RetrogeneDB ID: retro_opri_1013

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_573:291145..291370(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSOPRG00000001780
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_opri_1013
ATGGTCCAGCATTTGATATACCACCATAGACTTTCCTACAATACAGTCTCCAACAAAATCAGACTATCTCGAACTCCTGT
GAACAGAAATGTCTACCTTCATCCTAAGAAGGTTGGTAAGGTACCAAAGTCTGTGTGTGGAGTGTGCTCGGGCTAACTGT
GAGCAGTTCGTGCTATGAGACCTAGAGTTCTGATGCGGTTGTCTAAGAAGAAAAAAAACATGTCA

Alignment

ORF - retro_opri_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 84.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKT
          MVQ.L.Y..RLSYNT.SNK.RLSRTP.NR.VYL..KKVGK.PKS.CGVC.G.L..VRA.RP.VLMRLSK.
Retrocopy MVQHLIYHHRLSYNTVSNKIRLSRTPVNRNVYLHPKKVGKVPKSVCGVCSG*L*AVRAMRPRVLMRLSKK

Parental  KKHVS
          ....S
Retrocopy XXXMS

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_1013 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 21 parental genes, and 192 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009074	10 retrocopies	retro_chof_1313, retro_chof_1474, retro_chof_184, retro_chof_2249, retro_chof_2258, retro_chof_2260, retro_chof_2291, retro_chof_2411, retro_chof_281, retro_chof_324,
Callithrix jacchus	ENSCJAG00000015993	4 retrocopies	retro_cjac_130, retro_cjac_293, retro_cjac_83, retro_cjac_99,
Equus caballus	ENSECAG00000019719	1 retrocopy	retro_ecab_58,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Myotis lucifugus	ENSMLUG00000000464	4 retrocopies	retro_mluc_125, retro_mluc_1372, retro_mluc_1427, retro_mluc_1847,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Mustela putorius furo	ENSMPUG00000008873	17 retrocopies	retro_mputfur_1028, retro_mputfur_1095, retro_mputfur_1130, retro_mputfur_1170, retro_mputfur_12, retro_mputfur_1242, retro_mputfur_1305, retro_mputfur_1480, retro_mputfur_1501, retro_mputfur_360, retro_mputfur_378, retro_mputfur_475, retro_mputfur_517, retro_mputfur_557, retro_mputfur_562, retro_mputfur_852, retro_mputfur_923,
Mus musculus	ENSMUSG00000062006	26 retrocopies	retro_mmus_1064, retro_mmus_1283, retro_mmus_1513, retro_mmus_1603, retro_mmus_1658, retro_mmus_2115, retro_mmus_2116, retro_mmus_215, retro_mmus_2154, retro_mmus_2266, retro_mmus_2290, retro_mmus_2476, retro_mmus_2595, retro_mmus_2695, retro_mmus_2748, retro_mmus_2903, retro_mmus_2960, retro_mmus_3041, retro_mmus_3381, retro_mmus_3524, retro_mmus_467, retro_mmus_609, retro_mmus_640, retro_mmus_817, retro_mmus_823, retro_mmus_882,
Nomascus leucogenys	ENSNLEG00000012934	20 retrocopies	retro_nleu_1219, retro_nleu_1322, retro_nleu_1495, retro_nleu_150, retro_nleu_1617, retro_nleu_1703, retro_nleu_1839, retro_nleu_1915, retro_nleu_2101, retro_nleu_2260, retro_nleu_2268, retro_nleu_2575, retro_nleu_263, retro_nleu_2911, retro_nleu_2916, retro_nleu_2966, retro_nleu_3073, retro_nleu_38, retro_nleu_553, retro_nleu_861,
Otolemur garnettii	ENSOGAG00000006774	1 retrocopy	retro_ogar_44,
Ochotona princeps	ENSOPRG00000001780	11 retrocopies	retro_opri_1013 , retro_opri_142, retro_opri_303, retro_opri_311, retro_opri_344, retro_opri_365, retro_opri_39, retro_opri_610, retro_opri_771, retro_opri_907, retro_opri_933,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Rattus norvegicus	ENSRNOG00000016387	36 retrocopies	retro_rnor_1031, retro_rnor_1083, retro_rnor_1101, retro_rnor_1172, retro_rnor_1376, retro_rnor_1550, retro_rnor_1575, retro_rnor_1630, retro_rnor_1694, retro_rnor_1695, retro_rnor_1696, retro_rnor_1775, retro_rnor_1803, retro_rnor_1844, retro_rnor_1857, retro_rnor_2029, retro_rnor_2090, retro_rnor_2095, retro_rnor_2139, retro_rnor_2230, retro_rnor_2565, retro_rnor_2578, retro_rnor_2597, retro_rnor_2621, retro_rnor_2651, retro_rnor_2794, retro_rnor_282, retro_rnor_367, retro_rnor_500, retro_rnor_575, retro_rnor_605, retro_rnor_617, retro_rnor_672, retro_rnor_848, retro_rnor_866, retro_rnor_869,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,