RetrogeneDB ID: retro_mdom_1980

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:43356156..43356522(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000016340
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000003534
• Aliases: None
• Description: None

Sequence

>retro_mdom_1980
ATGGTGAGGTATTCTCTTGATCCAGAGAATCCTACAAAATCATGCAAGTCAAGGGGCTCAAATCTCCGGGTCCACTTGAA
GAACACCCGTGAAACAGACCAAGCTATCAAGGGCATGCATATCCGAAAAGCTACCAAATATTTGAAAGATGTCACGTTGA
AGAAACAGTGTGTTCCTTTCCATCGGTACAATGGTGGAGTTGGCAGGTGTGCCCAGGCTAAGCAGTGGGGTTGGACACAA
GGTCGTTGGCCCAAAAAGAGTGCTGAATTCTTGCTGCATATGCTTAAAAATGCAGAAAGTAATGCAGAACTTAAGGGTTT
GGATGTGGATTCTCTTGTCATTGAGCATATCCAGGTTAACAAAGCG

Alignment

ORF - retro_mdom_1980 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.54 %
• Parental protein coverage: 66.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVGRC
          MVRYSLDPENPTKSCKSRGSNLRVH.KNTRET.QAIKGMHIRKATKYLKDVTLKKQCVPF.RYNGGVGRC
Retrocopy MVRYSLDPENPTKSCKSRGSNLRVHLKNTRETDQAIKGMHIRKATKYLKDVTLKKQCVPFHRYNGGVGRC

Parental  AQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKA
          AQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKA
Retrocopy AQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKA

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	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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1980 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1980 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 478 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022902	5 retrocopies	retro_btau_164, retro_btau_221, retro_btau_4, retro_btau_50, retro_btau_75,
Choloepus hoffmanni	ENSCHOG00000007872	50 retrocopies	retro_chof_1020, retro_chof_1021, retro_chof_107, retro_chof_1232, retro_chof_130, retro_chof_137, retro_chof_1405, retro_chof_1432, retro_chof_1448, retro_chof_1453, retro_chof_1471, retro_chof_1475, retro_chof_153, retro_chof_1634, retro_chof_1671, retro_chof_1678, retro_chof_1754, retro_chof_1786, retro_chof_187, retro_chof_1871, retro_chof_1895, retro_chof_1901, retro_chof_1908, retro_chof_2038, retro_chof_204, retro_chof_2133, retro_chof_2140, retro_chof_221, retro_chof_2243, retro_chof_2415, retro_chof_2458, retro_chof_246, retro_chof_2489, retro_chof_2534, retro_chof_2570, retro_chof_2610, retro_chof_2640, retro_chof_463, retro_chof_507, retro_chof_564, retro_chof_65, retro_chof_690, retro_chof_716, retro_chof_759, retro_chof_775, retro_chof_798, retro_chof_875, retro_chof_899, retro_chof_945, retro_chof_953,
Echinops telfairi	ENSETEG00000011322	10 retrocopies	retro_etel_1787, retro_etel_1810, retro_etel_1900, retro_etel_1936, retro_etel_1954, retro_etel_207, retro_etel_396, retro_etel_470, retro_etel_565, retro_etel_831,
Homo sapiens	ENSG00000215472	1 retrocopy	retro_hsap_2367,
Latimeria chalumnae	ENSLACG00000008835	1 retrocopy	retro_lcha_38,
Macropus eugenii	ENSMEUG00000016709	26 retrocopies	retro_meug_1111, retro_meug_127, retro_meug_1285, retro_meug_1485, retro_meug_1821, retro_meug_188, retro_meug_1886, retro_meug_191, retro_meug_204, retro_meug_2159, retro_meug_2167, retro_meug_2183, retro_meug_257, retro_meug_326, retro_meug_355, retro_meug_373, retro_meug_410, retro_meug_413, retro_meug_509, retro_meug_58, retro_meug_703, retro_meug_738, retro_meug_740, retro_meug_779, retro_meug_81, retro_meug_934,
Microcebus murinus	ENSMICG00000017102	14 retrocopies	retro_mmur_1046, retro_mmur_1047, retro_mmur_107, retro_mmur_1305, retro_mmur_1360, retro_mmur_1614, retro_mmur_195, retro_mmur_325, retro_mmur_335, retro_mmur_427, retro_mmur_484, retro_mmur_754, retro_mmur_817, retro_mmur_855,
Myotis lucifugus	ENSMLUG00000025554	22 retrocopies	retro_mluc_1141, retro_mluc_1224, retro_mluc_1300, retro_mluc_1375, retro_mluc_1468, retro_mluc_1500, retro_mluc_1547, retro_mluc_1579, retro_mluc_1739, retro_mluc_1755, retro_mluc_1822, retro_mluc_1870, retro_mluc_1959, retro_mluc_2018, retro_mluc_2027, retro_mluc_2036, retro_mluc_2059, retro_mluc_2165, retro_mluc_2198, retro_mluc_719, retro_mluc_835, retro_mluc_929,
Myotis lucifugus	ENSMLUG00000029264	36 retrocopies	retro_mluc_1043, retro_mluc_1060, retro_mluc_1061, retro_mluc_1081, retro_mluc_1094, retro_mluc_1163, retro_mluc_1193, retro_mluc_1206, retro_mluc_123, retro_mluc_1230, retro_mluc_1241, retro_mluc_1416, retro_mluc_157, retro_mluc_1581, retro_mluc_1652, retro_mluc_1677, retro_mluc_1693, retro_mluc_170, retro_mluc_1711, retro_mluc_1848, retro_mluc_1890, retro_mluc_2003, retro_mluc_2064, retro_mluc_2095, retro_mluc_2125, retro_mluc_2387, retro_mluc_2636, retro_mluc_2637, retro_mluc_661, retro_mluc_734, retro_mluc_763, retro_mluc_779, retro_mluc_785, retro_mluc_807, retro_mluc_938, retro_mluc_977,
Macaca mulatta	ENSMMUG00000018837	26 retrocopies	retro_mmul_1015, retro_mmul_1046, retro_mmul_1205, retro_mmul_1216, retro_mmul_1225, retro_mmul_1441, retro_mmul_163, retro_mmul_172, retro_mmul_1784, retro_mmul_1858, retro_mmul_1952, retro_mmul_2006, retro_mmul_2008, retro_mmul_2257, retro_mmul_2268, retro_mmul_2284, retro_mmul_2304, retro_mmul_2512, retro_mmul_46, retro_mmul_474, retro_mmul_589, retro_mmul_652, retro_mmul_669, retro_mmul_825, retro_mmul_956, retro_mmul_971,
Monodelphis domestica	ENSMODG00000003534	11 retrocopies	retro_mdom_1153, retro_mdom_1194, retro_mdom_1437, retro_mdom_1734, retro_mdom_1783, retro_mdom_1980 , retro_mdom_321, retro_mdom_337, retro_mdom_491, retro_mdom_541, retro_mdom_91,
Oryctolagus cuniculus	ENSOCUG00000012485	2 retrocopies	retro_ocun_1433, retro_ocun_231,
Procavia capensis	ENSPCAG00000003103	8 retrocopies	retro_pcap_193, retro_pcap_196, retro_pcap_197, retro_pcap_200, retro_pcap_206, retro_pcap_250, retro_pcap_363, retro_pcap_52,
Pongo abelii	ENSPPYG00000009151	43 retrocopies	retro_pabe_1177, retro_pabe_1178, retro_pabe_1179, retro_pabe_1197, retro_pabe_1373, retro_pabe_1408, retro_pabe_1448, retro_pabe_1464, retro_pabe_1531, retro_pabe_1565, retro_pabe_1574, retro_pabe_1725, retro_pabe_1807, retro_pabe_1832, retro_pabe_1902, retro_pabe_2052, retro_pabe_2053, retro_pabe_2088, retro_pabe_2102, retro_pabe_2164, retro_pabe_2231, retro_pabe_2317, retro_pabe_2520, retro_pabe_2635, retro_pabe_2638, retro_pabe_2871, retro_pabe_2917, retro_pabe_2921, retro_pabe_2971, retro_pabe_3020, retro_pabe_3029, retro_pabe_3103, retro_pabe_3187, retro_pabe_3248, retro_pabe_3253, retro_pabe_3262, retro_pabe_3277, retro_pabe_347, retro_pabe_3493, retro_pabe_539, retro_pabe_567, retro_pabe_617, retro_pabe_882,
Pteropus vampyrus	ENSPVAG00000001969	76 retrocopies	retro_pvam_1003, retro_pvam_1005, retro_pvam_1020, retro_pvam_1036, retro_pvam_1037, retro_pvam_104, retro_pvam_1042, retro_pvam_1085, retro_pvam_1093, retro_pvam_1105, retro_pvam_1155, retro_pvam_1162, retro_pvam_1186, retro_pvam_1194, retro_pvam_1204, retro_pvam_1218, retro_pvam_1279, retro_pvam_1336, retro_pvam_1338, retro_pvam_1351, retro_pvam_1366, retro_pvam_1372, retro_pvam_138, retro_pvam_1392, retro_pvam_1397, retro_pvam_1407, retro_pvam_1409, retro_pvam_142, retro_pvam_143, retro_pvam_1452, retro_pvam_1454, retro_pvam_182, retro_pvam_206, retro_pvam_220, retro_pvam_263, retro_pvam_268, retro_pvam_278, retro_pvam_292, retro_pvam_309, retro_pvam_339, retro_pvam_348, retro_pvam_395, retro_pvam_40, retro_pvam_402, retro_pvam_417, retro_pvam_424, retro_pvam_439, retro_pvam_442, retro_pvam_455, retro_pvam_464, retro_pvam_497, retro_pvam_520, retro_pvam_55, retro_pvam_571, retro_pvam_577, retro_pvam_584, retro_pvam_588, retro_pvam_596, retro_pvam_604, retro_pvam_608, retro_pvam_654, retro_pvam_659, retro_pvam_684, retro_pvam_700, retro_pvam_701, retro_pvam_705, retro_pvam_712, retro_pvam_716, retro_pvam_726, retro_pvam_751, retro_pvam_756, retro_pvam_777, retro_pvam_862, retro_pvam_88, retro_pvam_925, retro_pvam_966,
Rattus norvegicus	ENSRNOG00000018680	48 retrocopies	retro_rnor_1028, retro_rnor_1146, retro_rnor_1256, retro_rnor_1281, retro_rnor_1297, retro_rnor_1419, retro_rnor_1469, retro_rnor_1470, retro_rnor_1495, retro_rnor_1504, retro_rnor_1533, retro_rnor_1587, retro_rnor_1603, retro_rnor_1629, retro_rnor_1678, retro_rnor_1856, retro_rnor_1900, retro_rnor_1902, retro_rnor_1911, retro_rnor_1912, retro_rnor_1942, retro_rnor_1980, retro_rnor_2011, retro_rnor_218, retro_rnor_2243, retro_rnor_2348, retro_rnor_242, retro_rnor_2519, retro_rnor_2570, retro_rnor_2572, retro_rnor_2634, retro_rnor_2796, retro_rnor_419, retro_rnor_441, retro_rnor_554, retro_rnor_613, retro_rnor_667, retro_rnor_738, retro_rnor_762, retro_rnor_774, retro_rnor_803, retro_rnor_815, retro_rnor_837, retro_rnor_877, retro_rnor_932, retro_rnor_934, retro_rnor_972, retro_rnor_982,
Sarcophilus harrisii	ENSSHAG00000003060	14 retrocopies	retro_shar_206, retro_shar_214, retro_shar_279, retro_shar_387, retro_shar_457, retro_shar_586, retro_shar_593, retro_shar_606, retro_shar_713, retro_shar_743, retro_shar_751, retro_shar_800, retro_shar_802, retro_shar_817,
Ictidomys tridecemlineatus	ENSSTOG00000005193	33 retrocopies	retro_itri_1006, retro_itri_1015, retro_itri_1066, retro_itri_1070, retro_itri_1148, retro_itri_1212, retro_itri_1238, retro_itri_1312, retro_itri_1351, retro_itri_1360, retro_itri_1385, retro_itri_1424, retro_itri_1451, retro_itri_1476, retro_itri_1479, retro_itri_1625, retro_itri_1648, retro_itri_1712, retro_itri_181, retro_itri_213, retro_itri_300, retro_itri_320, retro_itri_400, retro_itri_425, retro_itri_513, retro_itri_575, retro_itri_601, retro_itri_621, retro_itri_625, retro_itri_708, retro_itri_816, retro_itri_834, retro_itri_949,
Tarsius syrichta	ENSTSYG00000007402	20 retrocopies	retro_tsyr_1042, retro_tsyr_1298, retro_tsyr_1349, retro_tsyr_1416, retro_tsyr_1555, retro_tsyr_159, retro_tsyr_180, retro_tsyr_1801, retro_tsyr_1940, retro_tsyr_2021, retro_tsyr_2053, retro_tsyr_2088, retro_tsyr_253, retro_tsyr_304, retro_tsyr_693, retro_tsyr_752, retro_tsyr_77, retro_tsyr_819, retro_tsyr_860, retro_tsyr_868,
Tursiops truncatus	ENSTTRG00000005797	31 retrocopies	retro_ttru_1153, retro_ttru_1338, retro_ttru_1374, retro_ttru_1436, retro_ttru_1509, retro_ttru_1716, retro_ttru_1757, retro_ttru_178, retro_ttru_1784, retro_ttru_1811, retro_ttru_1854, retro_ttru_1856, retro_ttru_193, retro_ttru_1932, retro_ttru_232, retro_ttru_264, retro_ttru_299, retro_ttru_447, retro_ttru_49, retro_ttru_568, retro_ttru_609, retro_ttru_627, retro_ttru_636, retro_ttru_660, retro_ttru_691, retro_ttru_703, retro_ttru_747, retro_ttru_800, retro_ttru_836, retro_ttru_884, retro_ttru_992,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,