RetrogeneDB ID: retro_opri_414

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_11262:4628..5491(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAPDH
• Ensembl ID: ENSOPRG00000012514
• Aliases: None
• Description: glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]

Sequence

>retro_opri_414
GGTCACCAGGTCACCAGGGCTGCTTTCAACTCTGGCAAAGTGGACATTGTGGCCATCAATGACCCATTCATTGACTTCAA
CTACATGGTCTACATGTTCCAGTATGATTCCACCCACGGCAAGTTCCACGGCACAGTGAAGGCAGAGAACGGCAAACTTG
TCATCAACGGGAAAGCCATCACCATCTTCCAGGCGCGAGATCCTGCCAACATCAAATGGGGCGATGCTGGTGCCCAGTAT
ATGGTGGAGTCCACTGGCGTCTTCACCACTATGGAGAAGGCTGGGCCTCACCTGAAGGGTGGGGCCAAGAAGGTCATCAT
CTCTGCCCCCTCTGCTGACGCCCCCATGTTTGTGATGGGAGTGAACCACGAGAAGTATGACAATTCCTTCAAGATTGTCA
GCAACGCCTCCTGCACCACCAACTGCTTGGCTCCCCTGGCCAAGGTCATCCACGACAACTTTGGCATTGTGGAGGGCCTC
ATGACCACAGTACACGCCATCACCACCACCCAGAAGACAGTGGACGGCCCCTCCAGGAAGCTGTGGCGTGACGGCCGTGG
GGCTGCCCAGAACATCATCCTGGCTTCCACTGGTGCCGCCAAGGCCGTGAGCAAGGTCATCCCTGAGCTGAATGGGAAAC
TCACCGGCATGGCCTTCCGTGTGCCTACTCCCAACGTGTCCGTGGTGGACCTGTCTTACCGTTTGGAGAAAGCTGCTAAG
TATGATGACATCAAGAAGGTGGTGAAGCAGGCCTCCGAGGGCCCGCTGAAGGGCATCCTGGGTTACACTGAGGACCAGGT
TGTCCCCTGTGACTTCAACAGTGACTCCTCCACTTTTGATTTGGGGCTGGCATTGCCCTCAAT

Alignment

ORF - retro_opri_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 87.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDST-GKFHGTVKAENGKLVINGKAITIFQERDPAN
          G..VTRAAFNSGKVDIVAINDPFID.NYMVYMFQYDST.GKFHGTVKAENGKLVINGKAITIFQ.RDPAN
Retrocopy GHQVTRAAFNSGKVDIVAINDPFIDFNYMVYMFQYDSTHGKFHGTVKAENGKLVINGKAITIFQARDPAN

Parental  IKWGDAGAQYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEKYDNSLKIVSNASCTT
          IKWGDAGAQY.VESTGVFTTMEKAG.HLKGGAK.VIISAPSADAPMFVMGVNHEKYDNS.KIVSNASCTT
Retrocopy IKWGDAGAQYMVESTGVFTTMEKAGPHLKGGAKKVIISAPSADAPMFVMGVNHEKYDNSFKIVSNASCTT

Parental  NCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPEL
          NCLAPLAKVIHDNFGIVEGLMTTVHAIT.TQKTVDGPS.KLWRDGRGAAQNII.ASTGAAKAV.KVIPEL
Retrocopy NCLAPLAKVIHDNFGIVEGLMTTVHAITTTQKTVDGPSRKLWRDGRGAAQNIILASTGAAKAVSKVIPEL

Parental  NGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVSCDFNSDTHSST
          NGKLTGMAFRVPTPNVSVVDL..RLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVV.CDFNSD..SST
Retrocopy NGKLTGMAFRVPTPNVSVVDLSYRLEKAAKYDDIKKVVKQASEGPLKGILGYTEDQVVPCDFNSD--SST

Parental  FDA-GAGIALN
          FD..GAGIALN
Retrocopy FDL<GAGIALN

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_414 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 23 parental genes, and 390 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006675	5 retrocopies	retro_amel_1189, retro_amel_146, retro_amel_1792, retro_amel_1826, retro_amel_549,
Ailuropoda melanoleuca	ENSAMEG00000014329	35 retrocopies	retro_amel_1050, retro_amel_1082, retro_amel_1134, retro_amel_1174, retro_amel_1229, retro_amel_1235, retro_amel_1253, retro_amel_1308, retro_amel_1538, retro_amel_1550, retro_amel_1598, retro_amel_1605, retro_amel_1614, retro_amel_1658, retro_amel_1776, retro_amel_1801, retro_amel_1802, retro_amel_187, retro_amel_1900, retro_amel_1904, retro_amel_268, retro_amel_294, retro_amel_387, retro_amel_443, retro_amel_471, retro_amel_601, retro_amel_605, retro_amel_641, retro_amel_738, retro_amel_750, retro_amel_762, retro_amel_852, retro_amel_899, retro_amel_961, retro_amel_992,
Canis familiaris	ENSCAFG00000015077	4 retrocopies	retro_cfam_122, retro_cfam_214, retro_cfam_3, retro_cfam_7,
Callithrix jacchus	ENSCJAG00000008234	1 retrocopy	retro_cjac_1548,
Cavia porcellus	ENSCPOG00000026350	1 retrocopy	retro_cpor_125,
Equus caballus	ENSECAG00000022051	11 retrocopies	retro_ecab_1006, retro_ecab_1067, retro_ecab_1086, retro_ecab_1125, retro_ecab_143, retro_ecab_191, retro_ecab_225, retro_ecab_333, retro_ecab_546, retro_ecab_854, retro_ecab_907,
Felis catus	ENSFCAG00000006874	17 retrocopies	retro_fcat_1038, retro_fcat_1147, retro_fcat_1166, retro_fcat_1337, retro_fcat_1781, retro_fcat_1858, retro_fcat_1870, retro_fcat_1881, retro_fcat_2005, retro_fcat_2007, retro_fcat_411, retro_fcat_582, retro_fcat_719, retro_fcat_726, retro_fcat_731, retro_fcat_806, retro_fcat_847,
Gorilla gorilla	ENSGGOG00000009553	30 retrocopies	retro_ggor_1142, retro_ggor_1143, retro_ggor_1260, retro_ggor_1450, retro_ggor_1621, retro_ggor_1659, retro_ggor_1889, retro_ggor_1902, retro_ggor_1982, retro_ggor_2126, retro_ggor_2224, retro_ggor_2443, retro_ggor_2477, retro_ggor_2500, retro_ggor_2991, retro_ggor_3004, retro_ggor_341, retro_ggor_376, retro_ggor_412, retro_ggor_424, retro_ggor_427, retro_ggor_428, retro_ggor_429, retro_ggor_430, retro_ggor_431, retro_ggor_459, retro_ggor_804, retro_ggor_921, retro_ggor_922, retro_ggor_926,
Loxodonta africana	ENSLAFG00000002780	3 retrocopies	retro_lafr_421, retro_lafr_46, retro_lafr_954,
Myotis lucifugus	ENSMLUG00000014320	18 retrocopies	retro_mluc_1073, retro_mluc_1102, retro_mluc_1352, retro_mluc_1487, retro_mluc_1577, retro_mluc_1772, retro_mluc_1886, retro_mluc_2039, retro_mluc_2222, retro_mluc_2292, retro_mluc_2518, retro_mluc_569, retro_mluc_584, retro_mluc_657, retro_mluc_848, retro_mluc_898, retro_mluc_957, retro_mluc_976,
Macaca mulatta	ENSMMUG00000018679	33 retrocopies	retro_mmul_1016, retro_mmul_1469, retro_mmul_1529, retro_mmul_1535, retro_mmul_1713, retro_mmul_1776, retro_mmul_1812, retro_mmul_1833, retro_mmul_1839, retro_mmul_1893, retro_mmul_2056, retro_mmul_2116, retro_mmul_2133, retro_mmul_2134, retro_mmul_2220, retro_mmul_2252, retro_mmul_2253, retro_mmul_2413, retro_mmul_2430, retro_mmul_2461, retro_mmul_2562, retro_mmul_2572, retro_mmul_480, retro_mmul_494, retro_mmul_513, retro_mmul_523, retro_mmul_524, retro_mmul_525, retro_mmul_526, retro_mmul_605, retro_mmul_650, retro_mmul_776, retro_mmul_784,
Monodelphis domestica	ENSMODG00000018066	41 retrocopies	retro_mdom_1060, retro_mdom_1089, retro_mdom_1104, retro_mdom_1137, retro_mdom_1161, retro_mdom_1184, retro_mdom_1233, retro_mdom_1241, retro_mdom_1317, retro_mdom_1358, retro_mdom_1384, retro_mdom_142, retro_mdom_1494, retro_mdom_1544, retro_mdom_1610, retro_mdom_1631, retro_mdom_1661, retro_mdom_1691, retro_mdom_1698, retro_mdom_1743, retro_mdom_1810, retro_mdom_1908, retro_mdom_2022, retro_mdom_275, retro_mdom_310, retro_mdom_354, retro_mdom_382, retro_mdom_497, retro_mdom_531, retro_mdom_552, retro_mdom_584, retro_mdom_590, retro_mdom_591, retro_mdom_628, retro_mdom_678, retro_mdom_766, retro_mdom_816, retro_mdom_828, retro_mdom_832, retro_mdom_835, retro_mdom_863,
Mustela putorius furo	ENSMPUG00000016891	28 retrocopies	retro_mputfur_1027, retro_mputfur_105, retro_mputfur_1051, retro_mputfur_1091, retro_mputfur_1152, retro_mputfur_1197, retro_mputfur_1198, retro_mputfur_1229, retro_mputfur_1278, retro_mputfur_1422, retro_mputfur_1461, retro_mputfur_1483, retro_mputfur_1630, retro_mputfur_244, retro_mputfur_300, retro_mputfur_31, retro_mputfur_317, retro_mputfur_380, retro_mputfur_481, retro_mputfur_513, retro_mputfur_555, retro_mputfur_612, retro_mputfur_717, retro_mputfur_789, retro_mputfur_817, retro_mputfur_842, retro_mputfur_88, retro_mputfur_925,
Mus musculus	ENSMUSG00000057666	109 retrocopies	retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Ornithorhynchus anatinus	ENSOANG00000004492	1 retrocopy	retro_oana_81,
Ochotona princeps	ENSOPRG00000012514	10 retrocopies	retro_opri_1113, retro_opri_128, retro_opri_147, retro_opri_371, retro_opri_414 , retro_opri_420, retro_opri_47, retro_opri_557, retro_opri_832, retro_opri_988,
Procavia capensis	ENSPCAG00000006928	9 retrocopies	retro_pcap_199, retro_pcap_210, retro_pcap_267, retro_pcap_365, retro_pcap_369, retro_pcap_440, retro_pcap_446, retro_pcap_68, retro_pcap_93,
Pteropus vampyrus	ENSPVAG00000012570	14 retrocopies	retro_pvam_1250, retro_pvam_1292, retro_pvam_1303, retro_pvam_160, retro_pvam_199, retro_pvam_280, retro_pvam_284, retro_pvam_31, retro_pvam_387, retro_pvam_451, retro_pvam_581, retro_pvam_680, retro_pvam_845, retro_pvam_976,
Rattus norvegicus	ENSRNOG00000018630	4 retrocopies	retro_rnor_107, retro_rnor_335, retro_rnor_407, retro_rnor_91,
Rattus norvegicus	ENSRNOG00000030638	2 retrocopies	retro_rnor_1571, retro_rnor_1777,
Sarcophilus harrisii	ENSSHAG00000014953	4 retrocopies	retro_shar_178, retro_shar_330, retro_shar_40, retro_shar_533,
Ictidomys tridecemlineatus	ENSSTOG00000007538	9 retrocopies	retro_itri_1069, retro_itri_1308, retro_itri_1472, retro_itri_1679, retro_itri_1802, retro_itri_419, retro_itri_540, retro_itri_752, retro_itri_979,
Xenopus tropicalis	ENSXETG00000033975	1 retrocopy	retro_xtro_70,