RetrogeneDB ID: retro_opri_665

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_22685:1280..2170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000005256
• Aliases: None
• Description: None

Sequence

>retro_opri_665
AAGTATTTGGAAAGGCATTCGAGGATGAAATGAAAAAGCTTCTCCTCTTCCTTAAAGCCTTTTCTGAAACAGAGCAGACA
AAATTGGCGATGCTGTCCGGGATCCTGCTGGGCAATGGCACCCTTCCAGCCAGCATCCTCACCAGCCTCTTCACCGACAA
CCTGGTCAAGGAAGGCATCGCGGCCTCGTTTGCCGTCAAGCTCTTCAAGGCCTGGATGGCAGAGAAAGACGCCAACTCTG
TTACCTCCTCGCTGAGAAAAGCCAACCTTGACAAGAGGCTGCTTGAACTCTTTCCGGTTAACCGGCAGAGCGTGGATCAT
TTTGCTAAGTACTTCACTGACGCGGGCCTCAAGGAGCTGTCCGACTTCCTCCGGGTGCAGCAGTCCCTGGGCACCAGGAA
AGAGCTACAGAAGGAGCTCCAGGAGCGGCTCTCACAGGAGTGCCCCATCAAGGAGGTGGTGCTTTACGTCAAAGAAGAAA
TGAAGAGGAATGAGCTTCCGGAAACGGCGGTGATTGGACTCCTGTGGGCCTGCATCATGAATGCCGTGGAGTGGAACAAG
AAGGAAGAGCTGGTCGCCGAGCAAGCTCTCAAGCACCTGAAGCAATACGCTCCCCTCCTGGCTGTGTTCAGCTCCCAAGG
CCAGTCGGAGCTGGCCCTGCTGCAGAAGGTCCAGGAGTACTGCTACGACAACATCCACTTCATGAAGGCCTTTCAGAAGA
TCGTGGTTCTCTTCTACAAAGCTGATGTTCTGAGTGAAGAAGCAATACTGAAATGGTATAAAGAAGCCCACGTTGCCAAA
GGCAAAAGTGTTTTCCTTGACCAGATGAAGAAGTTTGTGGAGTGGTTGCAGAACGCAGAAGAAGAGTCTGAATCGGAAGG
TGAAGAAAAC

Alignment

ORF - retro_opri_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 70.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KYLE-KAFEDEMKKLLLFLKAFSETEQTKLAMLSGILLGNGTLPASILTSLFTDNLVKEGIAASFAVKL-
          KYLE.KAFEDEMKKLLLFLKAFSETEQTKLAMLSGILLGNGTLPASILTSLFTDNLVKEGIAASFAVKL.
Retrocopy KYLE<KAFEDEMKKLLLFLKAFSETEQTKLAMLSGILLGNGTLPASILTSLFTDNLVKEGIAASFAVKLF

Parental  KAWMAEKDANSVTSSLRKANLDKRLLELFPVNRQSVDHFAKYFTDAGLKELSDFLRVQQSLGTRKELQKE
          KAWMAEKDANSVTSSLRKANLDKRLLELFPVNRQSVDHFAKYFTDAGLKELSDFLRVQQSLGTRKELQKE
Retrocopy KAWMAEKDANSVTSSLRKANLDKRLLELFPVNRQSVDHFAKYFTDAGLKELSDFLRVQQSLGTRKELQKE

Parental  LQERLSQECPIKEVVLYVKEEMKRNELPETAVIGLLWACIMNAVEWNKKEELVAEQALKHLKQYAPLLAV
          LQERLSQECPIKEVVLYVKEEMKRNELPETAVIGLLWACIMNAVEWNKKEELVAEQALKHLKQYAPLLAV
Retrocopy LQERLSQECPIKEVVLYVKEEMKRNELPETAVIGLLWACIMNAVEWNKKEELVAEQALKHLKQYAPLLAV

Parental  FSSQGQSELALLQKVQEYCYDNIHFMKAFQKIVVLFYKADVLSEEAILKWYKEAHVAKGKSVFLDQMKKF
          FSSQGQSELALLQKVQEYCYDNIHFMKAFQKIVVLFYKADVLSEEAILKWYKEAHVAKGKSVFLDQMKKF
Retrocopy FSSQGQSELALLQKVQEYCYDNIHFMKAFQKIVVLFYKADVLSEEAILKWYKEAHVAKGKSVFLDQMKKF

Parental  VEWLQNAEEESESEGEEN
          VEWLQNAEEESESEGEEN
Retrocopy VEWLQNAEEESESEGEEN

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_665 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001663	4 retrocopies	retro_dnov_2177, retro_dnov_2422, retro_dnov_2649, retro_dnov_575,
Equus caballus	ENSECAG00000022038	1 retrocopy	retro_ecab_1121,
Macaca mulatta	ENSMMUG00000017045	1 retrocopy	retro_mmul_1457,
Ochotona princeps	ENSOPRG00000005256	2 retrocopies	retro_opri_665 , retro_opri_9,
Pongo abelii	ENSPPYG00000017763	1 retrocopy	retro_pabe_2385,
Pteropus vampyrus	ENSPVAG00000014571	1 retrocopy	retro_pvam_481,
Ictidomys tridecemlineatus	ENSSTOG00000002506	1 retrocopy	retro_itri_1286,
Tarsius syrichta	ENSTSYG00000009806	1 retrocopy	retro_tsyr_1923,
Tursiops truncatus	ENSTTRG00000009867	1 retrocopy	retro_ttru_162,