri_861

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_38549:9055..10165(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PAPOLG
Ensembl ID:ENSOPRG00000009630
Aliases:None
Description:poly(A) polymerase gamma [Source:HGNC Symbol;Acc:14982]


Retrocopy-Parental alignment summary:






>retro_opri_861
ATGCCGCCATTTCCAGTTACAACGCAGGGGTCAGAGCAAGTGCCCCAGAACCACTATGGCGTTACTTCTCCTATCAGCCT
AGCAGCCCCCAAGGAGACTGACTGCATCCTCACCCAGAAACTCATCGAGACTCTGAAGCCCTTTGGGGTGTTTGAAGAGG
AAGAGGAACTGCAGCGCAGAATTTTAATTTTGGAAAAATTAAATAACCTGGTTAAAGAGTGGATACATGAAATCAGTGAA
AGTAAGAATCGTCCACAGTCAGTGATTGAAAACGTTGGCGAAAAAATTGTTACATTTGGATCTTACAGATTAGGAGTACA
TACAAAACGTGCTGATATTGATGTGCTGTGTGTTGCACCAAGTCATGTTGATGAAAGTGACTTTTTCACCTCATTCTATG
ACAAGTTGAAATTATAGGAAGAAGTAAAGGATTTAAGAGCTGTTGAAGAGGCATTTGTACCAGTTATCAAACGTTGTTTT
GATGGGATAGAGATTGATATTTTGTTTGTAACATTAGCCCTGCAGACCATTCCCGAAGATTTGGACCTACAAGATGATAG
TCTACTTAAAAACTTAAACCATAAGATGCATAAGAAGTCTTAATGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTA
CCAAACACTGACAACTTCAGGTTAACACTGAGAGCTGTCAAACTGTGGGCCAAACGCCACAACTTCTATTCCAATGTATC
AGGTTTCCTCGGTCGTGTTTCCTGGGCCATGCTGATAGCAAGAACTTGTCAGCTTTATCCAAAGGCAATACCATCAGCTC
TTGTACTTAATTTTTTCTTGGTATTTTCTAAACGGGAATGGCCAAATCCAGAGCTATTGAAACAGCCTGAAGAATGCAAA
TTTAATTTGTCTTTATGGGATCCAAGGGTAAGCCCCAGTGATGGGTACCTTCTTATGCTACATATACACCAGCATACCCA
CAGCAGAACTCCATGTACAATGTGTCCGTTTCAACAAGGATGGTCATGGTTGAGAAGTTTAAACAAGGTCTTGCTATCAC
AGATGGAATTTTGCTGAGTAAGGCAGAGTGGTCCAAACTCTTTGAAGCTCCTAACTTCTTTCACAAGTAC

ORF - retro_opri_861 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.16 %
Parental protein coverage: 50.2 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMKEMSANTMLDSQRQQKHYGITSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNL
M......T....Q..Q.HYG.TSPISLA.PKE.D.I.TQKLI...KPFGVFE.EEEL..R...L.KLNNL
RetrocopyMPPFPVTTQGSEQVPQNHYGVTSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILEKLNNL
ParentalVKEWISDISESKNLPPSVVATVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQD
VKEWI..ISESKN.P.SV...VG.KI.TFGSYRLGVHTK.ADID.LCVAP.HV..SDFF.SF..KLK...
RetrocopyVKEWIHEISESKNRPQSVIENVGEKIVTFGSYRLGVHTKRADIDVLCVAPSHVDESDFFTSFYDKLKL*E
ParentalGIRNLRAVEDAFVPVIKFEFDGIEIDLVFARLAIQTISDNLDLRDDSRLRSLD-IRCIRSLNGCRVTDEI
....LRAVE.AFVPVIK..FDGIEID..F..LA.QTI...LDL.DDS.L..L..IRCIRSLNGCRVTDEI
RetrocopyEVKDLRAVEEAFVPVIKRCFDGIEIDILFVTLALQTIPEDLDLQDDSLLKNLN>IRCIRSLNGCRVTDEI
ParentalLHLVPNKETFRLTLRAVKLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWE
LHLVPN...FRLTLRAVKLWAKR...YSN..GFLG.VSWAML.ARTCQLYP.A..S.LV..FFLVFSK.E
RetrocopyLHLVPNTDNFRLTLRAVKLWAKRHNFYSNVSGFLGRVSWAMLIARTCQLYPKAIPSALVLNFFLVFSKRE
ParentalWPNPVLLKQPEESNLNLPVWDPRVNPSDRYHLMPII-TPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTD
WPNP.LLKQPEE...NL..WDPRV.PSD.Y.LM..I.TPAYPQQNS.YNVS.STR.VMVE.FKQGLA.TD
RetrocopyWPNPELLKQPEECKFNLSLWDPRVSPSDGYLLMLHI<TPAYPQQNSMYNVSVSTRMVMVEKFKQGLAITD
ParentalEILQGKSDWSKLLEPPNFFQKY
.IL..K..WSKL.E.PNFF.KY
RetrocopyGILLSKAEWSKLFEAPNFFHKY

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_861 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 4 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000140284 retrocopies
Ochotona princeps ENSOPRG00000009630 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000108611 retrocopy
Tursiops truncatus ENSTTRG000000062371 retrocopy



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