RetrogeneDB ID:

retro_mdom_309

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:79717623..79718068(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000004571
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_309
TTAAGGTGCTTTGGTGGTGAAGATGGTGCCACAGCTGCTTTGGCCCTCAAAACTGGTCCTTGGATTTGTTTCCCCAAAAG
GTTGGTGATGACATTGCCAAAGTGGCTAGTGACTGGAAAGGGTGAAGGATCACAGTGAAACTTACCACTCAGAGACAGAC
TTGGATTGAGGCTGTGCCTTATGCATCAACCTTGATCATCAAACCCTAAAGGAACTTTCTCAGGACAGAAAGAAGTAGAA
AACTAACAAACATAGTGGAGATATCAGTCTCGATGAGAGCATCAACATTGCTTGACAGATGAGGCACTGATGCCTCATAA
GAGACCTCTCTGGAACCATTAAAGAGATACTTGGAACTGTCCAATCTGTGGGCTGCAATATTGATGGCAGACACTCTCAT
GGTGTCATTGGAGACATCAATAATGATGCTATGGGATGCCCAGCC

ORF - retro_mdom_309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.71 %
Parental protein coverage: 90.91 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRCTGGEVGATSALAPKIGP-LGLSPKKVGDDIAKATGDWKGLRITVKLTIQNRQAQIEVVPSASALIIK
LRC.GGE.GAT.ALA.K.GP.L.L.P.KVGDDIAK...DWKG.RITVKLT.Q.RQ..IE.VP.AS.LIIK
RetrocopyLRCFGGEDGATAALALKTGP<LDLFPQKVGDDIAKVASDWKG*RITVKLTTQ-RQTWIEAVPYASTLIIK
Parental-ALKEPPRDRKKQKNIKHNGNISLDEIINIARQMRHRSLARDLSGTIKEILGTAQSVGCNIDGRHPHDVI
..LKE...DRKK.K..KH.G.ISLDE.INIA.QMRH..L.RDLSGTIKEILGT.QSVGCNIDGRH.H.VI
Retrocopy<TLKELSQDRKK*KTNKHSGDISLDESINIA*QMRH*CLIRDLSGTIKEILGTVQSVGCNIDGRHSHGVI
ParentalDDINSGAVECPA
.DIN..A..CPA
RetrocopyGDINNDAMGCPA

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






RNA-Seq - click to see more details

(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 499 .55 RPM
SRP007412_cerebellum 0 .00 RPM 537 .67 RPM
SRP007412_heart 0 .00 RPM 950 .51 RPM
SRP007412_kidney 0 .00 RPM 2993 .16 RPM
SRP007412_liver 0 .00 RPM 2286 .85 RPM
SRP007412_testis 0 .00 RPM 487 .16 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_309 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_309 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 35 parental genes, and 665 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001671215 retrocopies
retro_amel_1131, retro_amel_1172, retro_amel_1208, retro_amel_1400, retro_amel_1508, retro_amel_1558, retro_amel_17, retro_amel_174, retro_amel_1856, retro_amel_203, retro_amel_260, retro_amel_293, retro_amel_688, retro_amel_876, retro_amel_952,
Bos taurus ENSBTAG000000069633 retrocopies
retro_btau_102, retro_btau_2, retro_btau_5,
Canis familiaris ENSCAFG0000002013631 retrocopies
retro_cfam_1016, retro_cfam_1139, retro_cfam_1141, retro_cfam_1143, retro_cfam_1151, retro_cfam_1166, retro_cfam_1181, retro_cfam_1203, retro_cfam_1257, retro_cfam_1470, retro_cfam_1484, retro_cfam_1558, retro_cfam_1591, retro_cfam_1597, retro_cfam_1632, retro_cfam_1796, retro_cfam_1880, retro_cfam_1986, retro_cfam_2009, retro_cfam_2094, retro_cfam_2194, retro_cfam_437, retro_cfam_588, retro_cfam_706, retro_cfam_728, retro_cfam_748, retro_cfam_759, retro_cfam_76, retro_cfam_850, retro_cfam_950, retro_cfam_955,
Choloepus hoffmanni ENSCHOG0000000673232 retrocopies
retro_chof_1081, retro_chof_129, retro_chof_145, retro_chof_1469, retro_chof_147, retro_chof_1531, retro_chof_156, retro_chof_1666, retro_chof_1724, retro_chof_1843, retro_chof_1886, retro_chof_197, retro_chof_1992, retro_chof_2080, retro_chof_2152, retro_chof_2169, retro_chof_2279, retro_chof_2318, retro_chof_249, retro_chof_2599, retro_chof_2614, retro_chof_2656, retro_chof_295, retro_chof_310, retro_chof_354, retro_chof_386, retro_chof_484, retro_chof_592, retro_chof_677, retro_chof_831, retro_chof_916, retro_chof_925,
Callithrix jacchus ENSCJAG000000180821 retrocopy
retro_cjac_221,
Cavia porcellus ENSCPOG0000001376918 retrocopies
retro_cpor_1, retro_cpor_1069, retro_cpor_1108, retro_cpor_1373, retro_cpor_140, retro_cpor_1473, retro_cpor_1510, retro_cpor_1513, retro_cpor_1514, retro_cpor_313, retro_cpor_342, retro_cpor_553, retro_cpor_556, retro_cpor_664, retro_cpor_874, retro_cpor_910, retro_cpor_921, retro_cpor_954,
Dasypus novemcinctus ENSDNOG0000000841248 retrocopies
retro_dnov_1021, retro_dnov_1039, retro_dnov_1105, retro_dnov_1111, retro_dnov_1291, retro_dnov_1292, retro_dnov_1339, retro_dnov_1355, retro_dnov_1383, retro_dnov_1387, retro_dnov_1408, retro_dnov_1636, retro_dnov_1658, retro_dnov_1695, retro_dnov_1711, retro_dnov_1884, retro_dnov_2053, retro_dnov_2055, retro_dnov_2058, retro_dnov_210, retro_dnov_2165, retro_dnov_2196, retro_dnov_2199, retro_dnov_2222, retro_dnov_231, retro_dnov_2370, retro_dnov_2430, retro_dnov_2452, retro_dnov_2485, retro_dnov_2490, retro_dnov_260, retro_dnov_2603, retro_dnov_2637, retro_dnov_2639, retro_dnov_330, retro_dnov_343, retro_dnov_368, retro_dnov_387, retro_dnov_395, retro_dnov_455, retro_dnov_552, retro_dnov_560, retro_dnov_590, retro_dnov_597, retro_dnov_614, retro_dnov_634, retro_dnov_654, retro_dnov_677,
Equus caballus ENSECAG0000001062217 retrocopies
retro_ecab_1024, retro_ecab_1027, retro_ecab_1119, retro_ecab_157, retro_ecab_335, retro_ecab_379, retro_ecab_457, retro_ecab_475, retro_ecab_605, retro_ecab_666, retro_ecab_679, retro_ecab_699, retro_ecab_708, retro_ecab_843, retro_ecab_895, retro_ecab_967, retro_ecab_973,
Echinops telfairi ENSETEG000000069417 retrocopies
retro_etel_1508, retro_etel_1714, retro_etel_318, retro_etel_345, retro_etel_750, retro_etel_919, retro_etel_983,
Felis catus ENSFCAG0000001030231 retrocopies
retro_fcat_1078, retro_fcat_1115, retro_fcat_1118, retro_fcat_1149, retro_fcat_1206, retro_fcat_1276, retro_fcat_1288, retro_fcat_1298, retro_fcat_1376, retro_fcat_1482, retro_fcat_1527, retro_fcat_1637, retro_fcat_1638, retro_fcat_1676, retro_fcat_1854, retro_fcat_1873, retro_fcat_1977, retro_fcat_2009, retro_fcat_302, retro_fcat_35, retro_fcat_352, retro_fcat_359, retro_fcat_415, retro_fcat_455, retro_fcat_502, retro_fcat_509, retro_fcat_53, retro_fcat_638, retro_fcat_767, retro_fcat_819, retro_fcat_902,
Homo sapiens ENSG0000019795841 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,
Gorilla gorilla ENSGGOG0000000064834 retrocopies
retro_ggor_1024, retro_ggor_1059, retro_ggor_1086, retro_ggor_1207, retro_ggor_1242, retro_ggor_1377, retro_ggor_1389, retro_ggor_1449, retro_ggor_1511, retro_ggor_1516, retro_ggor_1530, retro_ggor_1645, retro_ggor_1740, retro_ggor_1753, retro_ggor_1806, retro_ggor_1845, retro_ggor_2158, retro_ggor_221, retro_ggor_2232, retro_ggor_2293, retro_ggor_2304, retro_ggor_232, retro_ggor_2334, retro_ggor_2394, retro_ggor_2414, retro_ggor_2506, retro_ggor_262, retro_ggor_2758, retro_ggor_2768, retro_ggor_2949, retro_ggor_541, retro_ggor_600, retro_ggor_637, retro_ggor_942,
Latimeria chalumnae ENSLACG000000153733 retrocopies
retro_lcha_31, retro_lcha_87, retro_lcha_92,
Loxodonta africana ENSLAFG0000001766910 retrocopies
retro_lafr_1, retro_lafr_193, retro_lafr_204, retro_lafr_286, retro_lafr_342, retro_lafr_41, retro_lafr_8, retro_lafr_802, retro_lafr_830, retro_lafr_984,
Macropus eugenii ENSMEUG0000000738012 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,
Myotis lucifugus ENSMLUG000000095512 retrocopies
retro_mluc_1222, retro_mluc_1797,
Myotis lucifugus ENSMLUG000000134041 retrocopy
retro_mluc_14,
Macaca mulatta ENSMMUG000000004222 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,
Mustela putorius furoENSMPUG0000001383234 retrocopies
retro_mputfur_1102, retro_mputfur_1104, retro_mputfur_1137, retro_mputfur_1192, retro_mputfur_1223, retro_mputfur_1283, retro_mputfur_1329, retro_mputfur_1467, retro_mputfur_1526, retro_mputfur_1580, retro_mputfur_260, retro_mputfur_331, retro_mputfur_363, retro_mputfur_445, retro_mputfur_489, retro_mputfur_500, retro_mputfur_508, retro_mputfur_521, retro_mputfur_533, retro_mputfur_534, retro_mputfur_544, retro_mputfur_559, retro_mputfur_594, retro_mputfur_61, retro_mputfur_622, retro_mputfur_632, retro_mputfur_651, retro_mputfur_824, retro_mputfur_828, retro_mputfur_843, retro_mputfur_868, retro_mputfur_884, retro_mputfur_913, retro_mputfur_977,
Mus musculus ENSMUSG000000389001 retrocopy
retro_mmus_28,
Oryctolagus cuniculus ENSOCUG000000049029 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 ENSOGAG00000000597120 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 ENSOPRG0000001107821 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,
Procavia capensis ENSPCAG000000074693 retrocopies
retro_pcap_135, retro_pcap_253, retro_pcap_306,
Pongo abelii ENSPPYG0000001962244 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 ENSPTRG000000228081 retrocopy
retro_ptro_21,
Pteropus vampyrus ENSPVAG0000000092515 retrocopies
retro_pvam_100, retro_pvam_1026, retro_pvam_1193, retro_pvam_209, retro_pvam_239, retro_pvam_483, retro_pvam_572, retro_pvam_590, retro_pvam_617, retro_pvam_630, retro_pvam_687, retro_pvam_747, retro_pvam_787, retro_pvam_846, retro_pvam_888,
Rattus norvegicus ENSRNOG000000162204 retrocopies
retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sarcophilus harrisii ENSSHAG000000178648 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,
Sus scrofa ENSSSCG0000000561214 retrocopies
retro_sscr_1111, retro_sscr_127, retro_sscr_189, retro_sscr_28, retro_sscr_439, retro_sscr_526, retro_sscr_551, retro_sscr_71, retro_sscr_715, retro_sscr_772, retro_sscr_773, retro_sscr_828, retro_sscr_832, retro_sscr_911,
Ictidomys tridecemlineatus ENSSTOG000000274257 retrocopies
retro_itri_1128, retro_itri_1197, retro_itri_1498, retro_itri_445, retro_itri_790, retro_itri_833, retro_itri_840,
Tupaia belangeri ENSTBEG0000000630425 retrocopies
retro_tbel_1270, retro_tbel_1487, retro_tbel_2032, retro_tbel_207, retro_tbel_2110, retro_tbel_2210, retro_tbel_2815, retro_tbel_2816, retro_tbel_2886, retro_tbel_2894, retro_tbel_3506, retro_tbel_358, retro_tbel_3702, retro_tbel_3725, retro_tbel_3911, retro_tbel_3972, retro_tbel_3973, retro_tbel_400, retro_tbel_4089, retro_tbel_4231, retro_tbel_4647, retro_tbel_4679, retro_tbel_560, retro_tbel_742, retro_tbel_754,
Tursiops truncatus ENSTTRG0000001570015 retrocopies
retro_ttru_1215, retro_ttru_1328, retro_ttru_1356, retro_ttru_1373, retro_ttru_1390, retro_ttru_1449, retro_ttru_1685, retro_ttru_1847, retro_ttru_187, retro_ttru_1942, retro_ttru_342, retro_ttru_421, retro_ttru_536, retro_ttru_65, retro_ttru_774,
Vicugna pacos ENSVPAG0000000512327 retrocopies
retro_vpac_158, retro_vpac_181, retro_vpac_189, retro_vpac_191, retro_vpac_194, retro_vpac_236, retro_vpac_268, retro_vpac_276, retro_vpac_291, retro_vpac_306, retro_vpac_323, retro_vpac_36, retro_vpac_37, retro_vpac_377, retro_vpac_413, retro_vpac_43, retro_vpac_432, retro_vpac_465, retro_vpac_482, retro_vpac_494, retro_vpac_506, retro_vpac_55, retro_vpac_569, retro_vpac_615, retro_vpac_80, retro_vpac_83, retro_vpac_90,


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