RetrogeneDB ID: retro_mmul_1221

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:25214997..25215414(+)
• Located in intron of: ENSMMUG00000012118

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME4
• Ensembl ID: ENSMMUG00000000612
• Aliases: None
• Description: nucleoside diphosphate kinase, mitochondrial [Source:RefSeq peptide;Acc:NP_001191390]

Sequence

>retro_mmul_1221
CAAGAGTGGACCCTGGTCTCACTGAAGCCAGATGGGGTCTTGTGGCAGTCTGTTAGGGATGTGATCCAGTGCTTTGGAGG
CAGGGATTCAAGCTGGTAGGGATGAAGATCCTGCGGCCCGCTGGAAAGCGTCCTTGCTGACCACTACTGGGGCCTGCGAA
GGAAGCTCTTCTACCCAGCCCTCCTTAGCTATGTGAGCTTCAGGCCTGTTGATGGCCATGGTCTGGGAAGGGTACAATGT
GATCCATGCCTCGAGGGCCATGATAGGATACACTGACAGGGCTGAGGCTGACTCTGTGACCATATGCGGAGACTTCATCG
ACGTCCACATCAGCAGGAATATCATTCACACCAGCTATTCAGGGTAAGGGGTCAGAAAGAGATCCAGCTGTGGTTTGAAA
GCAGTGAGCTGGTGAAC

Alignment

ORF - retro_mmul_1221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.03 %
• Parental protein coverage: 73.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RERTLVAVKPDGVQRRLVGDVIQRFE-RRGFTLVGMKMLQAP-ESVLAEHYQDLRRKPFYPALIRYMS-S
          .E.TLV..KPDGV....V.DVIQ.F..R.GF.LVGMK.L....ESVLA.HY..LRRK.FYPAL..Y.S.S
Retrocopy QEWTLVSLKPDGVLWQSVRDVIQCFG<RQGFKLVGMKILRPA>ESVLADHYWGLRRKLFYPALLSYVS>S

Parental  GPMVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDF-SVHISRNVIHASDSVEG-AQREIQLWFQSSE
          G...AMVWEGYNV..ASRAMIG.TD.AEA...TI.GDF..VHISRN.IH.S.S..G..Q.EIQLWF.SSE
Retrocopy GLLMAMVWEGYNVIHASRAMIGYTDRAEADSVTICGDFIDVHISRNIIHTSYSG*G<GQKEIQLWFESSE

Parental  LVS
          LV.
Retrocopy LVN

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	13.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.90 RPM
SRP007412_cerebellum	0.00 RPM	10.46 RPM
SRP007412_heart	0.00 RPM	49.40 RPM
SRP007412_kidney	0.00 RPM	46.36 RPM
SRP007412_liver	0.00 RPM	110.80 RPM
SRP007412_testis	0.15 RPM	23.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1221 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1221 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221 ,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,