RetrogeneDB ID: retro_mmul_1889

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:73053847..73054341(+)
• Located in intron of: ENSMMUG00000016358

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSMMUG00000021229
• Aliases: None
• Description: 39S ribosomal protein L22, mitochondrial [Source:RefSeq peptide;Acc:NP_001181513]

Sequence

>retro_mmul_1889
GGTCTCCTTCATCTCAGTGTTTCACCCCAATGCCAGGTCCCACAAGTGCTTCTCTTGACACTTCTCAAAAATGGGAGAAG
AAGAATAAAACTGTTTATCCTCCACAACCGCTATGCAGAACCTCAGAGACCAGCAGAAGTCTACCAACACCAAAGAAAAT
GAAAAGACAGCAAAGACAAGATGTTGCATTTGGCAAAATTGGTAGGAGAAATGTCCACTGACCAGGCTTAGCTCAACTGG
GATTCAGTGACAAAAAGGGACCCAGATCATTAAAGAGGTTCTCTTAGAAGCATAAGACATGGCAGTGAAAGACCACAATG
TGGAATTCAGATCCAGTTTATATATAACTGAGTCCACCTTAGGGGGAGGCCAGTGCCTGACAGGTCTTTGCTACCAAAGT
AGAGGTTGCTTTGGGATCATGAAGGTTTACTGCTATTATTTTATGAAGTTGATGGAAGGGCCTCCCACCTCCATGTGAGG
CACCAAAGATGGCG

Alignment

ORF - retro_mmul_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.25 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKLALGVLPQSYIH-TSASLDISRKWEKKNKIVYPPQ-LPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLV
          G.L.L.V.PQ.....TSASLD.S.KWEKKNK.VYPPQ....EP.RPAE.Y...R..K.SKDKM..LAKLV
Retrocopy GLLHLSVSPQCQVP<TSASLDTSQKWEKKNKTVYPPQ>RYAEPQRPAEVYQHQRK*KDSKDKMLHLAKLV

Parental  RGMSIDQA-LAQLEFSDKKGAK-IIKEVLLEAQDMAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRG
          ..MS.DQA.LAQL.FSDKKG...IIKEVLLEA.DMAV.DHNVEFRS.LYI.EST.G.GQCL....Y..RG
Retrocopy GEMSTDQA<LAQLGFSDKKGPR<IIKEVLLEA*DMAVKDHNVEFRSSLYITESTLGGGQCLTGLCYQSRG

Parental  HFGIMERVYCHYFVKLVEGP-PPPPEPPKTA
          .FGIM..VYC.YF.KL.EGP.PPP.E.PK.A
Retrocopy CFGIM-KVYCYYFMKLMEGP>PPPCEAPKMA

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	8.85 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	6.35 RPM
SRP007412_cerebellum	0.00 RPM	6.72 RPM
SRP007412_heart	0.00 RPM	10.30 RPM
SRP007412_kidney	0.12 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	7.80 RPM
SRP007412_testis	0.04 RPM	44.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1889 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1889 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3041
Pan troglodytes	retro_ptro_1997
Gorilla gorilla	retro_ggor_2095
Pongo abelii	retro_pabe_2436
Callithrix jacchus	retro_cjac_2187

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Bos taurus	ENSBTAG00000019457	1 retrocopy	retro_btau_1348,
Canis familiaris	ENSCAFG00000017605	2 retrocopies	retro_cfam_1456, retro_cfam_584,
Macaca mulatta	ENSMMUG00000021229	1 retrocopy	retro_mmul_1889 ,
Otolemur garnettii	ENSOGAG00000016777	1 retrocopy	retro_ogar_1042,
Vicugna pacos	ENSVPAG00000001170	1 retrocopy	retro_vpac_294,