RetrogeneDB ID: retro_mmul_2494

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:52151950..52152375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSMMUG00000015353
• Aliases: None
• Description: 28S ribosomal protein S18c, mitochondrial [Source:RefSeq peptide;Acc:NP_001253055]

Sequence

>retro_mmul_2494
GCTATGGTTGCTGTTTGCGGTGGTCTAGGGAGGAAGAAGTTGACACACCTGGTAACGGCTGCTGTCAGACTTACACATCC
CGGGACTCCCACGGTGCTTTTGAGAAGGGGTTGTTCACAATATAAACAGGTATCCAGCAATGAGGACCTGCCCACTCCAA
TGGAAAACCCTTATAAAGAACCTCTTAAGAAATGTATCTTGTGTGGAAAGCATGTAAATTATAAGAATGCATGGCTTTTG
TCCCAGTTTGTTTCTCCATTTACTGAATGCATTTATGGAGGCACATTACGGGTCTTTGTGGGAAGAAACAGAAAGAAATA
ACTAAAGCAATCAAGAGAGCTCAAATAATGGGGTTTATGCCAGTTACATACAAAGATCCTGCATATCTCAAGGACCCTAG
AGTTTGTAACATCAGATATCAGGAA

Alignment

ORF - retro_mmul_2494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 98.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMVAVCGGLGRKKLTRLVTAAVSLTHLGTQTVLWRRGCSQYKQVSSNEDLPITMENPYKEPLKKCILCGK
          AMVAVCGGLGRKKLT.LVTAAV.LTH.GT.TVL.RRGCSQYKQVSSNEDLP..MENPYKEPLKKCILCGK
Retrocopy AMVAVCGGLGRKKLTHLVTAAVRLTHPGTPTVLLRRGCSQYKQVSSNEDLPTPMENPYKEPLKKCILCGK

Parental  RVDYKNVQLLSQFVSPFTGCIYG-RHITGLCGKKQKEITKAIKRAQILGFMPVTYKDPAYLKDPKVCNIR
          .V.YKN..LLSQFVSPFT.CIYG.RHITGLCGKKQKEITKAIKRAQI.GFMPVTYKDPAYLKDP.VCNIR
Retrocopy HVNYKNAWLLSQFVSPFTECIYG<RHITGLCGKKQKEITKAIKRAQIMGFMPVTYKDPAYLKDPRVCNIR

Parental  YRE
          Y.E
Retrocopy YQE

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	11.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.03 RPM
SRP007412_cerebellum	0.00 RPM	10.98 RPM
SRP007412_heart	0.00 RPM	10.72 RPM
SRP007412_kidney	0.00 RPM	13.15 RPM
SRP007412_liver	0.00 RPM	10.33 RPM
SRP007412_testis	0.00 RPM	13.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2494 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2494 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4684
Gorilla gorilla	retro_ggor_2908
Pongo abelii	retro_pabe_70

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494 , retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,