RetrogeneDB ID: retro_mmul_2338

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:50051900..50052506(-)
• Located in intron of: ENSMMUG00000013149

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4Y1
• Ensembl ID: ENSMMUG00000003295
• Aliases: RPS4Y1, RPS4X
• Description: 40S ribosomal protein S4, X isoform [Source:RefSeq peptide;Acc:NP_001252551]

Sequence

>retro_mmul_2338
GAGAAGATTTGCATGCAGTGGTTCATTAAGATCAATGGCAATGTTCAAACTGATACAACCCATCCCACTGGATTCACAGA
CGTCATGGGCATTGACTAGATAGGAGAGAATTTTCGTCTCATCTATGATACCAAGGGTTGCTTTGCTGTACATCGTATTA
CACCTGAGGAGCCCAAGTACAAATTGTGCAAAGTGAGAAAAATCTTCGTGGGCACAAAAAGAATCCCTCATCTGGTGACT
CATGATGCTTGCATCATCTGCTACCCTGATCCCCTCCATCAAGGTGAATGATCCCATTCGGACTGAAATGGAAACTGGCA
AGATCACTGATTTCATCAAGTTTGGCACTGGTAACCTGTGGATGGTGAATGGAGGTGCTAACTTGGAAAGAATTGGTGTC
ATCACCCACAGAGAAAGGCACCCTTGATCTTTTGATGTGGTTCACATAAAAGATGCCAATGGCAACAGCTTTGCCACCCG
GCTTTCCAACATTTTTTCTACTGGCAAAGGCAACAAACCATGAATTTCTCTTCTCCGAGGAAAGGTATATGCCTCACCAT
TGCTGAAGAGAGAGACAAGAGACTGGCAGCCAAACAGAGCAGTGGG

Alignment

ORF - retro_mmul_2338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 76.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFV
          .KICMQ.FIKI.G.V.TD.T.P.GF.DV..ID..GENFRLIYDTKG.FAVHRITPEE.KYKLCKVRKIFV
Retrocopy EKICMQWFIKINGNVQTDTTHPTGFTDVMGID*IGENFRLIYDTKGCFAVHRITPEEPKYKLCKVRKIFV

Parental  GTKGIPHLVTHDARTIRYPDPL-IKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRER
          GTK.IPHLVTHDA..I.YPDPL.IKVND.I....ETGKITDFIKF.TGNL.MV.GGANL.RIGVIT.RER
Retrocopy GTKRIPHLVTHDACIICYPDPL>IKVNDPIRTEMETGKITDFIKFGTGNLWMVNGGANLERIGVITHRER

Parental  HPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG-KGIRLTIAEERDKRLAAKQSSG
          HP.SFDVVH.KDANGNSFATRLSNIF..GKGNKP.ISL.RG.KGI.LTIAEERDKRLAAKQSSG
Retrocopy HP*SFDVVHIKDANGNSFATRLSNIFSTGKGNKP*ISLLRG<KGICLTIAEERDKRLAAKQSSG

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	0.45 RPM	51.10 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	129.31 RPM
SRP007412_cerebellum	0.52 RPM	36.23 RPM
SRP007412_heart	0.41 RPM	82.85 RPM
SRP007412_kidney	0.12 RPM	77.70 RPM
SRP007412_liver	0.12 RPM	92.82 RPM
SRP007412_testis	0.08 RPM	10.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2338 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2338 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4051
Pongo abelii	retro_pabe_3325

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 129 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Felis catus	ENSFCAG00000012041	11 retrocopies	retro_fcat_1155, retro_fcat_1498, retro_fcat_1562, retro_fcat_1751, retro_fcat_1773, retro_fcat_2024, retro_fcat_229, retro_fcat_290, retro_fcat_454, retro_fcat_563, retro_fcat_766,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Macaca mulatta	ENSMMUG00000003295	7 retrocopies	retro_mmul_1243, retro_mmul_1589, retro_mmul_1895, retro_mmul_1999, retro_mmul_2338 , retro_mmul_43, retro_mmul_97,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Procavia capensis	ENSPCAG00000000761	3 retrocopies	retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Pteropus vampyrus	ENSPVAG00000012882	21 retrocopies	retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Tupaia belangeri	ENSTBEG00000002918	20 retrocopies	retro_tbel_1108, retro_tbel_1367, retro_tbel_1465, retro_tbel_1798, retro_tbel_2241, retro_tbel_2659, retro_tbel_2711, retro_tbel_2715, retro_tbel_2722, retro_tbel_2743, retro_tbel_2944, retro_tbel_310, retro_tbel_3172, retro_tbel_3232, retro_tbel_4263, retro_tbel_4569, retro_tbel_4572, retro_tbel_4648, retro_tbel_511, retro_tbel_877,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,