RetrogeneDB ID: retro_opri_987

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5297:73398..73674(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL19
• Ensembl ID: ENSOPRG00000007092
• Aliases: None
• Description: ribosomal protein L19 [Source:HGNC Symbol;Acc:10312]

Sequence

>retro_opri_987
CAGCAGATTAGGAATCTGATTAAGGATGGGCTGATTATCCACAAACCAGTGACCGTCCACTCCCGGGCTCAGTGCCAGAA
GAACACCCTGACCCGCAGAAAAGGCAGGCACATGGGCATAGAGAAGCATAAGGCTACAGCCAAAGCGCGCATGCTGGAAA
AGGTGACCTGGATGAGGAGGATGCGGATCCTGCGCCGCCTGCTCAGGAGATACCAGGAGTCCAAGAAGATTGACCGCCAC
AGGTACCAGAAGGTGAAGGGAAGCATGTTCAAAAAT

Alignment

ORF - retro_opri_987 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 60.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRR
          QQIR.LIKDGLII.KPVTVHSRA.C.KNTL.RRKGRHMGI.K.K.TA.ARM.EKVTWMRRMRILRRLLRR
Retrocopy QQIRNLIKDGLIIHKPVTVHSRAQCQKNTLTRRKGRHMGIEKHKATAKARMLEKVTWMRRMRILRRLLRR

Parental  YRESKKIDRHMYHSLYLKVKGNVFKN
          Y.ESKKIDRH.Y.....KVKG..FKN
Retrocopy YQESKKIDRHRYQ----KVKGSMFKN

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_987 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 11 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002060	5 retrocopies	retro_btau_1241, retro_btau_1254, retro_btau_1371, retro_btau_1480, retro_btau_761,
Callithrix jacchus	ENSCJAG00000008520	4 retrocopies	retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Microcebus murinus	ENSMICG00000002663	5 retrocopies	retro_mmur_1213, retro_mmur_231, retro_mmur_469, retro_mmur_520, retro_mmur_678,
Macaca mulatta	ENSMMUG00000004235	2 retrocopies	retro_mmul_283, retro_mmul_63,
Nomascus leucogenys	ENSNLEG00000000748	19 retrocopies	retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540, retro_nleu_656,
Ochotona princeps	ENSOPRG00000007092	2 retrocopies	retro_opri_1220, retro_opri_987 ,
Procavia capensis	ENSPCAG00000015228	1 retrocopy	retro_pcap_141,
Pongo abelii	ENSPPYG00000008492	20 retrocopies	retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Tupaia belangeri	ENSTBEG00000008077	31 retrocopies	retro_tbel_1024, retro_tbel_1150, retro_tbel_1200, retro_tbel_1248, retro_tbel_1507, retro_tbel_1620, retro_tbel_173, retro_tbel_1752, retro_tbel_1791, retro_tbel_1826, retro_tbel_1942, retro_tbel_199, retro_tbel_2166, retro_tbel_2529, retro_tbel_2558, retro_tbel_2687, retro_tbel_2751, retro_tbel_2855, retro_tbel_3256, retro_tbel_3347, retro_tbel_3493, retro_tbel_3758, retro_tbel_4501, retro_tbel_4606, retro_tbel_4631, retro_tbel_759, retro_tbel_799, retro_tbel_835, retro_tbel_867, retro_tbel_957, retro_tbel_988,
Tarsius syrichta	ENSTSYG00000008698	10 retrocopies	retro_tsyr_1164, retro_tsyr_1267, retro_tsyr_1310, retro_tsyr_1330, retro_tsyr_1770, retro_tsyr_1916, retro_tsyr_540, retro_tsyr_713, retro_tsyr_782, retro_tsyr_93,