RetrogeneDB ID:

retro_opri_939

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_4788:101889..102844(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TDP2
Ensembl ID:ENSOPRG00000016299
Aliases:None
Description:tyrosyl-DNA phosphodiesterase 2 [Source:HGNC Symbol;Acc:17768]


Retrocopy-Parental alignment summary:






>retro_opri_939
GCGATGGCAAAGTGCTACCTGGCCGAGGACGACTGGGAGATGGAAAAGGCGCTGGACTCCTACTTCGAGCGGCCGGCAGA
GGAGAGCGCCTCGCAGAGCCGCCCGGTGGAGCCCGCGGCCTGCGTTGACCTCACCAATGAAGAAACAAGTGACTCCATTA
GTTCTAAAACCAGCTGTCCCAGACCACCGCGCAGGAAGATGGCAGCATGTTCTCTCTCATTACCTGGAACATTGATGGAT
TGGATCTAAACCACCTGCAAGAGAGGGCTCCGGGAGTGTGTTCCTAGCTAGCTTTGTACTGCCCAGATGTGATATTTCTA
CAGGAAGTAATCCCACCGTATTGCAGCTACCTAAAGAAGCGAGCAAGTAATTATGAAATTATTGCAGGTAATGAAGAAGG
ATATTTCACAGCTATAATGTTGAAGAAACCCAGAGTGAAATTAAAAAGCCAAGAGATAATTCCTTTTCCAAATACCAAAA
TGATGAGGAACCTTTTGTGTGTGCAGGTGAGTTTGTCCGGGAATGAGCTTTACCTTACGACCTCACATTTGGAGAGCACC
AGGGGCCATGCCATGGAATGAATTAATCAGTTCAAAGCGGTCCTACAGAAAAGCCAGGAGGCTCCCAAATCAGCTACTGT
TATATTTGCAGGAGAGACAAATTTAAGAGATCAAGAAGTTACCAAATGTGATGGTTTACCCAACAACATCTTGGATGTCT
GGGAGTTTCCGGGCAAACCTAAGCATTGCCAGCATACATGGGACACCCGAGTGAACTCTAATCTGGGTATAGCTGCTCCT
TGCAAGCTGCGTTTTGATTGGATATTCTTCAGAGCAGCAGCAGACGTGGGCCACATTATTCCCGAAGTTTGGACCTCCTT
GGGTTGGAAAAACTGGACTGTGGTAGATTTCCTAGTGATCACTGGGGCCTTCTGTGCAACTTGGATGTTATATTG

ORF - retro_opri_939 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.72 %
Parental protein coverage: 91.93 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAVAQCYLAENDWEMERALDSYFERPAEESASQSGPAEPAACVDLTSEETSDSISSKTS-QSETTVQEDGS
A.A.CYLAE.DWEME.ALDSYFERPAEESASQS.P.EPAACVDLT.EETSDSISSKTS..S.TT.QEDGS
RetrocopyAMAKCYLAEDDWEMEKALDSYFERPAEESASQSRPVEPAACVDLTNEETSDSISSKTS<LSQTTAQEDGS
ParentalMFSLITWNIDGLDLNHLQERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRARDYEIIAGNEEGYFTAI
MFSLITWNIDGLDLNHLQERA.GVCS.LALY.PDVIFLQEVIPPY.SYLKKRA..YEIIAGNEEGYFTAI
RetrocopyMFSLITWNIDGLDLNHLQERAPGVCS*LALYCPDVIFLQEVIPPYCSYLKKRASNYEIIAGNEEGYFTAI
ParentalMLKKSRVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYLMTSHLESTRGHAVERMNQLKVVLQKIQEAP
MLKK.RVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYL.TSHLESTRGHA.E..NQ.K.VLQK.QEAP
RetrocopyMLKKPRVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYLTTSHLESTRGHAME*INQFKAVLQKSQEAP
ParentalESATVIFAGDTNLRDQEVTKCGGLPNNILDVWEFLGKPKHCQYTWDTRVNSNLGIAAPCKLRFDRIFFRA
.SATVIFAG.TNLRDQEVTKC.GLPNNILDVWEF.GKPKHCQ.TWDTRVNSNLGIAAPCKLRFD.IFFRA
RetrocopyKSATVIFAGETNLRDQEVTKCDGLPNNILDVWEFPGKPKHCQHTWDTRVNSNLGIAAPCKLRFDWIFFRA
ParentalAADEGHIIP-RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL
AAD.GHIIP.RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL
RetrocopyAADVGHIIP<RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL

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_939 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 6 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000120122 retrocopies
Callithrix jacchus ENSCJAG000000060741 retrocopy
Dasypus novemcinctus ENSDNOG000000101131 retrocopy
Ochotona princeps ENSOPRG00000016299 2 retrocopies
retro_opri_261, retro_opri_939 ,



Copyright © RetrogeneDB 2014-2017