RetrogeneDB ID: retro_opri_335

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_5354:471231..471780(+)
• Located in intron of: ENSOPRG00000001219

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000001234
• Aliases: None
• Description: None

Sequence

>retro_opri_335
GACGCGGAGGACGCGGTGCACGAGCGAGACGGCTACGATTACGACGGGTACCGTCTCCGGGTCGAGTTTCCACGGAGCGG
CCGCGGGCCGGGCCGAGGCGGAGGTGCAGGTGGATGGGGCGGAGCGCCCCGCGGCCGCTATGGCCCCCCATCCCGGCGGT
CCGACCACCGCGTGGTGGTCTCCGGACTGCCTCCGAGTGGAAGCTGGCAGGATTTGAAGGATCACATGCGCGAGGCGGGC
GATATATGTTACGCTGATGTCCACCGAGATGGCACCGGTGTCGTGGAGTTTGTACGGAAAGAAGATATGACCTATGCAGT
TCGAAAACTGGACAACACTAAGTTTAGATCTCACGTGGGAGAAACCGCCTACATCCGGGTGAAGGCTGATGGGCCCAGAA
GTCCCAGTTCTGGAAGATCTCCATCTCGAAGCCGCCGTCGCAGCCGAAGCCGTAGCAGAAGCAACAGCAGGAGTCGCAGT
TACTCCCCAAGGAGAAGCAGAGGATCACCACGCTATTCTCCCCGTCATAGCAGATCTCGCTCTCGTACA

Alignment

ORF - retro_opri_335 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGRGGGGGGGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQ
          DAEDAV..RDGYDYDGYRLRVEFPRSGRG.GRGGG.GG.GGAPRGRYGPPSRRS..RVVVSGLPPSGSWQ
Retrocopy DAEDAVHERDGYDYDGYRLRVEFPRSGRGPGRGGGAGGWGGAPRGRYGPPSRRSDHRVVVSGLPPSGSWQ

Parental  DLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRS
          DLKDHMREAGD.CYADV.RDGTGVVEFVRKEDMTYAVRKLDNTKFRSH.GETAYIRVK.DGPRSPS.GRS
Retrocopy DLKDHMREAGDICYADVHRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHVGETAYIRVKADGPRSPSSGRS

Parental  RSRSRSRSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT
          .SRSR.RSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT
Retrocopy PSRSRRRSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT

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_335 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009255	1 retrocopy	retro_eeur_180,
Myotis lucifugus	ENSMLUG00000011040	1 retrocopy	retro_mluc_307,
Otolemur garnettii	ENSOGAG00000025950	1 retrocopy	retro_ogar_2848,
Ochotona princeps	ENSOPRG00000001234	2 retrocopies	retro_opri_335 , retro_opri_625,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Ochotona princeps	ENSOPRG00000006006	3 retrocopies	retro_opri_1037, retro_opri_158, retro_opri_545,