RetrogeneDB ID: retro_opri_635

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_20626:3967..4843(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000004505
• Aliases: None
• Description: None

Sequence

>retro_opri_635
ATGTCCTGAGCCCTTGACGTCCTGCAGAGGAAGGCAGAGGAGGTCCTCAAATTCCTTGCTGCAGGAACCCACTTGGGAGG
CACCAACATCAACTTCCACATGGAGCAGTACATCTACAAAAGGAAAAGCCATGGCATCTACATCATCAACTTCAAGAAGA
ACTGGGAGAAGCTCCTGCTGGCGGCGTGGGTCATCGTGGCCATCGAGAACCCTGCGGACATCAGCGTAATCTCCTCCGGG
AACACTGGCCAGAGGGCTGTGCTGAAGTTTGCTGCTGCCACTGGAGCTACTCCCATCGCTGGCGCTTCATTCCTGGCACC
TTCAGTAACCAGATCCAGGCCACCTTCCAGGAGCCGCGGCTCCTGGTGGTGACAGATCCCAGGGCCGACAATCAGCCCCT
CATAGAGGCATCGTACGTGAACCTGCCTACCATCGCTCTGTGCAACATGAACTCTCCTCTGTGCTACGTGTACAATGTCA
TCCCGTGCAACAACGAGGGAGCCCACTCCGTGGGTTTGATGTAGTGGATGCTGGCCCGGGATGTTCTGTGCATGAACAGC
ACCGTCTCCCGTGAACACCCGTGGGAGGCCATGCCTGATCTCTACTTCTACAGTGATCTTAAAGAGATTGAAAAAAGAAG
AACAGGCTGCGGCTGAAAAGGCAGTGACCAAGGAGGAGTTCCAGGGTGAATGGACCACCCCCGCTCCCGAGTTCTTGGCT
ACCAAGCCCGAGGTTGCAGACTGCTCTGAGGGTGTGAAGGTGCCTTCTGTGACCATCCAGCTGTTCCCCACTGAAGACTG
GAGTGCCCAGCCTGCCACTGAAGACTGGTCTGCGGCCCCCACAGCTCAGGCCACTGGATGGATAGGAACAACCACC

Alignment

ORF - retro_opri_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
          MS.ALDVLQ.K.E.VLKFLAAGTHLGGTN..F.MEQYIYKRKS.GIYIIN.K..WEKLLLAA..IVAIEN
Retrocopy MS*ALDVLQRKAEEVLKFLAAGTHLGGTNINFHMEQYIYKRKSHGIYIINFKKNWEKLLLAAWVIVAIEN

Parental  PADVSVISSRNTGQRAVLKFAAATGATPIAG-RFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASY
          PAD.SVISS.NTGQRAVLKFAAATGATPIAG.RF.PGTF.NQIQA.F.EPRLLVVTDPRAD.QPL.EASY
Retrocopy PADISVISSGNTGQRAVLKFAAATGATPIAG<RFIPGTFSNQIQATFQEPRLLVVTDPRADNQPLIEASY

Parental  VNLPH-ALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEE
          VNLP..ALCN..SPL.YV...IPCNN.GAHSVGLM.WMLAR.VL.M..T.SREHPWE.MPDLYFY.D..E
Retrocopy VNLPTIALCNMNSPLCYVYNVIPCNNEGAHSVGLM*WMLARDVLCMNSTVSREHPWEAMPDLYFYSDLKE

Parental  IE-KEEQAAAEKAVTKEEFQGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSA
          IE.KEEQAAAEKAVTKEEFQGEWT.PAPEF.AT.PEVAD.SEGV.VPSV.IQ.FPTEDWSAQPATEDWSA
Retrocopy IE>KEEQAAAEKAVTKEEFQGEWTTPAPEFLATKPEVADCSEGVKVPSVTIQLFPTEDWSAQPATEDWSA

Parental  APTAQATEWVGTTT
          APTAQAT.W.GTTT
Retrocopy APTAQATGWIGTTT

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_635 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 30 parental genes, and 315 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 retrocopies	retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Canis familiaris	ENSCAFG00000005101	27 retrocopies	retro_cfam_1046, retro_cfam_1109, retro_cfam_1173, retro_cfam_1189, retro_cfam_1263, retro_cfam_1288, retro_cfam_1366, retro_cfam_1373, retro_cfam_1435, retro_cfam_1511, retro_cfam_1534, retro_cfam_1545, retro_cfam_1555, retro_cfam_1679, retro_cfam_1770, retro_cfam_1814, retro_cfam_1957, retro_cfam_1990, retro_cfam_2140, retro_cfam_512, retro_cfam_820, retro_cfam_828, retro_cfam_854, retro_cfam_928, retro_cfam_957, retro_cfam_980, retro_cfam_994,
Callithrix jacchus	ENSCJAG00000009675	15 retrocopies	retro_cjac_1113, retro_cjac_1572, retro_cjac_1595, retro_cjac_2265, retro_cjac_2438, retro_cjac_2500, retro_cjac_2502, retro_cjac_2750, retro_cjac_2897, retro_cjac_305, retro_cjac_3160, retro_cjac_4124, retro_cjac_53, retro_cjac_732, retro_cjac_958,
Cavia porcellus	ENSCPOG00000008715	7 retrocopies	retro_cpor_1206, retro_cpor_1255, retro_cpor_1293, retro_cpor_594, retro_cpor_624, retro_cpor_806, retro_cpor_958,
Dasypus novemcinctus	ENSDNOG00000004048	27 retrocopies	retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Dipodomys ordii	ENSDORG00000008267	1 retrocopy	retro_dord_548,
Equus caballus	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Erinaceus europaeus	ENSEEUG00000005292	2 retrocopies	retro_eeur_202, retro_eeur_679,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus	ENSFCAG00000002739	22 retrocopies	retro_fcat_1119, retro_fcat_1127, retro_fcat_1239, retro_fcat_1353, retro_fcat_1595, retro_fcat_1668, retro_fcat_1694, retro_fcat_1720, retro_fcat_1758, retro_fcat_1804, retro_fcat_1807, retro_fcat_1861, retro_fcat_1970, retro_fcat_239, retro_fcat_258, retro_fcat_384, retro_fcat_391, retro_fcat_551, retro_fcat_682, retro_fcat_722, retro_fcat_793, retro_fcat_906,
Homo sapiens	ENSG00000168028	2 retrocopies	retro_hsap_107, retro_hsap_3015,
Gorilla gorilla	ENSGGOG00000015038	11 retrocopies	retro_ggor_1069, retro_ggor_1095, retro_ggor_1110, retro_ggor_1277, retro_ggor_1729, retro_ggor_2325, retro_ggor_2461, retro_ggor_2671, retro_ggor_2804, retro_ggor_2811, retro_ggor_62,
Loxodonta africana	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Microcebus murinus	ENSMICG00000004518	32 retrocopies	retro_mmur_1031, retro_mmur_1042, retro_mmur_1120, retro_mmur_1310, retro_mmur_1357, retro_mmur_136, retro_mmur_1432, retro_mmur_1482, retro_mmur_1513, retro_mmur_1522, retro_mmur_1593, retro_mmur_1596, retro_mmur_1607, retro_mmur_1628, retro_mmur_196, retro_mmur_219, retro_mmur_284, retro_mmur_302, retro_mmur_367, retro_mmur_477, retro_mmur_522, retro_mmur_532, retro_mmur_559, retro_mmur_561, retro_mmur_604, retro_mmur_620, retro_mmur_714, retro_mmur_727, retro_mmur_753, retro_mmur_756, retro_mmur_821, retro_mmur_933,
Macaca mulatta	ENSMMUG00000007930	2 retrocopies	retro_mmul_1789, retro_mmul_592,
Macaca mulatta	ENSMMUG00000022965	19 retrocopies	retro_mmul_1008, retro_mmul_1167, retro_mmul_120, retro_mmul_1237, retro_mmul_136, retro_mmul_1527, retro_mmul_1678, retro_mmul_1755, retro_mmul_1879, retro_mmul_1909, retro_mmul_2274, retro_mmul_2388, retro_mmul_2538, retro_mmul_2541, retro_mmul_2622, retro_mmul_378, retro_mmul_789, retro_mmul_876, retro_mmul_911,
Monodelphis domestica	ENSMODG00000010967	2 retrocopies	retro_mdom_1244, retro_mdom_1726,
Mustela putorius furo	ENSMPUG00000002463	21 retrocopies	retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus	ENSMUSG00000032518	1 retrocopy	retro_mmus_219,
Otolemur garnettii	ENSOGAG00000028830	8 retrocopies	retro_ogar_1507, retro_ogar_1548, retro_ogar_2094, retro_ogar_2258, retro_ogar_3126, retro_ogar_327, retro_ogar_457, retro_ogar_567,
Ochotona princeps	ENSOPRG00000004505	16 retrocopies	retro_opri_1083, retro_opri_1167, retro_opri_207, retro_opri_223, retro_opri_281, retro_opri_32, retro_opri_362, retro_opri_423, retro_opri_475, retro_opri_483, retro_opri_491, retro_opri_510, retro_opri_518, retro_opri_635 , retro_opri_772, retro_opri_874,
Pongo abelii	ENSPPYG00000013993	4 retrocopies	retro_pabe_1085, retro_pabe_1142, retro_pabe_116, retro_pabe_818,
Pan troglodytes	ENSPTRG00000022841	1 retrocopy	retro_ptro_14,
Pteropus vampyrus	ENSPVAG00000007794	19 retrocopies	retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus	ENSRNOG00000018645	27 retrocopies	retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Sarcophilus harrisii	ENSSHAG00000006896	2 retrocopies	retro_shar_231, retro_shar_484,
Sus scrofa	ENSSSCG00000011266	9 retrocopies	retro_sscr_1022, retro_sscr_1180, retro_sscr_22, retro_sscr_269, retro_sscr_890, retro_sscr_926, retro_sscr_966, retro_sscr_967, retro_sscr_982,
Tarsius syrichta	ENSTSYG00000004458	6 retrocopies	retro_tsyr_115, retro_tsyr_1290, retro_tsyr_156, retro_tsyr_38, retro_tsyr_456, retro_tsyr_807,
Vicugna pacos	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,