RetrogeneDB ID: retro_mmul_1946

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:49265541..49266056(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.16776
• Ensembl ID: ENSMMUG00000005157
• Aliases: None
• Description: 28S ribosomal protein S25, mitochondrial [Source:RefSeq peptide;Acc:NP_001244599]

Sequence

>retro_mmul_1946
ATGCCCATGAAGGGCTGCTCCCCCATTGCCGCACCCTGCAGTTCCTGAGCCAGGGGGAGGTGGTGTTCAAAGACTTGGCG
AAGGTCATGATGGTGAATTACAAAACACATGGGGAGCTGGGTGAGGGCACCAGGAAATCCGTGTTTTCAACATATCTCAG
ATTCAATACAAAATCCCATGAATGCAGATCATGATGTTTAAGGACAGGATGTCATCACCCTTTCTGTCTCCACATCCACC
AATACATTCTGGGGAGCAAGTCCTGTTGGATGTGGAGACCAAGAACAATAAGGAGGTTATCGAGTACATCAAAAAATCTT
GGGGAAGAATGAGGAAACCCCCAAGAAAGAAGAGAAGGAGAAAAGCAGCTGTCTCATCCAGCCCACTTTGGCCCTGGAAA
GTACTGCCTGCAGGATTGTATCTGCAAAGTGGAAGGACAGATGCCCTGCCTAGGCCTGATACCCAAGGAGATGATGGGGA
AGTGCAGAGCCACTGTGAAAGTCAGTGCCCAAGAC

Alignment

ORF - retro_mmul_1946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPMKGRFPIR-RTLQYLSQGNVVFKESVKVMTVNYNTHGELGEGARKFVF-FNIPQIQYKNPWVQIMMFK
          MPMKG..PI..RTLQ.LSQG.VVFK...KVM.VNY.THGELGEG.RK.VF.FNI.QIQYK.P..QIMMFK
Retrocopy MPMKGCSPIA<RTLQFLSQGEVVFKDLAKVMMVNYKTHGELGEGTRKSVF<FNISQIQYKIP*MQIMMFK

Parental  NMTPSPFLRFY--LDSGEQVLVDVETKSNKEIMEHIR-KILGKNEETLREEEEKK-KELSHPANFGPRKY
          ....SPFL.......SGEQVL.DVETK.NKE..E.I..KILGKNEET...EE..K.K.LSHPA.FGP.KY
Retrocopy DRMSSPFLSPHPPIHSGEQVLLDVETKNNKEVIEYIK<KILGKNEETPKKEEKEK<KQLSHPAHFGPGKY

Parental  CLRECICEVEGQVPCPSVVPLPKEMRGKYKAILKASAQD
          CL..CIC.VEGQ.PC......PKEM.GK..A..K.SAQD
Retrocopy CLQDCICKVEGQMPCLGLI--PKEMMGKCRATVKVSAQD

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	18.04 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.54 RPM
SRP007412_cerebellum	0.00 RPM	14.85 RPM
SRP007412_heart	0.00 RPM	23.85 RPM
SRP007412_kidney	0.00 RPM	23.71 RPM
SRP007412_liver	0.00 RPM	29.57 RPM
SRP007412_testis	0.04 RPM	45.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1946 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1946 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946 , retro_mmul_874,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,