RetrogeneDB ID: retro_mmus_2338

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:32051811..32052209(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082398
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufs3
• Ensembl ID: ENSMUSG00000005510
• Aliases: Ndufs3, 0610010M09Rik, CI-30kD
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3 [Source:MGI Symbol;Acc:MGI:1915599]

Sequence

>retro_mmus_2338
GGGCGACCCTCAGTGTTGTTGCAGTGCGTAAGAAGGGAGAATGTGGTGGCTGAGAAGCGCCCCACTGTCAGACCCCAGAG
TGATATGACCCACAAGCAACTCTCAGCATTTGGAGAGCATGTGGCTGAAATCTTACCCAATTAAGTCCAACAAGTTTAGG
TGACCTGCCTTGATGAGTTAGAAATCTGTATCCATCCCGATGGAGTCATCCCAACACTGACGTTTCTCAGGGATCGCACC
AATGCACAATTCAGATCCTTGGCTGACTTGACACAGTGGATGTCCCAACTCGGCAGAACCGTTTTGATATTGTCTACAAC
CTGCTGTCTCTGTGGTTCAACTCTAGGATTTGGGTGAAGACCTATGTAGATGAGCTGACGTCCACTAACTCTATAGTT

Alignment

ORF - retro_mmus_2338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAFGEYVAEILPKYVQQVQVSCLDELEICIHPDGVI
          GRPSVL.Q.VRRE...A.KRPTVRP.SD.THKQLSAFGE.VAEILP..VQQV.V.CLDELEICIHPDGVI
Retrocopy GRPSVLLQCVRRENVVAEKRPTVRPQSDMTHKQLSAFGEHVAEILPN*VQQV*VTCLDELEICIHPDGVI

Parental  PTLTFLRDHTNAQFKSLADLT-AVDVPTRQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIV
          PTLTFLRD.TNAQF.SLADLT..VDVPTRQNRF.IVYNLLSL.FNSRI.VKTY.DELT...SIV
Retrocopy PTLTFLRDRTNAQFRSLADLT<TVDVPTRQNRFDIVYNLLSLWFNSRIWVKTYVDELTSTNSIV

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	42.82 RPM
SRP007412_cerebellum	0.00 RPM	40.47 RPM
SRP007412_heart	0.00 RPM	141.98 RPM
SRP007412_kidney	0.00 RPM	93.96 RPM
SRP007412_liver	0.00 RPM	49.65 RPM
SRP007412_testis	0.09 RPM	36.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2338 was not detected

EST

No EST(s) were mapped for retro_mmus_2338 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_104252	114 libraries	281 libraries	166 libraries	283 libraries	228 libraries

The graphical summary, for retro_mmus_2338 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_2338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338 , retro_mmus_792,