RetrogeneDB ID: retro_opri_157

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2989:89233..89469(-)
• Located in intron of: ENSOPRG00000003470

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000003411
• Aliases: None
• Description: None

Sequence

>retro_opri_157
CCCTGCAGCCTAGGAGGCTGCCAGGAAGCAGCACCCACAAAGCTGTACGCAGGAGCTGTTCTCAAAGTCGGCAGAAGAGA
ATGGAAAGGCTCCCGTCGAGTCCAGGCTTTCGTGAGGAGTGGTAAACCCAAACTAAACAGAGACTATAAGTCACGTGTGT
CTGAGGACCAGCCCCCGTGCTGAAGTGTTTTCATGACAAGGGGAAAATCGCTGGAGAACTCAGCATCCTGGAATAC

Alignment

ORF - retro_opri_157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 50.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDCRGCCQEEALETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRG-LQIKYVRGSDPVLKLLDDN
          P...G.CQE.A....KLYAGA.L.V..........VQAFVRS.KPKL.R..L....V.G..PVLK...D.
Retrocopy PCSLGGCQEAA--PTKLYAGAVLKVGRREWKGSRRVQAFVRSGKPKLNRD<L*VTCV*GPAPVLKCFHDK

Parental  GNIAEELSILKW
          G.IA.ELSIL..
Retrocopy GKIAGELSILEY

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_157 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004701	1 retrocopy	retro_dnov_2296,
Macropus eugenii	ENSMEUG00000005462	4 retrocopies	retro_meug_1005, retro_meug_2191, retro_meug_769, retro_meug_817,
Monodelphis domestica	ENSMODG00000008134	2 retrocopies	retro_mdom_1289, retro_mdom_1504,
Ochotona princeps	ENSOPRG00000003411	2 retrocopies	retro_opri_157 , retro_opri_897,
Vicugna pacos	ENSVPAG00000011775	1 retrocopy	retro_vpac_621,