RetrogeneDB ID: retro_mmus_3044

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:81161395..81161743(-)
• Located in intron of: ENSMUSG00000025726

Retrocopy information

• Ensembl ID: ENSMUSG00000083820
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufs6
• Ensembl ID: ENSMUSG00000021606
• Aliases: Ndufs6, BC059730, IP13
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 6 [Source:MGI Symbol;Acc:MGI:107932]

Sequence

>retro_mmus_3044
ATGGCGGTGGTACTGACCTTCCGCTGGCTGTTGACTCTCCCCAGGGCTGCGCGGGGTTTCAGGGTTCGAGTGTTGCCGAG
CGGGGAAAAGATCACGCATACCGGCCAGGTGTATGATGAAAAAGACTACAGGAGGATTCGTTTTGTAGATCGTCAGAAAG
AGGTGAATGAGAACTTTGCCATTGATTTGATAGCACAACAGCCTGTGAATGAGGTGGACCATCGTATCATAGCCTGCGAT
GGAGGCGGTGGTGCCCTGGGCCACCCTAAGGTGTACATAAACTTGGACAAAGAAACAAAAACGGGGACATGTGGCTACTG
CGGCCTGCAGTTCAAGCAGCACCATCAC

Alignment

ORF - retro_mmus_3044 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVLTFRRLLTLPRAARGFGVQVSPSGEKITHTGQVYDEKDYRRVRFVDRQKEVNENFAIDLIAQQPVN
          MA.VLTFR.LLTLPRAARGF.V.V.PSGEKITHTGQVYDEKDYRR.RFVDRQKEVNENFAIDLIAQQPVN
Retrocopy MAVVLTFRWLLTLPRAARGFRVRVLPSGEKITHTGQVYDEKDYRRIRFVDRQKEVNENFAIDLIAQQPVN

Parental  EVEHRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH
          EV.HRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH
Retrocopy EVDHRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH

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	24.20 RPM
SRP007412_cerebellum	0.04 RPM	30.18 RPM
SRP007412_heart	0.65 RPM	152.79 RPM
SRP007412_kidney	0.46 RPM	91.97 RPM
SRP007412_liver	0.11 RPM	36.46 RPM
SRP007412_testis	0.32 RPM	26.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3044 was not detected

EST

No EST(s) were mapped for retro_mmus_3044 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_137588	738 libraries	292 libraries	33 libraries	8 libraries	1 library

The graphical summary, for retro_mmus_3044 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3044 has 0 orthologous retrocopies within eutheria group .

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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,