RetrogeneDB ID: retro_mmul_1072

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:71570263..71570585(+)
• Located in intron of: ENSMMUG00000003142

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18955
• Ensembl ID: ENSMMUG00000015774
• Aliases: None
• Description: nucleoplasmin-3 [Source:RefSeq peptide;Acc:NP_001181431]

Sequence

>retro_mmul_1072
GCCAGCACTGCCACCACCTTGAGTCAGGAGAACCAAGCCCAGACTGGGGTGTTGGAAGTCTGGGGATTCCAGCCTCAGTC
ACTATGGACAGCTTTTTCTTTGTCTGTAGCTCTCTGGCCACACCCACTCCTTTACATTCAAGGTAGAGAAAGAAGATAAT
ATGAAGCATGTGCTGGCATTAATTATGCTCTGCTTCACCAAGGGGGCTAACAATGAGTGAAATGTGGTAGAAGTTGTAAC
CTGGAACTATGACCACCAGGAGATTACAGTCTCTGTGGCGAACCTCAAGTTGTCCTGTCAACCCGTTACAATACGCAATG
AT

Alignment

ORF - retro_mmul_1072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 60.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAALAFLSQESRTRAG-GVGGLRVSAPVTMDSFFFGCE-LSGHTRSFTFKVEEEDDAEHVLALTMLCLTE
          A.....LSQE.....G.GVG.L...A.VTMDSFFF.C..LSGHT.SFTFKVE.ED...HVLAL.MLC.T.
Retrocopy ASTATTLSQENQAQTG<GVGSLGIPASVTMDSFFFVCS<LSGHTHSFTFKVEKEDNMKHVLALIMLCFTK

Parental  GAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPMLSLDD
          GA..E.NVVEVV..N.DHQEI.V.VANLKLSCQP.....D
Retrocopy GANNE*NVVEVVTWNYDHQEITVSVANLKLSCQPVTIRND

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	0.11 RPM	4.93 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.63 RPM
SRP007412_cerebellum	0.26 RPM	1.42 RPM
SRP007412_heart	0.00 RPM	6.30 RPM
SRP007412_kidney	0.00 RPM	8.22 RPM
SRP007412_liver	0.00 RPM	10.73 RPM
SRP007412_testis	0.04 RPM	6.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1072 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1072 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_792
Pan troglodytes	retro_ptro_551
Pongo abelii	retro_pabe_706

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072 ,
Macaca mulatta	ENSMMUG00000015781	1 retrocopy	retro_mmul_203,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,