RetrogeneDB ID:

retro_opri_358

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_816:65925..67319(-)
Located in intron of:ENSOPRG00000016903
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:WEE2
Ensembl ID:ENSOPRG00000009103
Aliases:None
Description:WEE1 homolog 2 (S. pombe) [Source:HGNC Symbol;Acc:19684]


Retrocopy-Parental alignment summary:






>retro_opri_358
ATGGATGTGGAGAGCAGTAACAAACAGCTAAGTGGGAAATTAGGCTTGTTTCCTTGTGAACAGGGGACAGAGAACAAAGC
GCAGAGGGGAGCAGAAGAGGGTGAGGGAGTCCAGAGCCAGTCTCCGGAGAAGGAGGAGGTTCAGGACTCGGAGTCCTTCA
GGACACCCCTGAGGAGCGTAAGTGGGGTCCCTGGCACCTTTCAGAAAAGAGGCAAACCCATCCTAGGCCCAGTTCTGAGG
ACTCCAGTGTCAGCCTCTCCCACATGTCCTGAGACACCAGCTCTGCTGGAGAAAAGGAGCAAGATGCTGCATGCTGAGAG
CCCCTCCACTCTGAAAAACCTGCAGAGCCAGCCTCCAGCAATTTCTTCAACAGTGAAGCTCTCCTCCAGAGGCTCCAAGC
ATTTCAGGCACACGCCTGTTTCCCTCAGGGATGAGATGGCCTTGCTGGCTTTGGTCAATATTAATCCCTTCACTCCAGAG
TCCTTGAAAAAATTATTGCTTACACCCAATGGCAAGAGGAAAACCCGAGGAGATGTTGAGGAAACTGGTCCAGAAGAAGG
CAAATTAAAACAAGGGTTACCTGCCAAGAGATGTGTCATGAGAGAAACCAACATGGACACACACTATGAAAAGGAATTTT
TGGAGGTGGAAAAAATTGGAGTCGGGTCATTTGGTACAGTCTACAAATGCATTAAGAGGTTGGATGGATGTGTCTATGCA
ATAAAGCGTGCTACCAAGCCATCCACAGCATCTTCCAATGAAATTCAGATTTGCGAGAAGTCTATGCCCATGCAGTGCTA
GGCCATCACCCCCATGTAGTGCGTTACTACTCTGCCTGGTCAGAAGATGACTACATGATCATTCAGAATGAATACTGCAA
TGGTGGGAGTTTGCAAGCCGTTATATCTGAAAATACTAAGTCTGGTGATCATTTCCAAGAGCCCACACTCAGAGACATCC
TTCTGCAGATTTCCGTGGGAATTAAATACATCCACAACTCGGGGGTGGTGCACCTGGACATCAAACCTAGCAATATCTTC
ATTTGTCATAAGGTGCAAAGCGATTTTACTGACGTGCCAGAAGAGATTGAAAATGAAGCTGATTGGTTCATCTCTGCCAG
TGTGATATATAAAATTGGTGACCTGGGCCACGTATCATCCATAAGTGATCCCAGTGTAGAAGAAGGAGATATTCGCTTCC
TGGCTAATGAGGTTTTGCAAGAAGATTATCGACATCTTCCCAAGGCAGACATATTTGCCTTGGGCTTAACAATAGCGGTG
GCTGCGGGAGCCGGGGCGTTACCAGCCAACGGGGAGGCGTGGCATCACATCCGCAAGGGTAACCTTCCAGAAATTCCCCA
GAAACTCTCGGAAGACTTTCAAGATCTGCTCAAG

ORF - retro_opri_358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.85 %
Parental protein coverage: 81.8 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSEW--TPLRNVSGVPGTFQKR
MDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSE...TPLR.VSGVPGTFQKR
RetrocopyMDVESSNKQLSGKLGLFPCEQGTENKAQRGAEEGEGVQSQSPEKEEVQDSESFRTPLRSVSGVPGTFQKR
ParentalGKPILAPVLRTPVSASPTCPETPALLEKRSKMLHAESPSTPKNLQSQPPAISSTVKLSSRGSKHFRHTPV
GKPIL.PVLRTPVSASPTCPETPALLEKRSKMLHAESPST.KNLQSQPPAISSTVKLSSRGSKHFRHTPV
RetrocopyGKPILGPVLRTPVSASPTCPETPALLEKRSKMLHAESPSTLKNLQSQPPAISSTVKLSSRGSKHFRHTPV
ParentalSLRDEMASLALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDTRYE
SLRDEMA.LALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDT.YE
RetrocopySLRDEMALLALVNINPFTPESLKKLLLTPNGKRKTRGDVEETGPEEGKLKQGLPAKRCVMRETNMDTHYE
ParentalKEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE-NSDLREVYAHAVLGHHPHVVRYYSA
KEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE.NSDLREVYAHAVLGHHPHVVRYYSA
RetrocopyKEFLEVEKIGVGSFGTVYKCIKRLDGCVYAIKRATKPSTASSNE<NSDLREVYAHAVLGHHPHVVRYYSA
ParentalWSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVGLKYIHNSGVVHLDIKPSNIFIC
WSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVG.KYIHNSGVVHLDIKPSNIFIC
RetrocopyWSEDDYMIIQNEYCNGGSLQAVISENTKSGDHFQEPTLRDILLQISVGIKYIHNSGVVHLDIKPSNIFIC
ParentalHKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF
HKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF
RetrocopyHKVQSDFTDVPEEIENEADWFISASVIYKIGDLGHVSSISDPSVEEGDIRFLANEVLQEDYRHLPKADIF
ParentalALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK
ALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK
RetrocopyALGLTIAVAAGAGALPANGEAWHHIRKGNLPEIPQKLSEDFQDLLK

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_358 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 7 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000046581 retrocopy
Callithrix jacchus ENSCJAG000000136271 retrocopy
Dipodomys ordii ENSDORG000000151561 retrocopy
Gorilla gorilla ENSGGOG000000096091 retrocopy
Ochotona princeps ENSOPRG00000009103 2 retrocopies
retro_opri_358 , retro_opri_841,
Pongo abelii ENSPPYG000000180661 retrocopy
Pan troglodytes ENSPTRG000000283831 retrocopy



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