RetrogeneDB ID: retro_mmul_1539

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:157366343..157366814(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4300
• Ensembl ID: ENSMMUG00000016241
• Aliases: None
• Description: None

Sequence

>retro_mmul_1539
CTTCTCTGCACTGAAAGCAACTGTATTCCCATAGCCCCTTACCCCTAAAAATGTATGCCTGCTCCAAGTATGTCTCCATC
CACTCTTGGTCAAGAGCACCTCCCAGTTGCTGAGCTGTCTACTATCTGCAGTGGTGCTGAAATGAACAGAGACACTGATA
GATGAGAGCCTCAGCAGCTTGGCAGTCTCACATCCCCTTATCTCACTTGTCCCTGGCTGCAGCTCCAAACCAGTGCAATT
TCAAGAGACATTGACACAGCAGCCAAGTTTATTGGGGTTGGGGCTGCTACAGTCGGGGGGCTGGCTCTGGGGCTGGGATT
GGTTGGGATTGTGTTTGGGAGCCTCATCATTGGTTATGCCAGGAACCCTTCTCTGAAGCAACAACTATTCTATCCCATTC
TGGGTTTTGCCCTCTGGGAGGTAATGGGGCTGTTTTGCCTGATGGTAGCCTCTCTCATTCTTTTTGCCATG

Alignment

ORF - retro_mmul_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLCSGRSSPATAPHP-LKMFACSKFVST-PSLVKSTSQLLSRPLSAVVLKRPEILTDEGLSSLAVSRPLT
          LLC........AP.P.LKM.ACSK.VS..P.LVKSTSQLLS..LSAVVLK..E.L.DE.LSSLAVS.PL.
Retrocopy LLCTESNCIPIAPYP<LKMYACSKYVSI<PLLVKSTSQLLSCLLSAVVLK*TETLIDESLSSLAVSHPLI

Parental  SLVSSRS-FQTSATSRDIDTAAKFIGAGAATVGVAGSGAG-IGTVFGSLIIGYARNPSLKQQLFSYAILG
          SLV...S..QTSA.SRDIDTAAKFIG.GAATVG....G.G..G.VFGSLIIGYARNPSLKQQLF.Y.ILG
Retrocopy SLVPGCS<LQTSAISRDIDTAAKFIGVGAATVGGLALGLGLVGIVFGSLIIGYARNPSLKQQLF-YPILG

Parental  FALSEAMGLFCLMVAFLILFAM
          FAL.E.MGLFCLMVA.LILFAM
Retrocopy FALWEVMGLFCLMVASLILFAM

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	43.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	111.38 RPM
SRP007412_cerebellum	0.00 RPM	61.67 RPM
SRP007412_heart	0.00 RPM	156.52 RPM
SRP007412_kidney	0.00 RPM	103.64 RPM
SRP007412_liver	0.00 RPM	101.81 RPM
SRP007412_testis	0.00 RPM	45.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1539 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1539 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2703
Pan troglodytes	retro_ptro_1824
Pongo abelii	retro_pabe_2255

---

Parental genes homology:

Parental genes homology involve 33 parental genes, and 255 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000619	18 retrocopies	retro_amel_1077, retro_amel_1113, retro_amel_1166, retro_amel_1309, retro_amel_1317, retro_amel_1322, retro_amel_1323, retro_amel_1610, retro_amel_1851, retro_amel_209, retro_amel_227, retro_amel_244, retro_amel_342, retro_amel_363, retro_amel_578, retro_amel_632, retro_amel_770, retro_amel_919,
Bos taurus	ENSBTAG00000005735	11 retrocopies	retro_btau_1405, retro_btau_1414, retro_btau_733, retro_btau_734, retro_btau_735, retro_btau_737, retro_btau_739, retro_btau_740, retro_btau_741, retro_btau_742, retro_btau_994,
Cavia porcellus	ENSCPOG00000022889	3 retrocopies	retro_cpor_1495, retro_cpor_268, retro_cpor_492,
Dipodomys ordii	ENSDORG00000002955	1 retrocopy	retro_dord_610,
Equus caballus	ENSECAG00000023021	2 retrocopies	retro_ecab_373, retro_ecab_793,
Erinaceus europaeus	ENSEEUG00000003051	1 retrocopy	retro_eeur_79,
Echinops telfairi	ENSETEG00000005968	40 retrocopies	retro_etel_1001, retro_etel_1007, retro_etel_103, retro_etel_1191, retro_etel_1203, retro_etel_1259, retro_etel_1288, retro_etel_1301, retro_etel_1327, retro_etel_1332, retro_etel_1354, retro_etel_1374, retro_etel_1402, retro_etel_1404, retro_etel_1420, retro_etel_1427, retro_etel_144, retro_etel_1533, retro_etel_1535, retro_etel_1591, retro_etel_1662, retro_etel_1684, retro_etel_1712, retro_etel_1771, retro_etel_2011, retro_etel_2127, retro_etel_2128, retro_etel_2142, retro_etel_2207, retro_etel_2216, retro_etel_260, retro_etel_475, retro_etel_636, retro_etel_639, retro_etel_652, retro_etel_72, retro_etel_735, retro_etel_736, retro_etel_796, retro_etel_847,
Felis catus	ENSFCAG00000001502	13 retrocopies	retro_fcat_1126, retro_fcat_1345, retro_fcat_1611, retro_fcat_1785, retro_fcat_1952, retro_fcat_226, retro_fcat_351, retro_fcat_353, retro_fcat_363, retro_fcat_405, retro_fcat_668, retro_fcat_958, retro_fcat_999,
Homo sapiens	ENSG00000135390	6 retrocopies	retro_hsap_1332, retro_hsap_2195, retro_hsap_2703, retro_hsap_3782, retro_hsap_4813, retro_hsap_499,
Gorilla gorilla	ENSGGOG00000015641	5 retrocopies	retro_ggor_1039, retro_ggor_1737, retro_ggor_1884, retro_ggor_2543, retro_ggor_2999,
Macropus eugenii	ENSMEUG00000004661	67 retrocopies	retro_meug_1009, retro_meug_1030, retro_meug_113, retro_meug_1180, retro_meug_1187, retro_meug_1238, retro_meug_1258, retro_meug_1261, retro_meug_1265, retro_meug_1272, retro_meug_1284, retro_meug_1297, retro_meug_1322, retro_meug_1328, retro_meug_1361, retro_meug_1389, retro_meug_1413, retro_meug_1602, retro_meug_1626, retro_meug_1639, retro_meug_1653, retro_meug_1709, retro_meug_1752, retro_meug_177, retro_meug_1802, retro_meug_1843, retro_meug_1882, retro_meug_1885, retro_meug_1891, retro_meug_1903, retro_meug_1909, retro_meug_1919, retro_meug_193, retro_meug_1987, retro_meug_2014, retro_meug_2048, retro_meug_206, retro_meug_2073, retro_meug_2111, retro_meug_2115, retro_meug_2122, retro_meug_216, retro_meug_229, retro_meug_230, retro_meug_296, retro_meug_313, retro_meug_345, retro_meug_348, retro_meug_397, retro_meug_485, retro_meug_514, retro_meug_529, retro_meug_567, retro_meug_622, retro_meug_66, retro_meug_721, retro_meug_742, retro_meug_799, retro_meug_800, retro_meug_846, retro_meug_864, retro_meug_865, retro_meug_896, retro_meug_904, retro_meug_935, retro_meug_936, retro_meug_983,
Microcebus murinus	ENSMICG00000011686	4 retrocopies	retro_mmur_175, retro_mmur_373, retro_mmur_905, retro_mmur_977,
Myotis lucifugus	ENSMLUG00000011860	13 retrocopies	retro_mluc_106, retro_mluc_1215, retro_mluc_1335, retro_mluc_1337, retro_mluc_1496, retro_mluc_1633, retro_mluc_2151, retro_mluc_2186, retro_mluc_2257, retro_mluc_2273, retro_mluc_516, retro_mluc_575, retro_mluc_656,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Macaca mulatta	ENSMMUG00000016241	3 retrocopies	retro_mmul_1539 , retro_mmul_2173, retro_mmul_439,
Mustela putorius furo	ENSMPUG00000005927	6 retrocopies	retro_mputfur_1650, retro_mputfur_290, retro_mputfur_335, retro_mputfur_631, retro_mputfur_814, retro_mputfur_947,
Mus musculus	ENSMUSG00000062683	1 retrocopy	retro_mmus_6,
Nomascus leucogenys	ENSNLEG00000017686	4 retrocopies	retro_nleu_1576, retro_nleu_2187, retro_nleu_2403, retro_nleu_326,
Oryctolagus cuniculus	ENSOCUG00000008933	4 retrocopies	retro_ocun_1933, retro_ocun_450, retro_ocun_762, retro_ocun_794,
Otolemur garnettii	ENSOGAG00000003611	4 retrocopies	retro_ogar_142, retro_ogar_1620, retro_ogar_166, retro_ogar_2415,
Ochotona princeps	ENSOPRG00000002978	1 retrocopy	retro_opri_671,
Procavia capensis	ENSPCAG00000008679	3 retrocopies	retro_pcap_140, retro_pcap_189, retro_pcap_212,
Pongo abelii	ENSPPYG00000004586	7 retrocopies	retro_pabe_1211, retro_pabe_1212, retro_pabe_2073, retro_pabe_2255, retro_pabe_236, retro_pabe_3088, retro_pabe_3741,
Pan troglodytes	ENSPTRG00000005023	6 retrocopies	retro_ptro_1668, retro_ptro_1824, retro_ptro_2563, retro_ptro_3202, retro_ptro_376, retro_ptro_909,
Pteropus vampyrus	ENSPVAG00000012291	1 retrocopy	retro_pvam_146,
Rattus norvegicus	ENSRNOG00000015320	6 retrocopies	retro_rnor_1286, retro_rnor_1490, retro_rnor_1939, retro_rnor_2699, retro_rnor_2738, retro_rnor_2910,
Sorex araneus	ENSSARG00000001027	7 retrocopies	retro_sara_124, retro_sara_152, retro_sara_377, retro_sara_581, retro_sara_716, retro_sara_73, retro_sara_759,
Sarcophilus harrisii	ENSSHAG00000005726	4 retrocopies	retro_shar_163, retro_shar_417, retro_shar_653, retro_shar_678,
Ictidomys tridecemlineatus	ENSSTOG00000008217	3 retrocopies	retro_itri_1404, retro_itri_399, retro_itri_436,
Tupaia belangeri	ENSTBEG00000005748	4 retrocopies	retro_tbel_1358, retro_tbel_1467, retro_tbel_2095, retro_tbel_789,
Tarsius syrichta	ENSTSYG00000003433	4 retrocopies	retro_tsyr_147, retro_tsyr_795, retro_tsyr_876, retro_tsyr_915,
Vicugna pacos	ENSVPAG00000000409	1 retrocopy	retro_vpac_105,