RetrogeneDB ID: retro_opri_5

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6355:74670..75636(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000009687
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000015755
• Aliases: None
• Description: None

Sequence

>retro_opri_5
GATGAGCTGTGGAGGATCCAGGAGAAGTTGGAATGTTACTTTGGCTCCTTGGTTGGCTCAAATGTGTACATAACCCCTGC
CGGATCTCAGGGCCTCCCACCGCACTATGATGATGTTGAGGTTTTTATCCTGCAACTAGAAGGAGAGAAACATTGGCGCC
TCTACCACCCAACAGTGCCCCTGGCGCGGGAGTACAGCGTGGAAGCCGAGGATAGGATCGGCAGGCCGACACATGAGTTC
ACATTGAAGCCAGGTGATTTGTTGTACTTTCCCAGAGGGACCATTCACCAAGCAGACACTCCTCTGGGGCTGGCCCACTC
TACTCATGTGACTATCAGCACCTACCAAAACAGTTCATGGGGAGATTTCCTTTTGGACACCATTTCGGGGCTTGTGTTTG
ATGCTACAAAGGAAGATGTGACATTGCGGGCTGGCATACCCCGGCAACTGCTTCTGCAGGCAGAAACCACAACTGTTGCA
GCAAGGAGACTAAGTGGTTTTCTGAGGAGGCTTGCAGAGAGGCTGGAAGGCACCAAAGAACTCCTTTCATCAGACATGAA
GAAGGATTTTATTATGCATAGGTTGCCCCCATACCATGTGGGAGATGGAACAGAACTGACAACACCAGGTGGAGAGTTAC
CGAGGTTGAACAGCACAGTGACGCTGCAGTTTAAAGACCACATCATCCTCACAGTAGGGCCAGATCAGGACCGATCTGAT
GAAGCTCAAGAAAAGATGATTTACATCTATCATTCCTTAAAGAATAAGAGGGAGACACACATGATGGGAAGTGAGGAGGA
AACAGAGGCTCATGGACTTCGCTTTCCTTTGTCGCATATGGAGGCACTAAAGCAGATCTGGAACAGTACGACTGTTTCTG
TCAAGAGCCTGAAACTTGCAACAGATGAAGAAAAGGAAAGCCTGGTCTTATCCCTCTGGACAGAATGTTTAATCCAAGTA
GCCTAG

Alignment

ORF - retro_opri_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELWRIQEKLECYFGSLVGSNVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAE
          DELWRIQEKLECYFGSLVGSNVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAE
Retrocopy DELWRIQEKLECYFGSLVGSNVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAE

Parental  DRIGRPTHEFTLKPGDLLYFPRGTIHQADTPLGLAHSTHVTISTYQNSSWGDFLLDTISGLVFDATKEDV
          DRIGRPTHEFTLKPGDLLYFPRGTIHQADTPLGLAHSTHVTISTYQNSSWGDFLLDTISGLVFDATKEDV
Retrocopy DRIGRPTHEFTLKPGDLLYFPRGTIHQADTPLGLAHSTHVTISTYQNSSWGDFLLDTISGLVFDATKEDV

Parental  TLRAGIPRQLLLQAETTTVAARRLSGFLRRLAERLEGTKELLSSDMKKDFIMHRLPPYHVGDGTELTTPG
          TLRAGIPRQLLLQAETTTVAARRLSGFLRRLAERLEGTKELLSSDMKKDFIMHRLPPYHVGDGTELTTPG
Retrocopy TLRAGIPRQLLLQAETTTVAARRLSGFLRRLAERLEGTKELLSSDMKKDFIMHRLPPYHVGDGTELTTPG

Parental  GELPRLNSTVTLQFKDHIILTVGPDQDRSDEAQEKMIYIYHSLKNKRETHMMGSEEETEAHGLRFPLSHM
          GELPRLNSTVTLQFKDHIILTVGPDQDRSDEAQEKMIYIYHSLKNKRETHMMGSEEETEAHGLRFPLSHM
Retrocopy GELPRLNSTVTLQFKDHIILTVGPDQDRSDEAQEKMIYIYHSLKNKRETHMMGSEEETEAHGLRFPLSHM

Parental  EALKQIWNSTTVSVKSLKLATDEEKESLVLSLWTECLIQVA
          EALKQIWNSTTVSVKSLKLATDEEKESLVLSLWTECLIQVA
Retrocopy EALKQIWNSTTVSVKSLKLATDEEKESLVLSLWTECLIQVA

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_5 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015546	1 retrocopy	retro_btau_678,
Echinops telfairi	ENSETEG00000010104	1 retrocopy	retro_etel_1065,
Mus musculus	ENSMUSG00000022724	1 retrocopy	retro_mmus_2829,
Ochotona princeps	ENSOPRG00000015755	1 retrocopy	retro_opri_5 ,