RetrogeneDB ID:

retro_mdom_1624

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:6:226126510..226126979(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL6
Ensembl ID:ENSMODG00000003096
Aliases:None
Description:ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]


Retrocopy-Parental alignment summary:






>retro_mdom_1624
GTGGCTGAAAAGGTGGTGAAAAAGCCTCGAAAGTATTGCAGCCACAACTCAGTTCTGGCTAGAGGGATTGGTAGGTACTC
CAGGTCTACCATATATTCCCATCGAGCCAATATGCTGCACAAAGAACCCGGATTGAAAGGAAAAAGAAAAGAGAAGGTGC
CTGCTACTATCTCAAAGCCAGTTGGTGGTGATAAGAATGGAGGAACCTGTGTGGTAAAGATTCAGAAAATGCCTAGGTAT
TATCCTACTGAGGATGTGCCTAGAAAGCTGCTAAGTCGTGGGGAAAAGCCCTTCAGCCAGCATGTAAGGAGACTCTGGTC
TAGCATTACCCCCAGGAACAGTTCTAATCATGCTCACTGGCCGCCACAGGGAGAAGCAAGTGGTTTTCCTGAAGCAGCTG
GCAAGTGGCTTGCTACTGGTCACTGGACTGTTGACCATTAACTGTGTTCCTCTGTGAAGGACCCATCAG

ORF - retro_mdom_1624 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.88 %
Parental protein coverage: 56.14 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVAEKVVKKPRKHCSRNPVLARGIGRYSRSAMYSRRAMYKRKYAAPKTRIERKKKEKVPATISKPVGGDKN
VAEKVVKKPRK.CS.N.VLARGIGRYSRS..YS.RA....K....K.......KEKVPATISKPVGGDKN
RetrocopyVAEKVVKKPRKYCSHNSVLARGIGRYSRSTIYSHRANMLHKEPGLKGK----RKEKVPATISKPVGGDKN
ParentalGGNRVIKIRKMPRYYPTEDVPRKLLSHGKKPFSQHVRRLRSSIT-PGTVLIMLTGRHRGKRVVFLKQLAS
GG..V.KI.KMPRYYPTEDVPRKLLS.G.KPFSQHVRRL.SSIT.PGTVLIMLTGRHR.K.VVFLKQLAS
RetrocopyGGTCVVKIQKMPRYYPTEDVPRKLLSRGEKPFSQHVRRLWSSIT>PGTVLIMLTGRHREKQVVFLKQLAS
ParentalGLLLVTGPLTINRVPLRRTHQ
GLLLVTG.LTIN.VPL.RTHQ
RetrocopyGLLLVTGLLTINCVPL*RTHQ

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1624 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1624 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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.

Parental genes homology:
Parental genes homology involve 33 parental genes, and 835 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000030601 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000851010 retrocopies
Bos taurus ENSBTAG000000317236 retrocopies
Canis familiaris ENSCAFG000000088731 retrocopy
Choloepus hoffmanni ENSCHOG0000000291713 retrocopies
Callithrix jacchus ENSCJAG000000124507 retrocopies
Cavia porcellus ENSCPOG000000135268 retrocopies
Dasypus novemcinctus ENSDNOG000000170323 retrocopies
Dipodomys ordii ENSDORG000000057931 retrocopy
Equus caballus ENSECAG000000175141 retrocopy
Erinaceus europaeus ENSEEUG000000002813 retrocopies
Felis catus ENSFCAG0000000685812 retrocopies
Homo sapiens ENSG0000008900926 retrocopies
Gorilla gorilla ENSGGOG0000000337216 retrocopies
Loxodonta africana ENSLAFG000000022012 retrocopies
Microcebus murinus ENSMICG0000000296125 retrocopies
Macaca mulatta ENSMMUG000000074331 retrocopy
Monodelphis domestica ENSMODG00000003096 4 retrocopies
Mustela putorius furoENSMPUG000000025269 retrocopies
Mus musculus ENSMUSG0000002961413 retrocopies
Nomascus leucogenys ENSNLEG000000270932 retrocopies
Oryctolagus cuniculus ENSOCUG000000038025 retrocopies
Ochotona princeps ENSOPRG000000118002 retrocopies
Pongo abelii ENSPPYG0000002585513 retrocopies
Pteropus vampyrus ENSPVAG000000124092 retrocopies
Rattus norvegicus ENSRNOG000000259361 retrocopy
Sarcophilus harrisii ENSSHAG000000070962 retrocopies
Sus scrofa ENSSSCG000000248254 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000094093 retrocopies
Tupaia belangeri ENSTBEG00000008626605 retrocopies
retro_tbel_1003, retro_tbel_1011, retro_tbel_1018, retro_tbel_1025, retro_tbel_1035, retro_tbel_1039, retro_tbel_104, retro_tbel_1041, retro_tbel_1042, retro_tbel_105, retro_tbel_1064, retro_tbel_1074, retro_tbel_1077, retro_tbel_1080, retro_tbel_1085, retro_tbel_109, retro_tbel_1094, retro_tbel_1096, retro_tbel_1097, retro_tbel_111, retro_tbel_1110, retro_tbel_1116, retro_tbel_1124, retro_tbel_1131, retro_tbel_1142, retro_tbel_1145, retro_tbel_1157, retro_tbel_1159, retro_tbel_1163, retro_tbel_1172, retro_tbel_118, retro_tbel_1187, retro_tbel_1192, retro_tbel_1197, retro_tbel_120, retro_tbel_1211, retro_tbel_1212, retro_tbel_1214, retro_tbel_1221, retro_tbel_1234, retro_tbel_1236, retro_tbel_1238, retro_tbel_1240, retro_tbel_1242, retro_tbel_1252, retro_tbel_1253, retro_tbel_1256, retro_tbel_1276, retro_tbel_128, retro_tbel_1287, retro_tbel_1291, retro_tbel_1292, retro_tbel_1297, retro_tbel_1307, retro_tbel_1308, retro_tbel_1309, retro_tbel_1316, retro_tbel_132, retro_tbel_1321, retro_tbel_1325, retro_tbel_1326, retro_tbel_1339, retro_tbel_1341, retro_tbel_1342, retro_tbel_1353, retro_tbel_1376, retro_tbel_139, retro_tbel_1399, retro_tbel_1401, retro_tbel_1408, retro_tbel_1409, retro_tbel_1412, retro_tbel_1432, retro_tbel_1438, retro_tbel_144, retro_tbel_1440, retro_tbel_1441, retro_tbel_1445, retro_tbel_1447, retro_tbel_1453, retro_tbel_1455, retro_tbel_1458, retro_tbel_1464, retro_tbel_1495, retro_tbel_1496, retro_tbel_150, retro_tbel_1508, retro_tbel_1511, retro_tbel_1517, retro_tbel_1520, retro_tbel_1526, retro_tbel_1536, retro_tbel_1544, retro_tbel_1547, retro_tbel_1553, retro_tbel_1559, retro_tbel_1560, retro_tbel_1578, retro_tbel_158, retro_tbel_1581, retro_tbel_1582, retro_tbel_1585, retro_tbel_1598, retro_tbel_1628, retro_tbel_1631, retro_tbel_1640, retro_tbel_1648, retro_tbel_165, retro_tbel_1652, retro_tbel_1660, retro_tbel_1670, retro_tbel_1672, retro_tbel_1674, retro_tbel_1679, retro_tbel_1681, retro_tbel_1687, retro_tbel_1691, retro_tbel_1702, retro_tbel_1703, retro_tbel_1706, retro_tbel_1732, retro_tbel_1736, retro_tbel_1737, retro_tbel_1742, retro_tbel_1743, retro_tbel_1751, retro_tbel_1759, retro_tbel_1771, retro_tbel_1782, retro_tbel_1788, retro_tbel_1799, retro_tbel_1805, retro_tbel_181, retro_tbel_1816, retro_tbel_1828, retro_tbel_1834, retro_tbel_1843, retro_tbel_1850, retro_tbel_1854, retro_tbel_1859, retro_tbel_186, retro_tbel_1867, retro_tbel_187, retro_tbel_1884, retro_tbel_1898, retro_tbel_190, retro_tbel_1900, retro_tbel_1909, retro_tbel_191, retro_tbel_192, retro_tbel_1926, retro_tbel_1927, retro_tbel_1937, retro_tbel_1949, retro_tbel_1953, retro_tbel_1956, retro_tbel_1961, retro_tbel_1974, retro_tbel_1983, retro_tbel_1985, retro_tbel_1990, retro_tbel_2003, retro_tbel_2007, retro_tbel_2012, retro_tbel_2018, retro_tbel_2019, retro_tbel_2029, retro_tbel_203, retro_tbel_2038, retro_tbel_2041, retro_tbel_2052, retro_tbel_2056, retro_tbel_2064, retro_tbel_2066, retro_tbel_2070, retro_tbel_2082, retro_tbel_2092, retro_tbel_2096, retro_tbel_2097, retro_tbel_212, retro_tbel_214, retro_tbel_215, retro_tbel_2158, retro_tbel_218, retro_tbel_2181, retro_tbel_2184, retro_tbel_2185, retro_tbel_219, retro_tbel_2222, retro_tbel_2235, retro_tbel_2237, retro_tbel_2244, retro_tbel_225, retro_tbel_2250, retro_tbel_2256, retro_tbel_2269, retro_tbel_227, retro_tbel_2273, retro_tbel_2275, retro_tbel_2301, retro_tbel_2305, retro_tbel_231, retro_tbel_2321, retro_tbel_2323, retro_tbel_233, retro_tbel_2331, retro_tbel_2342, retro_tbel_2375, retro_tbel_2389, retro_tbel_2396, retro_tbel_2411, retro_tbel_242, retro_tbel_2421, retro_tbel_243, retro_tbel_2446, retro_tbel_2456, retro_tbel_2471, retro_tbel_2476, retro_tbel_2481, retro_tbel_2499, retro_tbel_2501, retro_tbel_2502, retro_tbel_2507, retro_tbel_2509, retro_tbel_2514, retro_tbel_252, retro_tbel_2523, retro_tbel_2527, retro_tbel_253, retro_tbel_2530, retro_tbel_2533, retro_tbel_2537, retro_tbel_2546, retro_tbel_255, retro_tbel_256, retro_tbel_2560, retro_tbel_2565, retro_tbel_2568, retro_tbel_2594, retro_tbel_2597, retro_tbel_260, retro_tbel_2632, retro_tbel_2633, retro_tbel_2639, retro_tbel_2642, retro_tbel_2643, retro_tbel_2645, retro_tbel_2648, retro_tbel_2650, retro_tbel_2676, retro_tbel_2678, retro_tbel_2679, retro_tbel_2684, retro_tbel_2695, retro_tbel_2708, retro_tbel_2717, retro_tbel_2724, retro_tbel_2740, retro_tbel_2742, retro_tbel_2750, retro_tbel_2754, retro_tbel_278, retro_tbel_2785, retro_tbel_2791, retro_tbel_2796, retro_tbel_2797, retro_tbel_2800, retro_tbel_2803, retro_tbel_2804, retro_tbel_2805, retro_tbel_2812, retro_tbel_2817, retro_tbel_284, retro_tbel_2842, retro_tbel_2843, retro_tbel_2845, retro_tbel_2858, retro_tbel_2861, retro_tbel_2866, retro_tbel_2867, retro_tbel_287, retro_tbel_2870, retro_tbel_2876, retro_tbel_288, retro_tbel_2887, retro_tbel_291, retro_tbel_2912, retro_tbel_2914, retro_tbel_2919, retro_tbel_2920, retro_tbel_2928, retro_tbel_2958, retro_tbel_2968, retro_tbel_297, retro_tbel_2987, retro_tbel_2997, retro_tbel_300, retro_tbel_3003, retro_tbel_3009, retro_tbel_3012, retro_tbel_3019, retro_tbel_3029, retro_tbel_3030, retro_tbel_3034, retro_tbel_3036, retro_tbel_3038, retro_tbel_3039, retro_tbel_3043, retro_tbel_3045, retro_tbel_3047, retro_tbel_3049, retro_tbel_3052, retro_tbel_3053, retro_tbel_3057, retro_tbel_3063, retro_tbel_3064, retro_tbel_3066, retro_tbel_3068, retro_tbel_3078, retro_tbel_308, retro_tbel_3083, retro_tbel_3086, retro_tbel_3113, retro_tbel_3124, retro_tbel_3128, retro_tbel_313, retro_tbel_3131, retro_tbel_3133, retro_tbel_3139, retro_tbel_3146, retro_tbel_3157, retro_tbel_3158, retro_tbel_3163, retro_tbel_3166, retro_tbel_3169, retro_tbel_3176, retro_tbel_3177, retro_tbel_3178, retro_tbel_318, retro_tbel_3185, retro_tbel_3199, retro_tbel_3206, retro_tbel_321, retro_tbel_3221, retro_tbel_3225, retro_tbel_3226, retro_tbel_3249, retro_tbel_3257, retro_tbel_3263, retro_tbel_327, retro_tbel_3275, retro_tbel_3278, retro_tbel_3279, retro_tbel_3289, retro_tbel_3296, retro_tbel_3308, retro_tbel_3312, retro_tbel_3319, retro_tbel_3322, retro_tbel_3326, retro_tbel_3328, retro_tbel_334, retro_tbel_3348, retro_tbel_3357, retro_tbel_3374, retro_tbel_3375, retro_tbel_3382, retro_tbel_3394, retro_tbel_3395, retro_tbel_3411, retro_tbel_3427, retro_tbel_3433, retro_tbel_3439, retro_tbel_3440, retro_tbel_3455, retro_tbel_3474, retro_tbel_351, retro_tbel_3511, retro_tbel_3518, retro_tbel_3521, retro_tbel_3532, retro_tbel_3533, retro_tbel_3551, retro_tbel_3553, retro_tbel_3563, retro_tbel_3569, retro_tbel_357, retro_tbel_3574, retro_tbel_3579, retro_tbel_3582, retro_tbel_3584, retro_tbel_3588, retro_tbel_3594, retro_tbel_3599, retro_tbel_3612, retro_tbel_3614, retro_tbel_3629, retro_tbel_3633, retro_tbel_3643, retro_tbel_3645, retro_tbel_3646, retro_tbel_365, retro_tbel_3668, retro_tbel_3672, retro_tbel_3673, retro_tbel_368, retro_tbel_369, retro_tbel_3706, retro_tbel_3714, retro_tbel_3740, retro_tbel_3746, retro_tbel_3753, retro_tbel_376, retro_tbel_3765, retro_tbel_3768, retro_tbel_3773, retro_tbel_3778, retro_tbel_3787, retro_tbel_380, retro_tbel_3804, retro_tbel_3811, retro_tbel_3817, retro_tbel_3819, retro_tbel_3825, retro_tbel_3842, retro_tbel_3845, retro_tbel_3857, retro_tbel_3902, retro_tbel_3904, retro_tbel_3906, retro_tbel_3908, retro_tbel_3909, retro_tbel_3942, retro_tbel_3943, retro_tbel_3952, retro_tbel_3953, retro_tbel_3965, retro_tbel_3978, retro_tbel_3985, retro_tbel_3990, retro_tbel_3991, retro_tbel_4000, retro_tbel_4001, retro_tbel_4009, retro_tbel_403, retro_tbel_4038, retro_tbel_4040, retro_tbel_4041, retro_tbel_4044, retro_tbel_4060, retro_tbel_409, retro_tbel_4108, retro_tbel_4109, retro_tbel_4112, retro_tbel_4132, retro_tbel_4140, retro_tbel_4146, retro_tbel_4152, retro_tbel_4156, retro_tbel_4159, retro_tbel_4178, retro_tbel_4201, retro_tbel_4218, retro_tbel_4232, retro_tbel_424, retro_tbel_4248, retro_tbel_4253, retro_tbel_4264, retro_tbel_4267, retro_tbel_4276, retro_tbel_4281, retro_tbel_4291, retro_tbel_4301, retro_tbel_4303, retro_tbel_4306, retro_tbel_4321, retro_tbel_4328, retro_tbel_4333, retro_tbel_434, retro_tbel_4344, retro_tbel_4349, retro_tbel_4353, retro_tbel_4359, retro_tbel_437, retro_tbel_4375, retro_tbel_4394, retro_tbel_4395, retro_tbel_4396, retro_tbel_4397, retro_tbel_4445, retro_tbel_4446, retro_tbel_4455, retro_tbel_4468, retro_tbel_4476, retro_tbel_4483, retro_tbel_4508, retro_tbel_4517, retro_tbel_452, retro_tbel_4544, retro_tbel_4559, retro_tbel_4576, retro_tbel_4580, retro_tbel_4582, retro_tbel_4591, retro_tbel_4594, retro_tbel_4598, retro_tbel_4603, retro_tbel_4618, retro_tbel_4619, retro_tbel_4633, retro_tbel_4637, retro_tbel_464, retro_tbel_4640, retro_tbel_4662, retro_tbel_469, retro_tbel_4691, retro_tbel_4694, retro_tbel_4701, retro_tbel_4702, retro_tbel_4704, retro_tbel_4709, retro_tbel_4717, retro_tbel_4721, retro_tbel_4722, retro_tbel_4731, retro_tbel_478, retro_tbel_486, retro_tbel_493, retro_tbel_497, retro_tbel_498, retro_tbel_505, retro_tbel_506, retro_tbel_515, retro_tbel_516, retro_tbel_520, retro_tbel_523, retro_tbel_524, retro_tbel_529, retro_tbel_533, retro_tbel_546, retro_tbel_548, retro_tbel_549, retro_tbel_554, retro_tbel_557, retro_tbel_562, retro_tbel_568, retro_tbel_571, retro_tbel_581, retro_tbel_589, retro_tbel_608, retro_tbel_624, retro_tbel_625, retro_tbel_629, retro_tbel_630, retro_tbel_642, retro_tbel_651, retro_tbel_652, retro_tbel_653, retro_tbel_656, retro_tbel_660, retro_tbel_663, retro_tbel_668, retro_tbel_672, retro_tbel_684, retro_tbel_685, retro_tbel_690, retro_tbel_693, retro_tbel_694, retro_tbel_699, retro_tbel_708, retro_tbel_712, retro_tbel_717, retro_tbel_719, retro_tbel_72, retro_tbel_723, retro_tbel_724, retro_tbel_731, retro_tbel_748, retro_tbel_75, retro_tbel_769, retro_tbel_77, retro_tbel_773, retro_tbel_775, retro_tbel_778, retro_tbel_785, retro_tbel_797, retro_tbel_81, retro_tbel_837, retro_tbel_847, retro_tbel_85, retro_tbel_855, retro_tbel_858, retro_tbel_86, retro_tbel_876, retro_tbel_879, retro_tbel_890, retro_tbel_894, retro_tbel_895, retro_tbel_896, retro_tbel_904, retro_tbel_933, retro_tbel_944, retro_tbel_948, retro_tbel_951, retro_tbel_977,
Tarsius syrichta ENSTSYG0000000949222 retrocopies
Tursiops truncatus ENSTTRG000000092687 retrocopies
Vicugna pacos ENSVPAG000000070005 retrocopies



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