RetrogeneDB ID: retro_opri_28

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1107:136856..137142(+)
• Located in intron of: ENSOPRG00000003846

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS14
• Ensembl ID: ENSOPRG00000008422
• Aliases: None
• Description: ribosomal protein S14 [Source:HGNC Symbol;Acc:10387]

Sequence

>retro_opri_28
ACTGGTGGAATGAAGGTGAAGGCTGATCGAGATGAATCCTCACCATATGCTGCCACGTTGGCTGCCCAGGATGTGGCCCA
GAGGTGCAAAGAGCTGGGCATCACTGCCCCCACATATCAAACTGCGGGCCACAGGAGGAAATAGGACCAAAACCCCTGGA
CCTGGAGCCCAGTCAGCTCTCAGAGCCCTTGCCCGCTCGGGGATGAACACTGGGCGAATTGAGGATGTCACCCCAAGCCC
CTCCGACAGCACCCGCAGGAAGGGGTGTCGCCGTGGTCACCGCCTG

Alignment

ORF - retro_opri_28 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.62 %
• Parental protein coverage: 62.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGGMKVKADRDESSPYAAMLAAQDVAQRCKELGITAL-HLKLRATGGNRTKTPGPGAQSALRALARSGMK
          TGGMKVKADRDESSPYAA.LAAQDVAQRCKELGITA..H.KLRATGGNRTKTPGPGAQSALRALARSGM.
Retrocopy TGGMKVKADRDESSPYAATLAAQDVAQRCKELGITAP>HIKLRATGGNRTKTPGPGAQSALRALARSGMN

Parental  IGRIEDVTPIPSDSTRRKGGRRGRRL
          .GRIEDVTP.PSDSTRRKG.RRG.RL
Retrocopy TGRIEDVTPSPSDSTRRKGCRRGHRL

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_28 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 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004644	2 retrocopies	retro_amel_1390, retro_amel_524,
Bos taurus	ENSBTAG00000008570	2 retrocopies	retro_btau_1109, retro_btau_213,
Canis familiaris	ENSCAFG00000018094	2 retrocopies	retro_cfam_1589, retro_cfam_301,
Callithrix jacchus	ENSCJAG00000020981	1 retrocopy	retro_cjac_89,
Equus caballus	ENSECAG00000024336	3 retrocopies	retro_ecab_127, retro_ecab_282, retro_ecab_522,
Latimeria chalumnae	ENSLACG00000016164	1 retrocopy	retro_lcha_12,
Loxodonta africana	ENSLAFG00000031195	2 retrocopies	retro_lafr_235, retro_lafr_67,
Myotis lucifugus	ENSMLUG00000013279	4 retrocopies	retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta	ENSMMUG00000002848	5 retrocopies	retro_mmul_1921, retro_mmul_1983, retro_mmul_358, retro_mmul_570, retro_mmul_90,
Mustela putorius furo	ENSMPUG00000013776	1 retrocopy	retro_mputfur_127,
Nomascus leucogenys	ENSNLEG00000010366	1 retrocopy	retro_nleu_101,
Oryctolagus cuniculus	ENSOCUG00000011509	1 retrocopy	retro_ocun_128,
Otolemur garnettii	ENSOGAG00000000721	1 retrocopy	retro_ogar_286,
Ochotona princeps	ENSOPRG00000008422	17 retrocopies	retro_opri_1012, retro_opri_1074, retro_opri_114, retro_opri_194, retro_opri_258, retro_opri_268, retro_opri_28 , retro_opri_306, retro_opri_376, retro_opri_428, retro_opri_707, retro_opri_825, retro_opri_842, retro_opri_876, retro_opri_882, retro_opri_919, retro_opri_971,