RetrogeneDB ID: retro_mmul_838

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:4428539..4428962(-)
• Located in intron of: ENSMMUG00000008548

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3952
• Ensembl ID: ENSMMUG00000003050
• Aliases: None
• Description: 40S ribosomal protein S15 [Source:RefSeq peptide;Acc:NP_001252851]

Sequence

>retro_mmul_838
ATGGCAGAGGTAGAGCAGAAGCTGACGTTCCGCAAATTCACCTACCGGGGCGTGGACTCGGACCAGCAGCTGTACATGAC
TCACCAGCAGCTGATGCAACCGTACAGTGCGTGCCAGCGGCAGAAGCTGAACCCGGGCCTGTGGCGGAAACAGCACTTGC
TGCCCAAGTGCCTGCGCAAGGCCACGAAGCCGGAAGTGGAGAAGCCGGAAGTAGTGAAGACGCACCTGGGGGACATGATC
ATCCTGCCCGAGATGGTGGGCAGCATGGTGGGCGTCTACAACGGCAAGACCTTCAACCAGGTGGAGATCAAGCCAGAGAT
GATCGGCCACTACCTGGGCGAGTTCTCCATCACCTACGAGCCGGTGAGGCACTGCCGGCCCGGCCTCAGGGCCACCCACT
CCTCCCGCTTCATCCCCCTCAAG

Alignment

ORF - retro_mmul_838 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPM
          MAEVEQK...TFRKFTYRGVD.DQ.L.M...QLMQ.YSA.QR..LN.GL.RKQH.L.K.LRKA.K..P..
Retrocopy MAEVEQKL--TFRKFTYRGVDSDQQLYMTHQQLMQPYSACQRQKLNPGLWRKQHLLPKCLRKATK--PEV

Parental  EKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSSR
          EKPEVVKTHL.DMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITY.PV.H.RPG..ATHSSR
Retrocopy EKPEVVKTHLGDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYEPVRHCRPGLRATHSSR

Parental  FIPLK
          FIPLK
Retrocopy FIPLK

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	46.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	156.20 RPM
SRP007412_cerebellum	0.00 RPM	47.01 RPM
SRP007412_heart	0.00 RPM	105.05 RPM
SRP007412_kidney	0.00 RPM	81.69 RPM
SRP007412_liver	0.59 RPM	220.92 RPM
SRP007412_testis	0.38 RPM	90.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_838 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_838 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_116

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005632	13 retrocopies	retro_cjac_143, retro_cjac_151, retro_cjac_1517, retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
Gorilla gorilla	ENSGGOG00000002818	4 retrocopies	retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Macaca mulatta	ENSMMUG00000003050	2 retrocopies	retro_mmul_2130, retro_mmul_838 ,
Mus musculus	ENSMUSG00000063457	8 retrocopies	retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786, retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys	ENSNLEG00000001651	8 retrocopies	retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii	ENSOGAG00000015776	4 retrocopies	retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii	ENSPPYG00000009317	4 retrocopies	retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes	ENSPTRG00000010200	1 retrocopy	retro_ptro_122,
Rattus norvegicus	ENSRNOG00000024603	8 retrocopies	retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,