RetrogeneDB ID: retro_mmul_1009

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:111271831..111272062(+)
• Located in intron of: ENSMMUG00000012115

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS26
• Ensembl ID: ENSMMUG00000017042
• Aliases: None
• Description: 40S ribosomal protein S26 [Source:RefSeq peptide;Acc:NP_001180510]

Sequence

>retro_mmul_1009
TTCATCATTCGAAACGTAGTGGAGGCTGCAGTAGTCAGGGACATTTCTGAAGCAAGTGTCTTCAATGCCTATGTGCTTCC
CAAGCTGTATGTGAAGCTAAATTACTGTGTGAGATGTGCGATTCACAGAAAAGTAGTCAAGAATCCATCTCGTAAAGCCC
ACAAGGACCAAACACGCCCACCCTGATTTAGATCTTCCGGTGCTGCCCCACAACCCCCACCAAAGCCCATG

Alignment

ORF - retro_mmul_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 66.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVIRNIVEAAAVRDISEASVFDAYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAP
          F.IRN.VEAA.VRDISEASVF.AYVLPKLYVKL.YCV.CAIH.KVV.N.SR.A.KD.T.PP.FR..GAAP
Retrocopy FIIRNVVEAAVVRDISEASVFNAYVLPKLYVKLNYCVRCAIHRKVVKNPSRKAHKDQTRPP*FRSSGAAP

Parental  RPPPKPM
          .PPPKPM
Retrocopy QPPPKPM

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	14.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	105.51 RPM
SRP007412_cerebellum	0.00 RPM	16.08 RPM
SRP007412_heart	0.06 RPM	46.93 RPM
SRP007412_kidney	0.00 RPM	32.75 RPM
SRP007412_liver	0.00 RPM	115.55 RPM
SRP007412_testis	0.04 RPM	31.74 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1009 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003260	7 retrocopies	retro_amel_1037, retro_amel_1240, retro_amel_303, retro_amel_777, retro_amel_926, retro_amel_927, retro_amel_928,
Bos taurus	ENSBTAG00000038896	3 retrocopies	retro_btau_191, retro_btau_25, retro_btau_724,
Cavia porcellus	ENSCPOG00000023630	6 retrocopies	retro_cpor_115, retro_cpor_1231, retro_cpor_134, retro_cpor_173, retro_cpor_48, retro_cpor_992,
Dipodomys ordii	ENSDORG00000001151	2 retrocopies	retro_dord_239, retro_dord_279,
Echinops telfairi	ENSETEG00000004510	35 retrocopies	retro_etel_1072, retro_etel_1145, retro_etel_1149, retro_etel_1175, retro_etel_1321, retro_etel_1357, retro_etel_1407, retro_etel_1423, retro_etel_1469, retro_etel_1498, retro_etel_155, retro_etel_162, retro_etel_1647, retro_etel_1691, retro_etel_1703, retro_etel_1734, retro_etel_1801, retro_etel_181, retro_etel_1859, retro_etel_1913, retro_etel_1963, retro_etel_2006, retro_etel_2043, retro_etel_2138, retro_etel_2146, retro_etel_2175, retro_etel_269, retro_etel_354, retro_etel_38, retro_etel_424, retro_etel_462, retro_etel_741, retro_etel_77, retro_etel_894, retro_etel_898,
Felis catus	ENSFCAG00000013977	10 retrocopies	retro_fcat_1211, retro_fcat_1332, retro_fcat_1460, retro_fcat_1728, retro_fcat_1851, retro_fcat_1948, retro_fcat_1949, retro_fcat_428, retro_fcat_508, retro_fcat_949,
Gorilla gorilla	ENSGGOG00000011566	6 retrocopies	retro_ggor_106, retro_ggor_121, retro_ggor_19, retro_ggor_55, retro_ggor_56, retro_ggor_63,
Loxodonta africana	ENSLAFG00000013329	8 retrocopies	retro_lafr_180, retro_lafr_240, retro_lafr_40, retro_lafr_464, retro_lafr_513, retro_lafr_768, retro_lafr_835, retro_lafr_962,
Myotis lucifugus	ENSMLUG00000029968	10 retrocopies	retro_mluc_1153, retro_mluc_149, retro_mluc_1925, retro_mluc_2065, retro_mluc_2163, retro_mluc_2462, retro_mluc_266, retro_mluc_309, retro_mluc_332, retro_mluc_477,
Macaca mulatta	ENSMMUG00000017042	7 retrocopies	retro_mmul_1009 , retro_mmul_1017, retro_mmul_1676, retro_mmul_1944, retro_mmul_2092, retro_mmul_294, retro_mmul_646,
Mus musculus	ENSMUSG00000025362	1 retrocopy	retro_mmus_115,
Pan troglodytes	ENSPTRG00000005075	1 retrocopy	retro_ptro_74,
Sus scrofa	ENSSSCG00000000374	2 retrocopies	retro_sscr_406, retro_sscr_650,
Ictidomys tridecemlineatus	ENSSTOG00000010559	12 retrocopies	retro_itri_1300, retro_itri_1446, retro_itri_1477, retro_itri_1488, retro_itri_289, retro_itri_418, retro_itri_469, retro_itri_470, retro_itri_643, retro_itri_652, retro_itri_729, retro_itri_871,