RetrogeneDB ID:

retro_opri_380

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_1043:109827..110265(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NFU1
Ensembl ID:ENSOPRG00000016760
Aliases:None
Description:NFU1 iron-sulfur cluster scaffold homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16287]


Retrocopy-Parental alignment summary:






>retro_opri_380
TTCACATTTATTCAAATACAAGATACCTCAAATCCTAAAGAGTTTAATGTTTAGACTAAGAAAATCAGTGCTTGAGATGA
GGACCATGGATTTTCCCACCCTTGCATCAGCATTTTGCTCCCCTTTGGCTAGCAATTAATTTGGATTGAAGGAGTAGAAA
GTGTCTTCATTGTATCAGATGTTATCACTGTCACAAAGGAGAATGGGGAGTTAGCATGGAGTTTACTGAGACCACGCATT
CATGCAAGTATTATGCATTTCTTTGCATCTGGTTTATCCCTAGTTACTGAGGAACCATCCCCAGGAAGAGCAGGGCCTGA
AGAAGACGGTGAAGTTGTGGCAATGATTAAAGAATCATTAGATACTAGACTACGGTTGATTGTGCAGGAAGATGGAGGAG
ATGTAATCAATAAAGGTTGTGGAGATGGCGTTGTACAA

ORF - retro_opri_380 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.24 %
Parental protein coverage: 57.25 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYMFIQTQDTPNPN-SLKFIPGKPVLETRTMDFPTPASAFRSPLAR-QLFRIEGVKSVFFGPDFITVTKDN
..FIQ.QDT.NP..SL.F...K.VLE.RTMDFPT.ASAF.SPLA..QL..IEGV.SVF...D.ITVTK.N
RetrocopyFTFIQIQDTSNPK>SLMFRLRKSVLEMRTMDFPTLASAFCSPLAS<QLIWIEGVESVFIVSDVITVTKEN
ParentalEELDWNLLKPDIYATIMDFFASGLPLVTEETSSGEAVSEEDDEVVAMIKELLDTRIRPTVQEDGGDVIFK
.EL.W.LL.P.I.A.IM.FFASGL.LVTEE.S.G.A..EED.EVVAMIKE.LDTR.R..VQEDGGDVI.K
RetrocopyGELAWSLLRPRIHASIMHFFASGLSLVTEEPSPGRAGPEEDGEVVAMIKESLDTRLRLIVQEDGGDVINK
ParentalGFEDGIVQ
G..DG.VQ
RetrocopyGCGDGVVQ

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_380 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 14 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000059781 retrocopy
Callithrix jacchus ENSCJAG000000191561 retrocopy
Echinops telfairi ENSETEG000000190021 retrocopy
Homo sapiens ENSG000001695991 retrocopy
Macaca mulatta ENSMMUG000000004351 retrocopy
Monodelphis domestica ENSMODG000000118051 retrocopy
Mustela putorius furoENSMPUG000000066631 retrocopy
Mus musculus ENSMUSG000000299931 retrocopy
Nomascus leucogenys ENSNLEG000000101011 retrocopy
Ochotona princeps ENSOPRG00000016760 2 retrocopies
retro_opri_380 , retro_opri_48,
Pongo abelii ENSPPYG000000123391 retrocopy
Pan troglodytes ENSPTRG000000120161 retrocopy
Tupaia belangeri ENSTBEG000000086161 retrocopy
Tarsius syrichta ENSTSYG000000137651 retrocopy



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