RetrogeneDB ID:

retro_opri_930

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_4673:39810..40704(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TRA2B
Ensembl ID:ENSOPRG00000007990
Aliases:None
Description:transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]


Retrocopy-Parental alignment summary:






>retro_opri_930
CAGCTTCGACGGAGGGCCAGCGAGCGGCGACAGCAGCCAGGCGTCATGAGCGACAGCGGCGAGCAGAACTACGGCGAGCA
GGGATCCCGCTCTGCTTCCCGAAGTGGAAGTGCTCACAGATCGGGGAATTCTGCAAGGCATAGCCCTGCAAGGTCTCACT
CCAAGGAAGATTCCAGGCGTTCCAGATCCAAGTCCAGGTCCAGATCCGAATCTAGGTCTAGATCCAGAAGAAGCTCGCGG
AAGCGTTACACGAGGTCGCGGTCCCGGTCCCGGTCCCATAGACGATCCCGTAGCAGGTCATACAGTCGCGATTATCGCAG
ACGGCATAGCCACAGCCATTCTCCCATGTCCACTCGTAGGCGCCACGTTGGGAACCAGGCAAACCCTGACCCCAACCGCT
GTCTTGGAGTATTTGGTTTGAGCTTGTACACCACAGAGAGAGATCTCAGAGAAGTGTTTTCTAAGTACGGGCCCATTGCC
GACGTGGCTGTCGTGTATGACCAGCAGTCGCGGCGCTCCCGAGGATTTGCCTTTGTTTATTTTGAGAGCGTAGATGATGC
CAAGGAAGCTAAGGAGCGCACCAATGGGATGGAGCTGGATGGGCGCAGGATCAGAGTTGATTTCTCTATAACAAAAAGAC
CACATACTCCAACACCAGGAATTTACATGGGGAGGCCCACGTATGGCAGTTCACGCCGTCGGGATTATTACGACCGAGGG
TATGACCGAGGCTATGACGACCGAGACTACTATAGCAGGCCGTATAGAGGGGGTGGCTGGAGAGCCGCCCAGGAGAGAGA
GGAGATCTATAGAAGACGCTCGCCTTCACCCTACTATAGTCGTGGCGGATACAGATCGCGCTCCAGGTCGCGCTCCTACT
CCCCCCGCCGCTAC

ORF - retro_opri_930 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.54 %
Parental protein coverage: 94.38 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQLRRKRGGR-QQPGVMSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSE
QLRR....R.QQPGVMSDSGEQNYGE..SRSASRSGSAH.SG.SARH.PARS.SKEDSRR..........
RetrocopyQLRRRASERRQQPGVMSDSGEQNYGEQGSRSASRSGSAHRSGNSARHSPARSHSKEDSRRXXXXXXXXXX
ParentalSRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGL
......RSSR..YT.........RRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGN.ANPDPN.CLGVFGL
RetrocopyXXXXXXRSSRKRYTXXXXXXXXXRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNQANPDPNRCLGVFGL
ParentalSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI
SLYTTERDLREVFSKYGPIADV..VYDQQSRRSRGFAFVYFE.VDDAKEAKER.NGMELDGRRIRVDFSI
RetrocopySLYTTERDLREVFSKYGPIADVAVVYDQQSRRSRGFAFVYFESVDDAKEAKERTNGMELDGRRIRVDFSI
ParentalTKRPHTPTPGIYMGRPTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSP
TKRPHTPTPGIYMGRPTYGSSRRRDY....YDRGYD.R.Y..R.Y......GGGWRAAQ.R..IYRRRSP
RetrocopyTKRPHTPTPGIYMGRPTYGSSRRRDY----YDRGYD-RGYDDRDYYSRPYRGGGWRAAQEREEIYRRRSP
ParentalSPYYSRGGYRSRSRSRSYSPRRY
SPYYSRGGYRSRSRSRSYSPRRY
RetrocopySPYYSRGGYRSRSRSRSYSPRRY

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_930 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 8 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000016972 retrocopies
Myotis lucifugus ENSMLUG000000057812 retrocopies
Mustela putorius furoENSMPUG000000031571 retrocopy
Mus musculus ENSMUSG000000228586 retrocopies
Ochotona princeps ENSOPRG00000007990 2 retrocopies
retro_opri_24, retro_opri_930 ,
Ochotona princeps ENSOPRG000000165931 retrocopy
Rattus norvegicus ENSRNOG000000017834 retrocopies
Tarsius syrichta ENSTSYG000000003881 retrocopy



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