RetrogeneDB ID: retro_mmul_1290

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:53489944..53490386(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1607
• Ensembl ID: ENSMMUG00000016981
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 10 [Source:RefSeq peptide;Acc:NP_001248034]

Sequence

>retro_mmul_1290
ATGTAGGGGTGTGTATCTAACCTAATGGTCTGCAACCTGGCCTACTGTGGGAAGCTGGAAGAGTTCAAGGAGAGTATTCT
GGCTGATAAATCCCTAACTACTAGCACTGACCAGGACAGCAGAACGGCATGCACTGGGCATGCTCAGCTGTACATACAGG
AATTGTTGAATTTTTGTTGCACCTTGGAGTGCCAGTGAATGATAAAGGTGATTCAGGTTGATCTCCTCTCATATTGCGGC
TTCTGCTGGCTGGGAGGAGATTGTAAAAACCCTTGTGGGAAAAGGTGCTCAAGTGAATGCTGTCAATCAAAATGGCTACA
CTCCCCTACATTATGCAGCTTTCAAAAATAGGCATGAGATTGCTGTCATGTTACTAGAAGGCAGGGCTAATCCTCATGCT
AAGGACCATTATGAGGCTACAGCATTGCACTGGGCAGCAGCC

Alignment

ORF - retro_mmul_1290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSGKLEELKESILADKSLATRTDQDRRTA-LHWACSAGHTEIVEFLLQLGVPVNDK
          M.GCVSNLMVCNLAY.GKLEE.KESILADKSL.T.TDQD.RTA..HWACSA.HT.IVEFLL.LGVPVNDK
Retrocopy M*GCVSNLMVCNLAYCGKLEEFKESILADKSLTTSTDQDSRTA<MHWACSAVHTGIVEFLLHLGVPVNDK

Parental  DDAGWSPL-HIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHY
          .D.G.SPL.HIAASAG..EIVK.L.GKGAQVNAVNQNG.TPLHYAA.KNRHEIAVMLLEG.ANP.AKDHY
Retrocopy GDSG*SPL<HIAASAGWEEIVKTLVGKGAQVNAVNQNGYTPLHYAAFKNRHEIAVMLLEGRANPHAKDHY

Parental  EATAMHRAAA
          EATA.H.AAA
Retrocopy EATALHWAAA

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	32.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.07 RPM
SRP007412_cerebellum	0.00 RPM	27.06 RPM
SRP007412_heart	0.00 RPM	9.95 RPM
SRP007412_kidney	0.00 RPM	15.96 RPM
SRP007412_liver	0.00 RPM	10.93 RPM
SRP007412_testis	0.00 RPM	9.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1290 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1290 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1214
Pan troglodytes	retro_ptro_831
Gorilla gorilla	retro_ggor_945
Pongo abelii	retro_pabe_1010

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Microcebus murinus	ENSMICG00000002059	1 retrocopy	retro_mmur_550,
Myotis lucifugus	ENSMLUG00000014534	1 retrocopy	retro_mluc_2008,
Macaca mulatta	ENSMMUG00000015254	2 retrocopies	retro_mmul_2397, retro_mmul_2444,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290 ,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,