RetrogeneDB ID: retro_opri_15

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_24541:8411..9701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000018715
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000005566
• Aliases: None
• Description: None

Sequence

>retro_opri_15
ATGTCTTGCCACCTCAATTCGGAAAACCACCTGGATCCAGGCCCCATCTATGTCCGAGAAAATGGACAGCTGCACATGGT
CAGCCTGGCTCTGAATGGTGTCAGGAGTGGCCAGCCGCAACCGAGGCCTTTCGGACTGTTTTCCAAAGGCTTCTCTGTTG
AGCTGTGCATGAACAGGGAAGACGACACTGCCCAGAAGGAGAAGACGGATCATTTCATCTTCACGTACACCCGGGAGGGC
AATCTCCGCTACTCCGCCAAGTCGCTCTTCAGCCTCGTCCTGGACTTCATCTCCGACAACATTGACCATGTCGATTCCCT
CATTGGCTTTCCCGAGCAGATTGCCGAGAGACTGTTCTCTGCAGCCGAAGCCAGACAAAAGTTCACGGAGCCGGGCACAG
GGCTGAGGGCCTTGCGGAAATTCACCGAGGCCTACGGGCGTCTGGTGCTCTGCTCACTATGTCTGCGGGACAGGTATCTG
GTGATTTCAGAGAAACTCGAGGAGATAAAGTCCTTCCGGGAGCTTACCTGCTTGGATCTTTCCTGTTGCAAGCTTGGAGA
TGAGCATGAGCTTCTAGAACACCTCACCAATGAGGCCCTGTCTAGTGTCACTCAGCTCCACCTGAAGGATAATTGTTTGT
CTGACGCCGGGGTGCGGAAAATGACAGCACCCGTTCGCGTGATGAAACGAGGCCTTGGGAATCTAACACTATTAGACTTA
TCCTGTAACCCTAAGATCACAGATGCAGGAATTGGATACCTGTTCTGTTTTAGAAAGCTAAGCTGCTTAGATATCTCTGG
GACAGGGCTCAAGGATGTAAACGCCATCAAGCACAAGCTGCAGGCCCGCATGGGCCTCGTCCTCTCCCAAGTGTCTCTGA
AGGAATTCGATCACACTAACTGCAAGACCGAGGGCTGGGCCGACCAGATTGTCCGGCAGTGGGAGCGCCTGACGGTGAAA
CCCCTGAAGAAAGCGGCTGTCGTGGAGCCTCGAAAGACAGCTCAGTACTTCTATGGCAACCGCTTCCTGGCCGAGGCCTC
TTTACGATGTCCCCTGGACGACACCTGCCTGGACGCCAGTGAGAAGCTCCAGTTCCGGAAAGAGAAGCCTACAGAGGCCC
AGGGGCCGTTGTTGAACTGTGACACTGCCATCTCAATGCAGGAGCCCCAGAAGAGCAAGAAGAGGACTTTTGAGGAGTCA
GAGAAGGAGCCGAGTAACTCCCCACAGGCTCCCAAGCAGAAGTATGTGTGCCTCACTGTGCAGGACTGGGACCTGCTGAA
TTCCTACTGA

Alignment

ORF - retro_opri_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCHLNSENHLDPGPIYVRENGQLHMVSLALNGVRSGQPQPRPFGLFSKGFSVELCMNREDDTAQKEKTD
          MSCHLNSENHLDPGPIYVRENGQLHMVSLALNGVRSGQPQPRPFGLFSKGFSVELCMNREDDTAQKEKTD
Retrocopy MSCHLNSENHLDPGPIYVRENGQLHMVSLALNGVRSGQPQPRPFGLFSKGFSVELCMNREDDTAQKEKTD

Parental  HFIFTYTREGNLRYSAKSLFSLVLDFISDNIDHVDSLIGFPEQIAERLFSAAEARQKFTEPGTGLRALRK
          HFIFTYTREGNLRYSAKSLFSLVLDFISDNIDHVDSLIGFPEQIAERLFSAAEARQKFTEPGTGLRALRK
Retrocopy HFIFTYTREGNLRYSAKSLFSLVLDFISDNIDHVDSLIGFPEQIAERLFSAAEARQKFTEPGTGLRALRK

Parental  FTEAYGRLVLCSLCLRDRYLVISEKLEEIKSFRELTCLDLSCCKLGDEHELLEHLTNEALSSVTQLHLKD
          FTEAYGRLVLCSLCLRDRYLVISEKLEEIKSFRELTCLDLSCCKLGDEHELLEHLTNEALSSVTQLHLKD
Retrocopy FTEAYGRLVLCSLCLRDRYLVISEKLEEIKSFRELTCLDLSCCKLGDEHELLEHLTNEALSSVTQLHLKD

Parental  NCLSDAGVRKMTAPVRVMKRGLGNLTLLDLSCNPKITDAGIGYLFCFRKLSCLDISGTGLKDVNAIKHKL
          NCLSDAGVRKMTAPVRVMKRGLGNLTLLDLSCNPKITDAGIGYLFCFRKLSCLDISGTGLKDVNAIKHKL
Retrocopy NCLSDAGVRKMTAPVRVMKRGLGNLTLLDLSCNPKITDAGIGYLFCFRKLSCLDISGTGLKDVNAIKHKL

Parental  QARMGLVLSQVSLKEFDHTNCKTEGWADQIVRQWERLTVKPLKKAAVVEPRKTAQYFYGNRFLAEASLRC
          QARMGLVLSQVSLKEFDHTNCKTEGWADQIVRQWERLTVKPLKKAAVVEPRKTAQYFYGNRFLAEASLRC
Retrocopy QARMGLVLSQVSLKEFDHTNCKTEGWADQIVRQWERLTVKPLKKAAVVEPRKTAQYFYGNRFLAEASLRC

Parental  PLDDTCLDASEKLQFRKEKPTEAQGPLLNCDTAISMQEPQKSKKRTFEESEKEPSNSPQAPKQKYVCLTV
          PLDDTCLDASEKLQFRKEKPTEAQGPLLNCDTAISMQEPQKSKKRTFEESEKEPSNSPQAPKQKYVCLTV
Retrocopy PLDDTCLDASEKLQFRKEKPTEAQGPLLNCDTAISMQEPQKSKKRTFEESEKEPSNSPQAPKQKYVCLTV

Parental  QDWDLLNSY
          QDWDLLNSY
Retrocopy QDWDLLNSY

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_15 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016552	1 retrocopy	retro_ogar_816,
Ochotona princeps	ENSOPRG00000005566	1 retrocopy	retro_opri_15 ,
Ictidomys tridecemlineatus	ENSSTOG00000022786	1 retrocopy	retro_itri_1536,