RetrogeneDB ID: retro_mmus_309

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:38487568..38487966(+)
• Located in intron of: ENSMUSG00000037138

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nme4
• Ensembl ID: ENSMUSG00000024177
• Aliases: Nme4, 2610027N22Rik, 2810024O08Rik, 5730493H09Rik, NM23-M4, Nm23M4
• Description: NME/NM23 nucleoside diphosphate kinase 4 [Source:MGI Symbol;Acc:MGI:1931148]

Sequence

>retro_mmus_309
TTTCAATGCCTGCTGGTGCACCCTAGTTCTGGAGAGCCCTCTTAGCCCCAAGAGTAGACCCTGGTTGCTGTAAAGCCACA
TGGGGTACAGCAGAGGCTGGTGGGGATTCTGATGTAATGCTTTGAGAGGTGGGGCTTCAAGATGGTAAGGATGAAGATGC
TGCAGGCACCGGAGAGCATCCTTGCTGAGCACTACCGGAACCTACAGAAGAAGCCATCCTATCTGGCCCTCATCAGCTAC
ATAAGCTCTGGGTCTATGGTGGCCATGGTCTGAGAAGTGTACAATATGCCCACATCTCAAGGGCTATGATAGAACACACT
GACTCAGCAGTGGTAGCCCCTGGGACAATCAGGGGCAACTTCAGTGTTCACATCAGCAGGAATGTCATCCATGCTAGC

Alignment

ORF - retro_mmus_309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.37 %
• Parental protein coverage: 71.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FQCLLVRPSSGGPPWPQERTLVAVKPDGVQRRLVGTVIQRFERRGFKLVGMKMLQAPESILAEHYRDLQR
          FQCLLV.PSSG.P..PQE.TLVAVKP.GVQ.RLVG.....FER.GFK.V.MKMLQAPESILAEHYR.LQ.
Retrocopy FQCLLVHPSSGEPS*PQE*TLVAVKPHGVQQRLVGILM*CFERWGFKMVRMKMLQAPESILAEHYRNLQK

Parental  KPFYPALISYMSSGPVVAMVWEGPNV-VHISRAMIGHTDSTEAAPGTIRGDFSVHISRNVIHAS
          KP.Y.ALISY.SSG..VAMV.E..N...HISRAMI.HTDS...APGTIRG.FSVHISRNVIHAS
Retrocopy KPSYLALISYISSGSMVAMV*EVYNM<AHISRAMIEHTDSAVVAPGTIRGNFSVHISRNVIHAS

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	0.02 RPM	1.64 RPM
SRP007412_cerebellum	0.00 RPM	1.39 RPM
SRP007412_heart	0.00 RPM	3.80 RPM
SRP007412_kidney	0.02 RPM	4.54 RPM
SRP007412_liver	0.00 RPM	0.96 RPM
SRP007412_testis	0.00 RPM	0.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_309 was not detected

EST

No EST(s) were mapped for retro_mmus_309 retrocopy.

TSS

No TSS is located nearby retro_mmus_309 retrocopy 5' end.

Lab

retro_mmus_309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_309 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2679

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 41 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,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309 ,
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
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,