RetrogeneDB ID: retro_mmul_2017

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:74414856..74415755(+)
• Located in intron of: ENSMMUG00000001360

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSMMUG00000013136
• Aliases: None
• Description: None

Sequence

>retro_mmul_2017
GACACTAAGCCTGGCACTACGGGCAGCCGCGCAGGGAGCTGTGGCCCGGGAGGCCTCACAAGGTCGGCGCCTGCCGACCA
AGAAGGTCATCCCAACGAAGGTTTTGGGAACAGTAAAATGGTTCAATGTAAGGAACGGATATGGTTTCATCAACAGGAAT
GACACCAAGGAAGATGTATTTGTACACCAGACTGCCATAAAGAAGAATAACCCCAGGAAGTAACTTCGCAGTGTAGGAGA
TGGAGAGACTGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGAAGGCAGCAAATGTTACAGGTCCTGGTGGTGGTC
CAGTTCAAGGCAGTAAATATGCAGCAGACCGTAACCATTACAGACGCTATCCACGTGGTAGGGGTCCTCCACGCAATTAC
CAGCAAAATTACCAGAATAGTGAGAGTGGGTAAAAGAACGAGCGATCGGAGGGGTGCTCCCGAAGTCCAGGCCCAACAAC
ACCGGCCCTACTGCAGGTGAAGGTTCCCACCTTACTACATGCGGAGACCCTATGGGCGTAGACCACAGTATTCCAACCCT
CCTGTGCAGGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTTCAGGAGAACAAGGTAGACCAGTGAGGCAGAATATGTA
TCGGGGATATAGACCACGATTCCGCAGGGGCCCTCCTCGCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAAGATAAAG
AAAATCAAGGAGATGAGACCCAAGGACAGCAGCCACCTTAACGTCGGTACCGCCGCAACTTCAATTACCCACGCAGACGC
CCAGAAAACCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCGGAGGC
TGAGCAGGGCGGGGCTGAG

Alignment

ORF - retro_mmul_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.11 %
• Parental protein coverage: 92.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTKPGTTGSGAGSGGPGGLTSAAPAGGD-KKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK
          DTKPGTT..G...G..G.......A..D.KKVI.TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK
Retrocopy DTKPGTT--GSRAGSCGPGGLTRSAPAD>KKVIPTKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK

Parental  KNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNY
          KNNPRK.LRSVGDGETVEFDVVEGEKGA.AANVTGPGG.PVQGSKYAADRNHYRRYPR.RGPPRNYQQNY
Retrocopy KNNPRK*LRSVGDGETVEFDVVEGEKGAKAANVTGPGGGPVQGSKYAADRNHYRRYPRGRGPPRNYQQNY

Parental  QNSESGEKNEGSES-APEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGR
          QNSESG.KNE.SE..APE.QAQQ.RPY.R.RFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQG.GEQGR
Retrocopy QNSESG*KNERSEG>APEVQAQQHRPYCR*RFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGSGEQGR

Parental  PVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGK
          PVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPP.RRYRRNFNY.RRRPENPKPQDGK
Retrocopy PVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPP*RRYRRNFNYPRRRPENPKPQDGK

Parental  ETKAADPPAENSSAPEAEQGGAE
          ETKAADPPAENSSAPEAEQGGAE
Retrocopy ETKAADPPAENSSAPEAEQGGAE

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	21.63 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	51.96 RPM
SRP007412_cerebellum	0.00 RPM	28.93 RPM
SRP007412_heart	0.18 RPM	270.76 RPM
SRP007412_kidney	0.00 RPM	55.75 RPM
SRP007412_liver	0.12 RPM	98.72 RPM
SRP007412_testis	3.32 RPM	1177.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2017 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2017 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 171 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000494	9 retrocopies	retro_amel_1280, retro_amel_1358, retro_amel_141, retro_amel_1486, retro_amel_215, retro_amel_418, retro_amel_625, retro_amel_837, retro_amel_909,
Canis familiaris	ENSCAFG00000002541	4 retrocopies	retro_cfam_1312, retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus	ENSCJAG00000003155	6 retrocopies	retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Cavia porcellus	ENSCPOG00000010888	3 retrocopies	retro_cpor_654, retro_cpor_833, retro_cpor_905,
Dipodomys ordii	ENSDORG00000016627	1 retrocopy	retro_dord_625,
Equus caballus	ENSECAG00000023592	20 retrocopies	retro_ecab_194, retro_ecab_228, retro_ecab_324, retro_ecab_389, retro_ecab_461, retro_ecab_538, retro_ecab_539, retro_ecab_712, retro_ecab_736, retro_ecab_756, retro_ecab_950, retro_ecab_963, retro_ecab_964, retro_ecab_965, retro_ecab_966, retro_ecab_982, retro_ecab_983, retro_ecab_984, retro_ecab_985, retro_ecab_992,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Felis catus	ENSFCAG00000022604	6 retrocopies	retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
Homo sapiens	ENSG00000065978	4 retrocopies	retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Microcebus murinus	ENSMICG00000014984	19 retrocopies	retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017 , retro_mmul_423, retro_mmul_861,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237,
Mustela putorius furo	ENSMPUG00000013922	6 retrocopies	retro_mputfur_1154, retro_mputfur_1332, retro_mputfur_1436, retro_mputfur_1627, retro_mputfur_215, retro_mputfur_293,
Nomascus leucogenys	ENSNLEG00000012324	7 retrocopies	retro_nleu_1053, retro_nleu_1188, retro_nleu_1312, retro_nleu_1601, retro_nleu_1749, retro_nleu_1888, retro_nleu_270,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115, retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Pongo abelii	ENSPPYG00000001466	7 retrocopies	retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pteropus vampyrus	ENSPVAG00000005504	7 retrocopies	retro_pvam_1255, retro_pvam_1348, retro_pvam_1391, retro_pvam_145, retro_pvam_405, retro_pvam_76, retro_pvam_971,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Sus scrofa	ENSSSCG00000028485	3 retrocopies	retro_sscr_1157, retro_sscr_255, retro_sscr_256,
Ictidomys tridecemlineatus	ENSSTOG00000000116	1 retrocopy	retro_itri_1532,
Tupaia belangeri	ENSTBEG00000015642	9 retrocopies	retro_tbel_1183, retro_tbel_1955, retro_tbel_2347, retro_tbel_2694, retro_tbel_2702, retro_tbel_2961, retro_tbel_3590, retro_tbel_4037, retro_tbel_4478,
Tarsius syrichta	ENSTSYG00000006915	6 retrocopies	retro_tsyr_1030, retro_tsyr_173, retro_tsyr_2037, retro_tsyr_610, retro_tsyr_840, retro_tsyr_996,
Tursiops truncatus	ENSTTRG00000001353	2 retrocopies	retro_ttru_461, retro_ttru_746,
Vicugna pacos	ENSVPAG00000000068	2 retrocopies	retro_vpac_235, retro_vpac_647,