RetrogeneDB ID: retro_opri_619

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_19592:3501..3716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSOPRG00000008599
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_opri_619
AAAACCATTCCCTGGAAGGGTTCCGTGGAGGGCTTCAAGCCGGCAGACAACAAGTGTCTGTTAAGAGCCACTGACGGGAA
GAGGAAGATCAGCACCGTGGTGAGCTCCAAAGAACTAAGTTTCAGATGGTCCTCTCCAACCTGCTGAGAGCGAGCATAGA
TGGGCTCAAGAGGCGGAACAGAAAGAGCACAAGCGGGAAGAGCGAACCAGCACAG

Alignment

ORF - retro_opri_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.16 %
• Parental protein coverage: 64.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSFPPKGSV-CFQSADNKCLLRTAGKRRNSTLVSSKEV-NKFQMAYSNLLRANMDGLKKRDKKSKSKKSK
          K..P.KGSV..F..ADNKCLLR.....R....V.S.....KFQM..SNLLRA..DGLK.R..KS.S.KS.
Retrocopy KTIPWKGSVEGFKPADNKCLLRATDGKRKISTVVSSKE<TKFQMVLSNLLRASIDGLKRRNRKSTSGKSE

Parental  PAQ
          PAQ
Retrocopy PAQ

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_619 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017231	1 retrocopy	retro_amel_1566,
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Erinaceus europaeus	ENSEEUG00000012759	1 retrocopy	retro_eeur_357,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Ochotona princeps	ENSOPRG00000008599	1 retrocopy	retro_opri_619 ,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Rattus norvegicus	ENSRNOG00000007512	1 retrocopy	retro_rnor_2702,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,