RetrogeneDB ID: retro_xtro_5

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172878.1:621965..622319(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000020482
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rpl34
• Ensembl ID: ENSXETG00000021095
• Aliases: None
• Description: ribosomal protein L34 [Source:Jamboree;Acc:XB-GENE-957318]

Sequence

>retro_xtro_5
ATGGTTCAGCGCCTCACATACCGTCGTAGGCTGTCCTACAATGCAGCCTCCAACAAAACAAGACTATCTCGAACACCAGG
TAACAGAATTGTGTACCTGTACACCAAGAAAGTTGGGAAAGCACCCAAGTCAGCATGTGGCATCTGCCCTGGAAGACTCC
GTGGTATCCGTGCTGTTAGACCTAAAGTACTTATGAGACTGTCAAAGACTAAGAAGCACGTCAGCAGAGCTTATGGTGAA
ACCATGTGTGCAAAATGTGTTCGTGATAGGATTAAGAGGGCATTCCTCATTGAGGAGCAGAAGATCGTTGTGAAAGTATT
GAAGGCACAGGCACAAAGCCAAAAGGCAAAGTAA

Alignment

ORF - retro_xtro_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.44 %
• Parental protein coverage: 84.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGICPGRLRGIRAVRPKVLMRLSKT
          MVQRLTYRRRLSYN.ASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGICPGRLRGIRAVRPKVLMRLSKT
Retrocopy MVQRLTYRRRLSYNAASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGICPGRLRGIRAVRPKVLMRLSKT

Parental  KKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
          KKHVSRAYG..MCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
Retrocopy KKHVSRAYGETMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	17.52 RPM	85.44 RPM
SRP007412_heart	37.16 RPM	89.44 RPM
SRP007412_kidney	37.16 RPM	89.44 RPM
SRP007412_liver	122.32 RPM	1312.52 RPM
SRP007412_skeletal_muscle	14.12 RPM	33.91 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_5 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_5 was not experimentally validated.

Homology

Retrocopy orthology:

Xenopus tropicalis 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 40 parental genes, and 548 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001758	20 retrocopies	retro_amel_1151, retro_amel_1298, retro_amel_1402, retro_amel_147, retro_amel_1595, retro_amel_1670, retro_amel_1678, retro_amel_1755, retro_amel_240, retro_amel_368, retro_amel_388, retro_amel_410, retro_amel_477, retro_amel_655, retro_amel_690, retro_amel_739, retro_amel_874, retro_amel_936, retro_amel_949, retro_amel_978,
Bos taurus	ENSBTAG00000014226	13 retrocopies	retro_btau_1017, retro_btau_1141, retro_btau_1280, retro_btau_1303, retro_btau_1372, retro_btau_1476, retro_btau_1738, retro_btau_288, retro_btau_404, retro_btau_465, retro_btau_628, retro_btau_712, retro_btau_904,
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,
Cavia porcellus	ENSCPOG00000000802	6 retrocopies	retro_cpor_139, retro_cpor_1494, retro_cpor_402, retro_cpor_485, retro_cpor_694, retro_cpor_732,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Equus caballus	ENSECAG00000019719	1 retrocopy	retro_ecab_58,
Erinaceus europaeus	ENSEEUG00000010390	5 retrocopies	retro_eeur_169, retro_eeur_175, retro_eeur_373, retro_eeur_82, retro_eeur_89,
Echinops telfairi	ENSETEG00000003715	53 retrocopies	retro_etel_106, retro_etel_107, retro_etel_1125, retro_etel_1140, retro_etel_1182, retro_etel_1187, retro_etel_1232, retro_etel_124, retro_etel_1303, retro_etel_1324, retro_etel_145, retro_etel_1483, retro_etel_1515, retro_etel_1545, retro_etel_1547, retro_etel_158, retro_etel_170, retro_etel_1745, retro_etel_1767, retro_etel_179, retro_etel_1795, retro_etel_1890, retro_etel_1967, retro_etel_1973, retro_etel_2066, retro_etel_2094, retro_etel_217, retro_etel_2191, retro_etel_273, retro_etel_274, retro_etel_299, retro_etel_327, retro_etel_344, retro_etel_362, retro_etel_380, retro_etel_388, retro_etel_416, retro_etel_418, retro_etel_429, retro_etel_464, retro_etel_494, retro_etel_533, retro_etel_726, retro_etel_74, retro_etel_756, retro_etel_759, retro_etel_774, retro_etel_863, retro_etel_870, retro_etel_914, retro_etel_927, retro_etel_938, retro_etel_974,
Felis catus	ENSFCAG00000015502	16 retrocopies	retro_fcat_1240, retro_fcat_1334, retro_fcat_1401, retro_fcat_1453, retro_fcat_1492, retro_fcat_1508, retro_fcat_1619, retro_fcat_2010, retro_fcat_368, retro_fcat_434, retro_fcat_518, retro_fcat_544, retro_fcat_640, retro_fcat_941, retro_fcat_953, retro_fcat_956,
Homo sapiens	ENSG00000109475	33 retrocopies	retro_hsap_1245, retro_hsap_126, retro_hsap_1265, retro_hsap_1417, retro_hsap_1636, retro_hsap_1735, retro_hsap_1756, retro_hsap_1921, retro_hsap_1987, retro_hsap_2041, retro_hsap_2145, retro_hsap_232, retro_hsap_2570, retro_hsap_258, retro_hsap_2624, retro_hsap_2695, retro_hsap_288, retro_hsap_2997, retro_hsap_3090, retro_hsap_3463, retro_hsap_3550, retro_hsap_3689, retro_hsap_4055, retro_hsap_4091, retro_hsap_4314, retro_hsap_520, retro_hsap_720, retro_hsap_769, retro_hsap_830, retro_hsap_853, retro_hsap_927, retro_hsap_941, retro_hsap_977,
Gorilla gorilla	ENSGGOG00000007650	32 retrocopies	retro_ggor_1097, retro_ggor_1236, retro_ggor_1401, retro_ggor_1471, retro_ggor_1604, retro_ggor_1657, retro_ggor_1878, retro_ggor_2123, retro_ggor_2249, retro_ggor_226, retro_ggor_2262, retro_ggor_2336, retro_ggor_2397, retro_ggor_2494, retro_ggor_2723, retro_ggor_2744, retro_ggor_2884, retro_ggor_3042, retro_ggor_308, retro_ggor_327, retro_ggor_462, retro_ggor_479, retro_ggor_561, retro_ggor_607, retro_ggor_638, retro_ggor_680, retro_ggor_696, retro_ggor_747, retro_ggor_760, retro_ggor_781, retro_ggor_975, retro_ggor_995,
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,
Microcebus murinus	ENSMICG00000002180	32 retrocopies	retro_mmur_1029, retro_mmur_1274, retro_mmur_1302, retro_mmur_1328, retro_mmur_134, retro_mmur_1366, retro_mmur_1412, retro_mmur_1424, retro_mmur_147, retro_mmur_1495, retro_mmur_1541, retro_mmur_187, retro_mmur_221, retro_mmur_286, retro_mmur_309, retro_mmur_336, retro_mmur_417, retro_mmur_494, retro_mmur_57, retro_mmur_643, retro_mmur_67, retro_mmur_677, retro_mmur_686, retro_mmur_737, retro_mmur_745, retro_mmur_76, retro_mmur_763, retro_mmur_789, retro_mmur_823, retro_mmur_864, retro_mmur_879, retro_mmur_980,
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,
Ornithorhynchus anatinus	ENSOANG00000007856	1 retrocopy	retro_oana_92,
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,
Pan troglodytes	ENSPTRG00000016353	31 retrocopies	retro_ptro_1105, retro_ptro_1210, retro_ptro_1224, retro_ptro_1285, retro_ptro_133, retro_ptro_1358, retro_ptro_1500, retro_ptro_1570, retro_ptro_1819, retro_ptro_201, retro_ptro_2087, retro_ptro_218, retro_ptro_2302, retro_ptro_2347, retro_ptro_237, retro_ptro_2502, retro_ptro_2748, retro_ptro_2775, retro_ptro_2922, retro_ptro_3244, retro_ptro_388, retro_ptro_468, retro_ptro_513, retro_ptro_538, retro_ptro_580, retro_ptro_592, retro_ptro_643, retro_ptro_651, retro_ptro_674, retro_ptro_856, retro_ptro_865,
Pteropus vampyrus	ENSPVAG00000005914	9 retrocopies	retro_pvam_1078, retro_pvam_1114, retro_pvam_1394, retro_pvam_189, retro_pvam_192, retro_pvam_225, retro_pvam_264, retro_pvam_312, retro_pvam_361,
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,
Sorex araneus	ENSSARG00000000177	8 retrocopies	retro_sara_111, retro_sara_218, retro_sara_411, retro_sara_538, retro_sara_565, retro_sara_591, retro_sara_645, retro_sara_726,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Sus scrofa	ENSSSCG00000009146	8 retrocopies	retro_sscr_1013, retro_sscr_1014, retro_sscr_1024, retro_sscr_522, retro_sscr_697, retro_sscr_703, retro_sscr_845, retro_sscr_929,
Ictidomys tridecemlineatus	ENSSTOG00000025964	14 retrocopies	retro_itri_1144, retro_itri_1207, retro_itri_1234, retro_itri_1249, retro_itri_1406, retro_itri_1508, retro_itri_1521, retro_itri_1542, retro_itri_209, retro_itri_267, retro_itri_344, retro_itri_766, retro_itri_898, retro_itri_967,
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,
Tarsius syrichta	ENSTSYG00000001781	34 retrocopies	retro_tsyr_1071, retro_tsyr_1087, retro_tsyr_1141, retro_tsyr_1249, retro_tsyr_1253, retro_tsyr_1292, retro_tsyr_1328, retro_tsyr_1375, retro_tsyr_140, retro_tsyr_1414, retro_tsyr_1425, retro_tsyr_1514, retro_tsyr_1573, retro_tsyr_164, retro_tsyr_1702, retro_tsyr_1849, retro_tsyr_2033, retro_tsyr_2035, retro_tsyr_2094, retro_tsyr_211, retro_tsyr_2172, retro_tsyr_220, retro_tsyr_221, retro_tsyr_254, retro_tsyr_300, retro_tsyr_375, retro_tsyr_49, retro_tsyr_59, retro_tsyr_597, retro_tsyr_678, retro_tsyr_812, retro_tsyr_853, retro_tsyr_872, retro_tsyr_897,
Tursiops truncatus	ENSTTRG00000003443	6 retrocopies	retro_ttru_1667, retro_ttru_1831, retro_ttru_355, retro_ttru_710, retro_ttru_717, retro_ttru_821,
Vicugna pacos	ENSVPAG00000005953	9 retrocopies	retro_vpac_134, retro_vpac_280, retro_vpac_309, retro_vpac_414, retro_vpac_421, retro_vpac_430, retro_vpac_514, retro_vpac_537, retro_vpac_84,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5 ,