RetrogeneDB ID: retro_opri_1198

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_93326:247..435(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000002972
• Aliases: None
• Description: None

Sequence

>retro_opri_1198
GGAGCGTTCTAGAGTGTGAAGAAGGACAGAGTCGGACATTTGCTGCAGTCGGCCTGCCTGCTGCAGGAAGGAAAGGAGAT
GGGCAGTGTTTGAAGGACGGCTATTGCCAAGCGTTGAAGTACTTCTTCTTTGAGTGTAAAAGATCAATGCTGGAAGACAG
GTCAAGTTTCAGAGGAAGAAAAGGATAT

Alignment

ORF - retro_opri_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 85.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GACSGVKEDLGACLLQSDCVLQEGKS-PRQCLKEGHCQALKYSFFECKRSMLEDRSSFRGRKGY
          GA...VK.D....LLQS.C.LQEGK....QCLK.G.CQALKY.FFECKRSMLEDRSSFRGRKGY
Retrocopy GAF*SVKKDRVGHLLQSACLLQEGKE<DGQCLKDGYCQALKYFFFECKRSMLEDRSSFRGRKGY

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_1198 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007139	1 retrocopy	retro_cjac_1382,
Cavia porcellus	ENSCPOG00000009263	1 retrocopy	retro_cpor_270,
Equus caballus	ENSECAG00000004183	1 retrocopy	retro_ecab_295,
Echinops telfairi	ENSETEG00000013626	1 retrocopy	retro_etel_757,
Felis catus	ENSFCAG00000004424	1 retrocopy	retro_fcat_201,
Homo sapiens	ENSG00000183513	1 retrocopy	retro_hsap_204,
Gorilla gorilla	ENSGGOG00000006019	1 retrocopy	retro_ggor_278,
Myotis lucifugus	ENSMLUG00000013167	2 retrocopies	retro_mluc_1336, retro_mluc_1760,
Monodelphis domestica	ENSMODG00000001197	1 retrocopy	retro_mdom_1413,
Nomascus leucogenys	ENSNLEG00000001998	1 retrocopy	retro_nleu_1854,
Ochotona princeps	ENSOPRG00000002972	3 retrocopies	retro_opri_1198 , retro_opri_1203, retro_opri_391,
Pongo abelii	ENSPPYG00000012085	1 retrocopy	retro_pabe_435,
Pan troglodytes	ENSPTRG00000012267	1 retrocopy	retro_ptro_340,
Pteropus vampyrus	ENSPVAG00000001578	1 retrocopy	retro_pvam_460,
Sorex araneus	ENSSARG00000006275	1 retrocopy	retro_sara_61,