RetrogeneDB ID: retro_mmus_1290

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:72840721..72841150(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufaf4
• Ensembl ID: ENSMUSG00000028261
• Aliases: Ndufaf4, 1110007M04Rik, 3000003G13Rik, AW214064
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 4 [Source:MGI Symbol;Acc:MGI:1915743]

Sequence

>retro_mmus_1290
AAGCACTCTTATCCCTGCAGCCTCCTAAGCAAGCAGCTGAGACACCATCCAGAAATCAAAGAAGTTGCTAGAAAAGGTAA
AAAGTTGTTGTCATTACTAAACAATGTATATATGTCGATCCTAAAGTTCTGGCATCTTCCTTGCAAGTAAAAGATATTGA
ACCATAACAAGAACCAAAAGAATTCAGATTGGAGATATGACATCACTTTGATATGAATATTATGGGTGTTTCCAAAGGCA
AATTACTATTATAGAAGTATTGACCCTTCTCAATAACCATACATTTTCTCAAGAAAGACAGACAGCTGGGAAATACTACA
AAAGAATTCTATTTAGAACTAAAATATGTAAATTCCCTTCTCAACTATTTAGTTACTTTTAATGTCAAAAATCTTTCCTT
TTGAAGAAAAGAAAGTAATATGATCAAAA

Alignment

ORF - retro_mmus_1290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.38 %
• Parental protein coverage: 82.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KHPSTRDLLQEHRSQYPEIEEVVSKKDNKLLSL-LRDVYVDSKDPVPALPVK-VEPRQEPKEFRLPIGNH
          KH.....LL.......PEI.EV..K....L..L.....YVD.K.....L.VK..EP.QEPKEFRL.I..H
Retrocopy KHSYPCSLLSKQLRHHPEIKEVARKGKKLLSLL<KQCIYVDPKVLASSLQVKDIEP*QEPKEFRLEI*HH

Parental  FDKNITDIPKGK-ITVVEALTLLNNHKLSPETWTAEK-IAQEYYLELKDVNSLLKYFVTFEV-KILPPED
          FD.NI....KGK.IT..E.LTLLNNH..S.E..TA.K....E.YLELK.VNSLL.Y.VTF.V.KI.P.E.
Retrocopy FDMNIMGVSKGK<ITIIEVLTLLNNHTFSQERQTAGK>TTKEFYLELKYVNSLLNYLVTFNV>KIFPFEE

Parental  RKAIQSK
          .K.I.SK
Retrocopy KKVI*SK

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	24.95 RPM
SRP007412_cerebellum	0.00 RPM	18.58 RPM
SRP007412_heart	0.00 RPM	39.22 RPM
SRP007412_kidney	0.00 RPM	30.09 RPM
SRP007412_liver	0.00 RPM	24.77 RPM
SRP007412_testis	0.09 RPM	2.10 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1290 was not detected

EST

No EST(s) were mapped for retro_mmus_1290 retrocopy.

TSS

No TSS is located nearby retro_mmus_1290 retrocopy 5' end.

Lab

retro_mmus_1290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003174	1 retrocopy	retro_btau_1763,
Choloepus hoffmanni	ENSCHOG00000005145	2 retrocopies	retro_chof_2271, retro_chof_891,
Callithrix jacchus	ENSCJAG00000001235	2 retrocopies	retro_cjac_1613, retro_cjac_1700,
Cavia porcellus	ENSCPOG00000007618	1 retrocopy	retro_cpor_425,
Homo sapiens	ENSG00000123545	4 retrocopies	retro_hsap_1494, retro_hsap_2774, retro_hsap_3761, retro_hsap_477,
Gorilla gorilla	ENSGGOG00000012070	4 retrocopies	retro_ggor_1147, retro_ggor_1931, retro_ggor_2529, retro_ggor_451,
Microcebus murinus	ENSMICG00000015734	1 retrocopy	retro_mmur_1624,
Macaca mulatta	ENSMMUG00000018843	4 retrocopies	retro_mmul_1717, retro_mmul_2138, retro_mmul_578, retro_mmul_734,
Mus musculus	ENSMUSG00000028261	3 retrocopies	retro_mmus_1153, retro_mmus_1290 , retro_mmus_3668,
Nomascus leucogenys	ENSNLEG00000013568	4 retrocopies	retro_nleu_171, retro_nleu_1716, retro_nleu_678, retro_nleu_890,
Oryctolagus cuniculus	ENSOCUG00000002152	1 retrocopy	retro_ocun_1162,
Pongo abelii	ENSPPYG00000016857	4 retrocopies	retro_pabe_1244, retro_pabe_2241, retro_pabe_257, retro_pabe_3160,
Pan troglodytes	ENSPTRG00000018435	4 retrocopies	retro_ptro_1013, retro_ptro_1877, retro_ptro_2552, retro_ptro_358,
Rattus norvegicus	ENSRNOG00000007506	3 retrocopies	retro_rnor_1617, retro_rnor_2973, retro_rnor_675,
Tursiops truncatus	ENSTTRG00000010911	1 retrocopy	retro_ttru_628,