RetrogeneDB ID: retro_mmul_1834

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:59907631..59908249(-)
• Located in intron of: ENSMMUG00000029597

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1876
• Ensembl ID: ENSMMUG00000008069
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 E3 [Source:RefSeq peptide;Acc:NP_001244500]

Sequence

>retro_mmul_1834
ATGTCCAGTGATAGGCAAAGGTCCGATGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCGGACCAGCGAGACCC
AGCCTCTCTAGAGCCTGAAGAACAAGAGGAAAGAAAACCTTCTGCCTCCCAGCAGAAGAAAAACACCAAACTCTCCAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAAGAATTCAGAAGAGCTAGCTGAAATAACCCTTGATCCTCCTCCTAACT
GCAGTGCTGGGCCTAAAGGAGCTAACATTTATGAATGGAGATGAACTATACTTGGTCCGCTGGGTTCTGTCTATGAAGGT
GGTGTGTTTTTTCTGGATATCACATTTTCAACAGATTATCCATTTAAGCTACCAAAGGTTACTTCTGCACCGGAATCTAT
CACTGCAACATCAACAGTTAAGGAGTCATCTGTCTGGACATCCTTAAAGACAACTGGAGTCCCGCTTTGACTATTTCAAA
GGTTTTGCTGTCTGTTTGTTCCCTTTTGACAGACTGCAACCCTGCGGATCCTCTGGTTGGAAGCATAGCCACTCAGTATT
TAACCACCGAGCAGAACACGACAGGCTAGCCAGACAGTGGACCAAGAGACACGCAACA

Alignment

ORF - retro_mmul_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSAAQQKKNTKLSSKTTAKLSTSAKRIQK-E
          MSSDRQRSDDESPSTSSGSSDADQRDPA..EPEEQEERKPSA.QQKKNTKLSSKTTAKLSTSAKRIQK.E
Retrocopy MSSDRQRSDDESPSTSSGSSDADQRDPASLEPEEQEERKPSASQQKKNTKLSSKTTAKLSTSAKRIQK<E

Parental  LAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPFKPPKVT-FRTRIYHCNI
          LAEITLDPPPNCSAGPKG.NIYEWR.TILGP.GSVYEGGVFFLDITFS.DYPFK.PKVT.F.T.IYHCNI
Retrocopy LAEITLDPPPNCSAGPKGANIYEWR*TILGPLGSVYEGGVFFLDITFSTDYPFKLPKVT<FCTGIYHCNI

Parental  NSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLT-NRAEHDRIARQWTKRYAT
          NS.GVICLDILKDNWSPALTISKVLLS.CSLLTDCNPADPLVGSIATQYLT..RAEHDR.ARQWTKR.AT
Retrocopy NS*GVICLDILKDNWSPALTISKVLLSVCSLLTDCNPADPLVGSIATQYLT<HRAEHDRLARQWTKRHAT

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	0.45 RPM	41.01 RPM
SRP007412_brain_prefrontal_cortex	1.03 RPM	40.22 RPM
SRP007412_cerebellum	0.06 RPM	54.31 RPM
SRP007412_heart	0.00 RPM	16.13 RPM
SRP007412_kidney	0.00 RPM	26.29 RPM
SRP007412_liver	0.20 RPM	9.26 RPM
SRP007412_testis	0.45 RPM	15.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1834 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834 ,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,