RetrogeneDB ID: retro_opri_533

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1547:81348..81967(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CEP44
• Ensembl ID: ENSOPRG00000007618
• Aliases: None
• Description: centrosomal protein 44kDa [Source:HGNC Symbol;Acc:29356]

Sequence

>retro_opri_533
TGTGATATTTTGAATTTTGTTATGAAAAAGCACAAGGAGTTGAGTGGTCAGCAGAAGGCTCCATCGCAACAAAGAGAGAA
TATTGTTTTTAAGTCAGAACCTTCTTCAAGCAGTGAGAAAACATCTGAAGAACCTGTTGGTGTTGATATTACTGGCAAGT
TTCTGACTTCAGGAAAGAAAAAGTGGTGGTGATCCGTCATCTGTATGATGAAGATAATGTTGAAATTCCTGAAGATACAT
CAAGTACAGTGACAGAGGTTAAAGAAACATTTGATGTGAATGACGTAAATAGTACTGAAATAGACATTCCTGAAGTAAAG
GACCCTGAAGTCAAGGCTGAGCAGCAAGATAGAAATATTACTCCTGAGATCACTGTGCTACAGACTATGCTTGCTGAGTG
CCAAGAAAAGCTTAAGAAACTTACTTTCTTGGAGAACAGGTTAGACTATTTAGAGGAAAAATGAAAGGAAAAGTGATGGT
TAATGAAAAGACCTGGATTAACCTCCTAACTTGCGTCACTCTTCTTGAAACAGAAATGCTTTTATCAAAAAAGAATGATA
ACTACATAGAGCTTAATGAAATAAATGAGGACCATGCTTCTACCAGTAGCATGAATCCT

Alignment

ORF - retro_opri_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CDILNG-RKKHKELSGQQKAPSQQREKIVFKSEPSSSSEKTSEEPVGVDITGKFLTSGKK-KVVVIRHLY
          CDILN...KKHKELSGQQKAPSQQRE.IVFKSEPSSSSEKTSEEPVGVDITGKFLTSGKK.KVVVIRHLY
Retrocopy CDILNFVMKKHKELSGQQKAPSQQRENIVFKSEPSSSSEKTSEEPVGVDITGKFLTSGKK<KVVVIRHLY

Parental  DEDNVEIPEDTSSTVTEVKETFDVNDVNTTEIDIPEVKDPEVKAEQQDINITPEITVLQTMLAECQEKLK
          DEDNVEIPEDTSSTVTEVKETFDVNDVN.TEIDIPEVKDPEVKAEQQD.NITPEITVLQTMLAECQEKLK
Retrocopy DEDNVEIPEDTSSTVTEVKETFDVNDVNSTEIDIPEVKDPEVKAEQQDRNITPEITVLQTMLAECQEKLK

Parental  KLTFLENRLDYLEE-KMKGKVMINEKTWINLLSRVTLLETEMLLSKKNDNYIELNEINEDHASTSSMNP
          KLTFLENRLDYLEE.KMKGKVM.NEKTWINLL..VTLLETEMLLSKKNDNYIELNEINEDHASTSSMNP
Retrocopy KLTFLENRLDYLEE<KMKGKVMVNEKTWINLLTCVTLLETEMLLSKKNDNYIELNEINEDHASTSSMNP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_533 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000007618	1 retrocopy	retro_opri_533 ,