RetrogeneDB ID:

retro_opri_941

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_48132:12325..12705(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUB1
Ensembl ID:ENSOPRG00000012887
Aliases:None
Description:SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]


Retrocopy-Parental alignment summary:






>retro_opri_941
ATGCTGAAGTCAGAGGAACTTGTGTCTTCAAGCTCGTCTGGCAGCGATTCTGACAGTGAAGGGGACAAAAAGTTAAAGAG
CAAAAAGCAAGTCGCTCAGGAAAAGCCTGTGAAGAAGCAGAAGACGGGCGAGACCTCCGAGTCCTGTCCTCTCCCAAACA
GAGCAGCAGCAGCAGAGACGACAACATGTTCCAGATTGGGAAAATGAGGTACGTCAGTGTTTGAGACTTTAAGGGGAAAG
TTCTGATTGATATTCGAGAATACTGCATGGATTCAGAAGGTGAAATGAAGCCAGGAAGAAAAGGCATTTCTCTAAATCCA
GAGCAGTGGAGCCAGCTGAAGGAACAGATTTCTGACATTGATGATGCAGTAAGGAAACTG

ORF - retro_opri_941 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPKSKELVSSSSSGSDSDSEVDKKLKRKKQVAQEKPVKKQKTGETS-RVLSSPKQSSSSRDDNMFQIGKM
M.KS.ELVSSSSSGSDSDSE.DKKLK.KKQVAQEKPVKKQKTGETS.RVLSSPKQSSSSRDDNMFQIGKM
RetrocopyMLKSEELVSSSSSGSDSDSEGDKKLKSKKQVAQEKPVKKQKTGETS<RVLSSPKQSSSSRDDNMFQIGKM
ParentalRYVSVRDFKGKVLIDIREYWMDSEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
RYVSV.DFKGKVLIDIREY.MDSEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
RetrocopyRYVSV*DFKGKVLIDIREYCMDSEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL

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






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.