RetrogeneDB ID: retro_mmul_1580

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:46524639..46525012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17989
• Ensembl ID: ENSMMUG00000016085
• Aliases: None
• Description: ubiquitin A-52 residue ribosomal protein fusion product 1 [Source:RefSeq peptide;Acc:NP_001182685]

Sequence

>retro_mmul_1580
ATGTGGATCTTTGTGAAGACCCTCACAGGCAAGACCATCGCCCTTGAGGTCGAGCCGAGTGACGCCACTGAGAATGCCAA
AGCCAAAATTCAAGACAAGTAGGGCATCCTACCTGACCAGCAGTGTCTGATAATTTGAGGTCAAATCGCTGGAGGATGGC
CGCACTCTCTCAGACTACAACATCCAGAAAGAGTCCACCCTGCACCTGATGCTGCGCCTGCGAGGTGGCATTACGGAGCC
TTCCCTCTGCCACCTTGCCAAGAAATACAACTGTGACAAGATGATCTGCCACAAGAGCTGTGCTTGCCTGCGCCCCCATG
CTGTCAACTACTGCAAGAAGTGTGGCCACACCAACAACCTACGTCCCAAAAAG

Alignment

ORF - retro_mmul_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 97.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAG-KQLEDGRTLSDYNIQKESTLHL
          M.IFVKTLTGKTI.LEVEPSD..EN.KAKIQDK.GI.PDQQ.LI..G.K.LEDGRTLSDYNIQKESTLHL
Retrocopy MWIFVKTLTGKTIALEVEPSDATENAKAKIQDK*GILPDQQCLII*G>KSLEDGRTLSDYNIQKESTLHL

Parental  VLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKK
          .LRLRGGI.EPSL..LA.KYNCDKMIC.K..A.L.P.AVN...KKCGHTNNLRPKK
Retrocopy MLRLRGGITEPSLCHLAKKYNCDKMICHKSCACLRPHAVN-YCKKCGHTNNLRPKK

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	0.34 RPM	54.23 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	96.70 RPM
SRP007412_cerebellum	0.26 RPM	45.07 RPM
SRP007412_heart	0.18 RPM	105.46 RPM
SRP007412_kidney	0.59 RPM	99.65 RPM
SRP007412_liver	0.51 RPM	248.19 RPM
SRP007412_testis	0.38 RPM	230.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1580 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1580 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1142
Gorilla gorilla	retro_ggor_1265
Callithrix jacchus	retro_cjac_2002

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 135 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014723	8 retrocopies	retro_cfam_1671, retro_cfam_1725, retro_cfam_1879, retro_cfam_1933, retro_cfam_2205, retro_cfam_600, retro_cfam_654, retro_cfam_873,
Cavia porcellus	ENSCPOG00000000351	3 retrocopies	retro_cpor_1454, retro_cpor_1471, retro_cpor_1502,
Echinops telfairi	ENSETEG00000003392	35 retrocopies	retro_etel_1121, retro_etel_113, retro_etel_1165, retro_etel_1229, retro_etel_1520, retro_etel_1521, retro_etel_1598, retro_etel_1618, retro_etel_1623, retro_etel_1644, retro_etel_1657, retro_etel_1707, retro_etel_1709, retro_etel_174, retro_etel_1756, retro_etel_1760, retro_etel_1785, retro_etel_1854, retro_etel_196, retro_etel_2027, retro_etel_2101, retro_etel_2123, retro_etel_2158, retro_etel_2166, retro_etel_268, retro_etel_376, retro_etel_386, retro_etel_406, retro_etel_660, retro_etel_690, retro_etel_70, retro_etel_755, retro_etel_807, retro_etel_843, retro_etel_859,
Gorilla gorilla	ENSGGOG00000004630	8 retrocopies	retro_ggor_1021, retro_ggor_1045, retro_ggor_1265, retro_ggor_1835, retro_ggor_2579, retro_ggor_2687, retro_ggor_2782, retro_ggor_905,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Macropus eugenii	ENSMEUG00000013159	5 retrocopies	retro_meug_1812, retro_meug_1868, retro_meug_441, retro_meug_513, retro_meug_750,
Microcebus murinus	ENSMICG00000017583	5 retrocopies	retro_mmur_143, retro_mmur_1486, retro_mmur_150, retro_mmur_633, retro_mmur_708,
Myotis lucifugus	ENSMLUG00000029594	5 retrocopies	retro_mluc_1995, retro_mluc_2057, retro_mluc_2203, retro_mluc_44, retro_mluc_829,
Macaca mulatta	ENSMMUG00000016085	7 retrocopies	retro_mmul_1184, retro_mmul_1580 , retro_mmul_1625, retro_mmul_2183, retro_mmul_2311, retro_mmul_232, retro_mmul_896,
Monodelphis domestica	ENSMODG00000003499	1 retrocopy	retro_mdom_867,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Otolemur garnettii	ENSOGAG00000028000	10 retrocopies	retro_ogar_1345, retro_ogar_1419, retro_ogar_1583, retro_ogar_1604, retro_ogar_1792, retro_ogar_2026, retro_ogar_2370, retro_ogar_2485, retro_ogar_2544, retro_ogar_3337,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Pteropus vampyrus	ENSPVAG00000024217	19 retrocopies	retro_pvam_1029, retro_pvam_1102, retro_pvam_1146, retro_pvam_1164, retro_pvam_1320, retro_pvam_1325, retro_pvam_1361, retro_pvam_1434, retro_pvam_1447, retro_pvam_211, retro_pvam_327, retro_pvam_517, retro_pvam_528, retro_pvam_600, retro_pvam_632, retro_pvam_655, retro_pvam_749, retro_pvam_987, retro_pvam_994,
Sorex araneus	ENSSARG00000000984	11 retrocopies	retro_sara_145, retro_sara_164, retro_sara_192, retro_sara_256, retro_sara_281, retro_sara_331, retro_sara_344, retro_sara_599, retro_sara_67, retro_sara_687, retro_sara_94,
Sus scrofa	ENSSSCG00000013907	1 retrocopy	retro_sscr_988,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Tursiops truncatus	ENSTTRG00000021461	1 retrocopy	retro_ttru_1582,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,