RetrogeneDB ID: retro_mmul_2154

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:63844172..63844650(+)
• Located in intron of: ENSMMUG00000000617

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18030
• Ensembl ID: ENSMMUG00000016494
• Aliases: None
• Description: None

Sequence

>retro_mmul_2154
CGAGATGCAGAGGATGCTATTTATGGAAGAAATGGTTATGATTATGGCCAGTGTTGGCTTCGTGTGGAGTTCCCCAGGAC
TTATGGAGGTCGGGGTGGGTGGCCCCATGGTGGGGGGAATTGACCTTCTACAAGAAGATCTGATTTCCGAGTTCTTGTTT
CAGCACTTCCTCCATCAGGCAGCTGGCAGGACCTGAAGGATCACATGCGAGCAGTTTGGGATGTCTGTTATGCCCACGTG
CAGAAGGATGGTGTGGGGATGGTTGAGTATCTCAGAAAAGCAGACATGGAATATGCCCTGCGTAAACTGGATGACATCAA
ATTCTACTCTCATGATAGTGAAACTTCCTACATCCGAGTTTATCCTGAGAGAAGGACCAGCTATGGCTACTCACGGTCTC
GGTCTGGGTCAAGGGGCCGTGACTCTCCATACTAAAGCAGGGGTTTCCCCACACCACTTCTCTCCTTTCAGGCCCTAC

Alignment

ORF - retro_mmul_2154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDAEDAIYGRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMR
          RDAEDAIYGRNGYDYGQC.LRVEFPRTYGGRGGWP.GG.N.P.TRRSDFRVLVS.LPPSGSWQDLKDHMR
Retrocopy RDAEDAIYGRNGYDYGQCWLRVEFPRTYGGRGGWPHGGGN*PSTRRSDFRVLVSALPPSGSWQDLKDHMR

Parental  EAGDVCYADVQKDGVGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGR
          ...DVCYA.VQKDGVGMVEYLRK.DMEYALRKLDD.KF.SH..ETSYIRVYPER.TSYGYSRSRSGSRGR
Retrocopy AVWDVCYAHVQKDGVGMVEYLRKADMEYALRKLDDIKFYSHDSETSYIRVYPERRTSYGYSRSRSGSRGR

Parental  DSPYQSRG-SPHYFSPFRPY
          DSPY.SRG.SPH.FSPFRPY
Retrocopy DSPY*SRG>SPHHFSPFRPY

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	1.01 RPM	24.43 RPM
SRP007412_brain_prefrontal_cortex	2.62 RPM	27.13 RPM
SRP007412_cerebellum	1.23 RPM	24.60 RPM
SRP007412_heart	0.35 RPM	15.13 RPM
SRP007412_kidney	0.35 RPM	36.97 RPM
SRP007412_liver	1.07 RPM	24.58 RPM
SRP007412_testis	1.13 RPM	27.78 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2154 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000014306	4 retrocopies	retro_mmul_1007, retro_mmul_1042, retro_mmul_1642, retro_mmul_2359,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154 ,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,