RetrogeneDB ID:

retro_opri_242

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_4158:84846..85900(+)
Located in intron of:ENSOPRG00000004660
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MAPK1
Ensembl ID:ENSOPRG00000014484
Aliases:None
Description:mitogen-activated protein kinase 1 [Source:HGNC Symbol;Acc:6871]


Retrocopy-Parental alignment summary:






>retro_opri_242
CCGAAAATTGTCAGCGGGCAGGGTTCCGACGTGGGGGCCTACCTACCCAAACCTCTTCTTCCTCGGCGGAGGGGGCCTAC
GGCATGGTGTGCTTTTGCTTATGATAACGTCAACAAAGTTCGAGTGGCTATCAAAGAAAATCAGTCCTTTTGAGCACCAG
ACCTATTGCCAGAGGACCCTGAGGGAGATCAAGATCTTGCTGCGTTTCAGACATGAACACATCATTGGGATCAATGACAT
CATCCGCGCACCGACCATCGAGCAGATGAAAGATGTATACATAGTACAGGACCTAATGGAGACAGATCTCTACAAGTTCT
TGAAGACACAGCACCTCAGCAACGACCATATCTGCTATTTTCTTTACCAGATCCTGCGAGGATTAAAATACATTCACTCA
GCTAACGTTCTGCACCGCGACCTCAAGCCTTCCAACCTGCTGCTCAACACCACCTGTGATCTCAAGATCTGTGACTTTGG
CTTGGCCCGCTTTGCAGATCCGGACAACGACCACACAGGGTTCCTGACAGAGTATGTAGCCACCCGTTGGTACAGGGCTC
CAGAAATTATGTTGAATTCCAAGGGCTACACCAAGTCCATCGACATCTGGTCTGTGGGCTGCATGCTGGCGGAGATGCTC
TCCAACCGGCCCATCTTCCCGGGGAAGCACTACCTCGACCAGCTGAACCACATTCTGGGTATTCTTGGTTCCCCATCACA
AGAAGACCTGAACTGTATAATAAATTTAAAAGCTAGAAACTATTTGCTTTCTCTTCCACACAAAAACAAGGTGCCATGGA
ACAGGTTGTTCCCAAATGCCAACTCCAAAGCTCTGGACTTGCTGGACAAAATGTTGACATTCAACCCTCACAAGAGGATC
GAGGTCGAACAGGCTCTGGCGCACCCCTATCTGGAGCAATATTATGACCCCAGTGACGAGCCAATTGCCGAAGCTCCATT
CAAGTTTGACTTGGAATTAGATGACTTGCCCAAGGAAAAACTCAAGGAGCTCATTTTTGAAGAGACTGCAAGATTCCAGC
CAGGATACAGATCT

ORF - retro_opri_242 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.79 %
Parental protein coverage: 97.49 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalPEMVRGQVFDVG-PRYTNLSYIG-EGAYGMVCS-AYDNVNKVRVAIK-KISPFEHQTYCQRTLREIKILL
P..V.GQ..DVG.P.Y.NL...G.EGAYGMVC..AYDNVNKVRVAIK.KISPFEHQTYCQRTLREIKILL
RetrocopyPKIVSGQGSDVG>PTYPNLFFLG>EGAYGMVCF>AYDNVNKVRVAIK>KISPFEHQTYCQRTLREIKILL
ParentalRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVL
RFRHE.IIGINDIIRAPTIEQMKDVYIVQDLMETDLYK.LKTQHLSNDHICYFLYQILRGLKYIHSANVL
RetrocopyRFRHEHIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKFLKTQHLSNDHICYFLYQILRGLKYIHSANVL
ParentalHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC
HRDLKPSNLLLNTTCDLKICDFGLAR.ADPD.DHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC
RetrocopyHRDLKPSNLLLNTTCDLKICDFGLARFADPDNDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC
ParentalILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKA
.LAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNA.SKA
RetrocopyMLAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNANSKA
ParentalLDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQP
LDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFD.ELDDLPKEKLKELIFEETARFQP
RetrocopyLDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDLELDDLPKEKLKELIFEETARFQP
ParentalGYRS
GYRS
RetrocopyGYRS

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_242 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 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000103121 retrocopy
Ficedula albicollis ENSFALG000000079351 retrocopy
Gallus gallus ENSGALG000000015011 retrocopy
Myotis lucifugus ENSMLUG000000059521 retrocopy
Monodelphis domestica ENSMODG000000177221 retrocopy
Ochotona princeps ENSOPRG00000014484 2 retrocopies
retro_opri_242 , retro_opri_615,



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