RetrogeneDB ID: retro_mmul_900

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:3144484..3144965(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSMMUG00000006525
• Aliases: None
• Description: 28S ribosomal protein S18b, mitochondrial [Source:RefSeq peptide;Acc:NP_001098635]

Sequence

>retro_mmul_900
AAAGTTGCTGGGAATCCCTGCCCCATCTGCCAAGATCACAAGTTACATGTTGATTTTAGGATTGTTAAGCTCTCGGAACA
GTTTGTCAGTGCCCACACGGGTATTATTTTCCATGCTCCATACACAGGAGTCCGTATGAAGCAGCATAAGATGTTGACCC
ATGTCATCCAGAAAGTCAGAGATCATGGTCTCCTCAGTTACCACATCTCCCAAGTTGAACCCCGGGACCTTGATTTTAGT
GCCTCTCATGGAGCTATGAGTGCTTCTCTGCCAGTCCCCACCCTGGTCTCAGGTGAACCCTGGTACCCATGGTACAGCTG
TAAACAGCCATCAGAGAGTGAACTGTCTCCCCTTTGCCAGCTCTATCAGGGTTATCTCTAAGAAGAGAGTAACCCCCGCA
CCTGAGTCAATGCCCAAGATGCTCTCAACACCACCAGTGGAAGCCTCCTTCACTGAAGAGACAGGCCCCTAGTGTGCTCT
G

Alignment

ORF - retro_mmul_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 62.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVAGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFHSLYTGVCVKQHKRLTQAIQKARDHGLLIYHIP
          KVAGNPCPIC.DHKLHVDFR.VKL.EQFV.AHTGIIFH..YTGV..KQHK.LT..IQK.RDHGLL.YHI.
Retrocopy KVAGNPCPICQDHKLHVDFRIVKLSEQFVSAHTGIIFHAPYTGVRMKQHKMLTHVIQKVRDHGLLSYHIS

Parental  QVEPRDRDFSISHGAVSATPPAPTLISGDPWYPWYNWKQPPERELSRLRRLYQGHLREESG-PPPESMPK
          QVEPRD.DFS.SHGA.SA..P.PTL.SG.PWYPWY..KQP.E.ELS.L..LYQG.L.EES..P.PESMPK
Retrocopy QVEPRDLDFSASHGAMSASLPVPTLVSGEPWYPWYSCKQPSESELSPLCQLYQGYL*EESN>PAPESMPK

Parental  MPPTAPVEASFTGQTDPQSAL
          M..T.PVEASFT..T.P..AL
Retrocopy MLSTPPVEASFTEETGP*CAL

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	17.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.37 RPM
SRP007412_cerebellum	0.00 RPM	18.66 RPM
SRP007412_heart	0.00 RPM	24.26 RPM
SRP007412_kidney	0.00 RPM	25.94 RPM
SRP007412_liver	0.00 RPM	32.97 RPM
SRP007412_testis	0.00 RPM	8.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_900 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_900 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900 ,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,