RetrogeneDB ID: retro_mmul_2540

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:132876671..132877252(+)
• Located in intron of: ENSMMUG00000023039

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSMMUG00000011870
• Aliases: None
• Description: 40S ribosomal protein S7 [Source:RefSeq peptide;Acc:NP_001253725]

Sequence

>retro_mmul_2540
ATGTTCAGTTTGAACACCAGGATCAAGAAGCCCAAAGGCAAGAAGCCAGACAAGTTCAAGTTCGGCATCTCCCAGGCTCT
TCTGGAGCCAAAGATGAACGTGGACCTCAAGACTCAGCTCAGGGAGCTGAATATCATAGCAGCCAAGGAAACTGAAGTTG
GTGGTAGTCAGAAAGCTATCATAATCTTTGTTCCTGTTTCTCAACTGAAATCTTCCCAGAAAATCCAAGTCTGGCTAGTA
CGTGAATTGGAGAAAGAGTTCAGTGAGAAGCATGTTGTCTTTATTACTCAGAGGAGAATTCTGCCTAAGCCAACTTGAAA
AAGCCATACAAAAAATAAGCAAAAGCATCACGGGAGCCATACTCTGATAGCTGTGTACCATGCGATCTTGAGGACTTGAT
CTTTCCAAGTTAAATTGTGGGCAAGAGAATCCACTTGAAACTGGATGGCAGCTGCCTCGCAAAGGTTCATTTGGACAAAG
CACAGCAAAACAATGTGGCACACAAGGTTGAAATTTTTTCTGGTGTCTATAAGAAGCTCATAGGTAATGATGTTAATTTT
GAATTCCCAGAGTTTCACTTG

Alignment

ORF - retro_mmul_2540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK
          MFS....I.KP.G.KPD.F..GISQALLE..MN.DLK.QLRELNI.AAKE.EVGG..KAIIIFVPV.QLK
Retrocopy MFSLNTRIKKPKGKKPDKFKFGISQALLEPKMNVDLKTQLRELNIIAAKETEVGGSQKAIIIFVPVSQLK

Parental  SFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAI-LEDLVFPSEI
          S.QKIQV.LVRELEK.FS.KHVVFI.QRRILPKPT.KS.TKNKQK...S.TL.AV..AI.LEDL.FPS.I
Retrocopy SSQKIQVWLVRELEKEFSEKHVVFITQRRILPKPT*KSHTKNKQKHHGSHTLIAVYHAI<LEDLIFPS*I

Parental  VGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL
          VGKRI..KLDGS.L.KVHLDKAQQNNV.HKVE.FSGVYKKL.G.DVNFEFPEF.L
Retrocopy VGKRIHLKLDGSCLAKVHLDKAQQNNVAHKVEIFSGVYKKLIGNDVNFEFPEFHL

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	129.19 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	100.51 RPM
SRP007412_cerebellum	0.00 RPM	117.59 RPM
SRP007412_heart	0.00 RPM	165.12 RPM
SRP007412_kidney	0.00 RPM	162.44 RPM
SRP007412_liver	0.00 RPM	98.56 RPM
SRP007412_testis	0.00 RPM	191.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2540 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2540 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4760
Gorilla gorilla	retro_ggor_2965

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018435	2 retrocopies	retro_amel_391, retro_amel_914,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Dasypus novemcinctus	ENSDNOG00000013285	14 retrocopies	retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus	ENSECAG00000020253	2 retrocopies	retro_ecab_276, retro_ecab_396,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Homo sapiens	ENSG00000171863	14 retrocopies	retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925, retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540 , retro_mmul_357,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810,
Nomascus leucogenys	ENSNLEG00000015407	10 retrocopies	retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Ochotona princeps	ENSOPRG00000005085	3 retrocopies	retro_opri_1036, retro_opri_415, retro_opri_500,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Sus scrofa	ENSSSCG00000027353	5 retrocopies	retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus	ENSSTOG00000024830	3 retrocopies	retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus	ENSTTRG00000001616	6 retrocopies	retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,