RetrogeneDB ID:

retro_opri_329

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_5261:259488..259842(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2E2
Ensembl ID:ENSOPRG00000010615
Aliases:None
Description:ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]


Retrocopy-Parental alignment summary:






>retro_opri_329
ACTGCTGCTAAATTATCCGCTGGTGCTAAAAGAATTCAGAAGGAGCTAGCTGAAATAACCTGCGATCCTGTTCCAAACTG
TAGCGCTGGGCCTGAAGGAGATAACATTTATGAGTGGAGATCGACTATACTTGGCCCACTAGGTTCTGTATATAAAGGTG
ATGTGTTTTTTTTCTGGATATCACATTTTCCTCAGATTATCCATTTAAAATTGCCAAAGGTTACGTTCCGAACCAGTATC
TATAACTGTAACATCAACAGTCAGGGAGTCATCTGTTTGGACATCCTTAAGGACAACTGAACTATCTCAAAGGTTTTGCT
GTCGATTTGTTCCCTTTTGAAAGATTGCAATCCC

ORF - retro_opri_329 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.1 %
Parental protein coverage: 70. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTAAKLSTSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPD-YPFK
TAAKLS..AKRIQKELAEIT.DP.PNCSAGP.GDNIYEWRSTILGP.GSVY.G.V....I...P.....K
RetrocopyTAAKLSAGAKRIQKELAEITCDPVPNCSAGPEGDNIYEWRSTILGPLGSVYKGDVXXXWISHFPQIIHLK
ParentalPPKXXXRTRIYHC---ISGVIC-DIRHSDLTISKVSL-ICSLLTDCNP
.PK...RT.IY.C.....GVIC.DI.....TISKV.L.ICSLL.DCNP
RetrocopyLPKVTFRTSIYNCNINSQGVICLDILKDN*TISKVLLSICSLLKDCNP

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_329 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 10 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000103412 retrocopies
Ciona intestinalis ENSCING000000068601 retrocopy
Dasypus novemcinctus ENSDNOG000000054487 retrocopies
Felis catus ENSFCAG000000077482 retrocopies
Microcebus murinus ENSMICG000000167993 retrocopies
Myotis lucifugus ENSMLUG000000251441 retrocopy
Ochotona princeps ENSOPRG00000010615 2 retrocopies
retro_opri_329 , retro_opri_788,
Ochotona princeps ENSOPRG000000116959 retrocopies
Tursiops truncatus ENSTTRG000000051561 retrocopy
Vicugna pacos ENSVPAG000000070073 retrocopies



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