RetrogeneDB ID: retro_opri_100

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2247:67068..67563(-)
• Located in intron of: ENSOPRG00000004429

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSOPRG00000011078
• Aliases: None
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_opri_100
ATGCCACCCAAGTTCGACCCTAACGAGATTAAAGTCGTGTACCTGCGGTGCACCGGCGGCGAGGTGGGTGCCACGTCTGC
CCTGGCCCCCAAGATCGGCCCCCTGGGCCTGTCTCCAAAGAAGGTGGGAGATGACATTGCCAAGGCCACCGGGGACTGGA
AGGGCCTGCGGATCACGGTGAAGCTGACCATCCAGAACCGACAAGCGCAGATCGAGGTGGTGCCGTCGGCCTCTGCCCTG
ATCATCAAGGCCCTCAAGGAGCCGCCCAGGGACCGCAAGAAGCAGAAGAACATCAAACACAGCGGGAACATCACATTTGA
TGAAATTGTCAACATCGCCCGGCAGATGCGCCACCGATCCTTAGCCAGAGAACTTTCCGGAACCATCAAAGAGATTCTGG
GGACTGCCCAGTCGGTGGGCTGCAATGTGGATGGCCGCCACCCACACGACATCATAGATGACATCAACAGTGGTGCAGTG
GAATGCCCAGCTAGC

Alignment

ORF - retro_opri_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
          MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ
Retrocopy MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQ

Parental  IEVVPSASALII-ALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG
          IEVVPSASALII.ALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG
Retrocopy IEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTIKEILGTAQSVG

Parental  CNVDGRHPHDIIDDINSGAVECPAS
          CNVDGRHPHDIIDDINSGAVECPAS
Retrocopy CNVDGRHPHDIIDDINSGAVECPAS

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_100 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 279 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006963	3 retrocopies	retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus	ENSCJAG00000018082	1 retrocopy	retro_cjac_221,
Homo sapiens	ENSG00000197958	41 retrocopies	retro_hsap_1064, retro_hsap_117, retro_hsap_1210, retro_hsap_127, retro_hsap_1311, retro_hsap_1359, retro_hsap_137, retro_hsap_1401, retro_hsap_1592, retro_hsap_1644, retro_hsap_1790, retro_hsap_1850, retro_hsap_1880, retro_hsap_1895, retro_hsap_2005, retro_hsap_2031, retro_hsap_2099, retro_hsap_2123, retro_hsap_2202, retro_hsap_2311, retro_hsap_2381, retro_hsap_2428, retro_hsap_2436, retro_hsap_2456, retro_hsap_2642, retro_hsap_3388, retro_hsap_3405, retro_hsap_3458, retro_hsap_3544, retro_hsap_3578, retro_hsap_3709, retro_hsap_4107, retro_hsap_4121, retro_hsap_4746, retro_hsap_584, retro_hsap_643, retro_hsap_705, retro_hsap_719, retro_hsap_768, retro_hsap_868, retro_hsap_983,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta	ENSMMUG00000000422	2 retrocopies	retro_mmul_1823, retro_mmul_53,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus	ENSMUSG00000038900	1 retrocopy	retro_mmus_28,
Oryctolagus cuniculus	ENSOCUG00000004902	9 retrocopies	retro_ocun_1246, retro_ocun_1632, retro_ocun_1895, retro_ocun_318, retro_ocun_329, retro_ocun_520, retro_ocun_556, retro_ocun_677, retro_ocun_880,
Otolemur garnettii	ENSOGAG00000000597	120 retrocopies	retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Ochotona princeps	ENSOPRG00000011078	21 retrocopies	retro_opri_100 , retro_opri_1018, retro_opri_1066, retro_opri_1110, retro_opri_1210, retro_opri_1217, retro_opri_221, retro_opri_265, retro_opri_336, retro_opri_353, retro_opri_418, retro_opri_461, retro_opri_479, retro_opri_576, retro_opri_638, retro_opri_648, retro_opri_658, retro_opri_672, retro_opri_835, retro_opri_905, retro_opri_986,
Pongo abelii	ENSPPYG00000019622	44 retrocopies	retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes	ENSPTRG00000022808	1 retrocopy	retro_ptro_21,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sarcophilus harrisii	ENSSHAG00000017864	8 retrocopies	retro_shar_140, retro_shar_266, retro_shar_284, retro_shar_335, retro_shar_346, retro_shar_453, retro_shar_508, retro_shar_646,