RetrogeneDB ID:

retro_opri_827

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_3486:117314..118925(+)
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_827
AAGCGCTACGGCATCTCCTCGCCCATCAGCCTGGCCACCCCCAAGGAGACGGACTGCGCGCTCACCCAGAAGCTCATCGA
GACCCTGCGGCCCTTCGGCGTGTTCGAGGAGGAGGAGGAGCTGCAGGGCCGGAGCCTGATCCTGGAGAAGTTGAACAAGT
TGGTGAAGGAGTGGATCCGCGAAGTCAGTGCGAGCAAGAGCCTGCCCGAGGTGCTGGTGGAGAGCGTGGGCGGCCGGCTC
TTCACCTTCGGCTCCTACCGCCTGGGCGTGCACACCAAGGGCGCCGACATCGACGCGCTGTGCGTGGCGCCCAGGCACGT
GGACCGCAGCGACTTCTTCACCTCCTTCTACGACAAGCTGAAGCTGCAGGAGGAGGTGAAGGACCTGCGGGCCGTGGAGG
AGGCGTTCGTGCCGGTCATAAAGCTGTGTTTTGATGGGGTAGAGATCGACATTTTGTTTGCAAGGTTGGCGCTGCAGACC
ATTCCAGAAGACTTGGATTTGAGGGATGACAGTTTGCTCAAGAACTTAGATATCAGATGCATCAGGAGTCTTAACGGTTG
CCGGGTAACCGATGAGATATTACACCTGGTCCCAGACATGGACAACTTCAGGTTAACGCTGAGAGCTATCAAGCTGTGGG
CCAAGTGCCACAATATCTACTCCAACATACTCGGCTTCCTGGGCGGCGTTTCCTGGGCCATGCTGGTGGCGAGAACCTGC
CAGCTCTACCCGAATGCGGTAGCCTCCACTCTGGTGCGTAAATTTTTCTTGGTGTTTTCGGAATGGGAGTGGCCCAACCC
GGTGCTGCTCAAAGAGCCGGAGGAGCGGAACCTGAACCTGCCGGTCTGGGACCCGAGAGTGAACCCCAGTGACCGCTACC
ACCTGATGCCGATCATCACCCCGGCATACCCGCAGCAGAACTCCACCTACAACGTGTCCGTCTCCACCAGGAGGGTCATG
GTGGAGGAGTTTAAACAAGGCCTCGCCATCACACACGAGATCCTGCTCAACAAGGCAGAGTGGTCTAAACTTTTTGAAGC
TCCAAGCTTCTTCCAGAAGTACAAGCACTACATCGTTCTTATAGCAAGTGCGCCGACGGAGAAGCAGCATCTGGAGTGGG
TCGGCCTGGTGGAGTCCAAGATCCGGATCCTAGTCGGGAGCCTGGAGAAGAATGAGTTCATCACCCTGGCGCACGTGAAC
CCCCAGTCGTACCCGGCACCCAAAGAGAAGCCCAAGCAGGAGGAGTTCTGCACCATGTGGGTGATCGGGCTGGTGCTGAA
GAGGCCCGAGAACTCCGAGGTGCTCAGCGTGGACCTCACCTACGACATCCAGTCGTTCACTGACACCGTGTATCGGCAGG
CCATCAACAGCAAGATGTTTGAGATGGATATGAAAGTTGCTGCCATGCATTTGAGAAAGAAAGAGCTCCAGGAGCTGCTC
CCGAACCACGTATTTCAGAAAAAGAAGACCCACCCGGCAGAGGGCGTCACCCTGACAGCCACGAGTGATGATGGCAGTGT
CGGGACAGACAGCGAAGACAGCGTGTCCACACCCTTGCCCCCTGGCCTCTTGACTGGCAGCTCCCAGGACACCAGCAGCC
CCGCCCCACCC

ORF - retro_opri_827 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.77 %
Parental protein coverage: 72.59 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKHYGITSPISLACPKEIDHIYTQKLIDAMKPFGVFEDEEELNHRLVVLGKLNNLVKEWISDISESKNLPP
K.YGI.SPISLA.PKE.D...TQKLI....PFGVFE.EEEL..R...L.KLN.LVKEWI...S.SK.LP.
RetrocopyKRYGISSPISLATPKETDCALTQKLIETLRPFGVFEEEEELQGRSLILEKLNKLVKEWIREVSASKSLPE
ParentalSVVATVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVERSDFFQSFFEKLKHQDGIRNLRAVEDAFVPVI
..V..VGG..FTFGSYRLGVHTKGADIDALCVAPRHV.RSDFF.SF..KLK.Q.....LRAVE.AFVPVI
RetrocopyVLVESVGGRLFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVI
ParentalKFEFDGIEIDLVFARLAIQTISDNLDLRDDSRLRSLDIRCIRSLNGCRVTDEILHLVPNKETFRLTLRAV
K..FDG.EID..FARLA.QTI...LDLRDDS.L..LDIRCIRSLNGCRVTDEILHLVP....FRLTLRA.
RetrocopyKLCFDGVEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPDMDNFRLTLRAI
ParentalKLWAKRRGIYSNMLGFLGGVSWAMLVARTCQLYPNAAASTLVHKFFLVFSKWEWPNPVLLKQPEESNLNL
KLWAK...IYSN.LGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPNPVLLK.PEE.NLNL
RetrocopyKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWPNPVLLKEPEERNLNL
ParentalPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSTSTRTVMVEEFKQGLAVTDEILQGKSDWSKLLEPPNF
PVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS.STR.VMVEEFKQGLA.T.EIL..K..WSKL.E.P.F
RetrocopyPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRRVMVEEFKQGLAITHEILLNKAEWSKLFEAPSF
ParentalFQKYRHYIVLTASASTEEHHLEWVGLVESKIRVLVGNLERNEFITLAHVNPQSFPGNKEHHKDNNYVSMW
FQKY.HYIVL.ASA.TE..HLEWVGLVESKIR.LVG.LE.NEFITLAHVNPQS.P..KE..K......MW
RetrocopyFQKYKHYIVLIASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSYPAPKEKPKQEEFCTMW
ParentalFLGIIFRRVENAESVNIDLTYDIQSFTDTVYRQA-NNIMLKEGMK-EATHVKKKQLHHYLPAEILQKKKK
..G....R.EN.E....DLTYDIQSFTDTVYRQA.N..M....MK..A.H..KK.L...LP....QKKK.
RetrocopyVIGLVLKRPENSEVLSVDLTYDIQSFTDTVYRQAINSKMFEMDMKVAAMHLRKKELQELLPNHVFQKKKT
ParentalQSLSDVSRSGLQSKRSSLDSNCLDS-SRDTDNGTPFNSPVSTDKPSKP
.....V......S...S......DS.S.....G....S...T..P..P
RetrocopyHPAEGVTLTA-TSDDGSVGTDSEDSVSTPLPPGLLTGSSQDTSSPAPP

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_827 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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