RetrogeneDB ID: retro_mmul_1473

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:151857646..151858010(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.354
• Ensembl ID: ENSMMUG00000004447
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001181243]

Sequence

>retro_mmul_1473
GCAGCAGCAATGATTTACCAGCTGCTGGTCTGGAGCAGCATACTGGTGTTGAGCCTGCCCTCAGGTGCCAGGTGTTTTGG
GGTATGGGCCTTGCCAACTGGAGACAAGGTCATGCATGCTAGCCAGGTTGATGATAATAAAGACTCCAGGAAAATTCGGT
TTGTGGGTTGTCAGGAAGAGGTGAATGTAAACTTTGCCACTGATTTGATAACAGAGCAACCTATGAGTGAAGTAGAGTGT
TGGGTAGTATTGTGTAACTGGTTGAGGAGCTCTTGGCTACCCAAAAGTGTATGTAAACATAGACAAAGAAACAAAAACTG
GGATATGTGGTTATTGCGGTCTGTAGTTCAAAAAACACCATCAT

Alignment

ORF - retro_mmul_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.35 %
• Parental protein coverage: 98.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASVTFYRLLSRCGKAALSRPLGARCFGVRVSPTGEKITHTGQVYDDKDYRRIRFVDRQKEVNENFAIDLI
          A....Y.LL.......LS.P.GARCFGV...PTG.K..H..QV.D.KD.R.IRFV..Q.EVN.NFA.DLI
Retrocopy AAAMIYQLLVWSSILVLSLPSGARCFGVWALPTGDKVMHASQVDDNKDSRKIRFVGCQEEVNVNFATDLI

Parental  AEQPVSEVQTRVIACD-GGGGALGHPKVYINLDKETKTGTCGYCGLQFRQHPH
          .EQP.SEV...V..C..G.G.ALG.PKVY.N.DKETKTG.CGYCGL.F..H.H
Retrocopy TEQPMSEVECWVVLCN>G*G-ALGYPKVYVNIDKETKTGICGYCGL*FKKHHH

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	11.77 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.42 RPM
SRP007412_cerebellum	0.00 RPM	9.43 RPM
SRP007412_heart	0.00 RPM	76.61 RPM
SRP007412_kidney	0.00 RPM	31.10 RPM
SRP007412_liver	0.00 RPM	29.45 RPM
SRP007412_testis	0.00 RPM	80.17 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1473 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1473 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2838
Pan troglodytes	retro_ptro_1924
Pongo abelii	retro_pabe_2350
Callithrix jacchus	retro_cjac_1552

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010930	2 retrocopies	retro_amel_213, retro_amel_228,
Bos taurus	ENSBTAG00000009914	2 retrocopies	retro_btau_302, retro_btau_333,
Callithrix jacchus	ENSCJAG00000019382	1 retrocopy	retro_cjac_1552,
Equus caballus	ENSECAG00000021690	3 retrocopies	retro_ecab_701, retro_ecab_838, retro_ecab_917,
Homo sapiens	ENSG00000145494	1 retrocopy	retro_hsap_2838,
Latimeria chalumnae	ENSLACG00000004625	1 retrocopy	retro_lcha_95,
Loxodonta africana	ENSLAFG00000005708	1 retrocopy	retro_lafr_5,
Myotis lucifugus	ENSMLUG00000016888	1 retrocopy	retro_mluc_1750,
Macaca mulatta	ENSMMUG00000004447	1 retrocopy	retro_mmul_1473 ,
Monodelphis domestica	ENSMODG00000001425	1 retrocopy	retro_mdom_207,
Mus musculus	ENSMUSG00000021606	1 retrocopy	retro_mmus_3044,
Nomascus leucogenys	ENSNLEG00000011199	1 retrocopy	retro_nleu_1593,
Oryctolagus cuniculus	ENSOCUG00000004581	2 retrocopies	retro_ocun_1011, retro_ocun_1624,
Pongo abelii	ENSPPYG00000015323	1 retrocopy	retro_pabe_2350,
Pan troglodytes	ENSPTRG00000016706	1 retrocopy	retro_ptro_1924,
Rattus norvegicus	ENSRNOG00000023387	1 retrocopy	retro_rnor_1619,
Rattus norvegicus	ENSRNOG00000049394	1 retrocopy	retro_rnor_1618,
Sarcophilus harrisii	ENSSHAG00000017779	1 retrocopy	retro_shar_176,
Ictidomys tridecemlineatus	ENSSTOG00000003715	1 retrocopy	retro_itri_496,