RetrogeneDB ID:

retro_opri_79

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_2010:104569..105113(-)
Located in intron of:ENSOPRG00000010208
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1
Ensembl ID:ENSOPRG00000006107
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A1 [Source:HGNC Symbol;Acc:5031]


Retrocopy-Parental alignment summary:






>retro_opri_79
GAGCTTCCCAAAGAGCCCGAACAGCCACGGAATCTTTCCATCAAAGGGCTGAGCTTCCAAATAAGTCCTGAGAGTTTATG
GAGCCATTTTAAGCAGTGAGGAATGCTCACGGACTGTGTGGGATGAGATATGAACACCAAGCACTCCAGTGGCTGAAGGG
TTGTTACCTACGCCACCATGGAGGCGTGGACACAGCCATGAATGCAAGGCCATACTAGTGGATGGAAAAGTGCTGGAACC
AAAGAGGGCTGACCCCAGAGAAAATTCTCCAAGATCCAGTGCCAATCTAACTGTGAAAAAGAGCTTTACTGGGAGCATTT
CTTTAATCTGCCTAGACACTGAAGAGAATTACCTCCCACGTTATTTTAAGCAATACAGGAAAATCAAAATGACTGAGATC
ATGACTGATAGAAGCAATGGCAAGAAGAGGGCTTTTGCTTTTGGTACTTCTGATGACTGTGACTCCGTGGATAAGACTGC
CACTCAGAAATACCGTACTGTGAATGGTCACAACTGTGGAGTAAGAAAGGCCCTGTTCAAGCAA

ORF - retro_opri_79 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.24 %
Parental protein coverage: 51.43 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE-VDAAMN
E.PKEPEQ.R.L.I.GLSF....ESL.SHF.Q.G.LTDCV...D.NTK.S.G...VTYAT.E..VD.AMN
RetrocopyELPKEPEQPRNLSIKGLSFQISPESLWSHFKQ*GMLTDCVG*-DMNTKHSSG*RVVTYATMEA<VDTAMN
ParentalARPH-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVEGIKE---DTEEHHLRDYFEQYGKIEVIEIMTD
ARP...VDG.V.EPKRA..RE.S.R..A.LTVKK.F...I.....DTEE..L..YF.QY.KI...EIMTD
RetrocopyARPY<LVDGKVLEPKRADPRENSPRSSANLTVKKSFTGSISLICLDTEENYLPRYFKQYRKIKMTEIMTD
ParentalRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ
R..GKKR.FAF.T.DD.DSVDK...QKY.TVNGHNC.VRKAL.KQ
RetrocopyRSNGKKRAFAFGTSDDCDSVDKTATQKYRTVNGHNCGVRKALFKQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide