RetrogeneDB ID: retro_mmus_3152

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:85824329..85824542(+)
• Located in intron of: ENSMUSG00000031703

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atp5k
• Ensembl ID: ENSMUSG00000050856
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1F0 complex, subunit e [Source:MGI Symbol;Acc:MGI:106636]

Sequence

>retro_mmus_3152
ATGGTGCCCCTGGTTCAGGTCTCTCCACTCATCAAGTTCGGCCGGTACTCCGCTCTGATCCTTGGCATGGCATAGGGTGC
CAAGCGCTACAGTTACCTAAAACCCCTGGCAGAGGAGGAGAGGAGAATAGCAGCAGAGGAAAAGAAGAGACTAGATGAAT
TGAAACGGATTGAGAGAGAACTGGCAGAAGCTCAAGATGACAGCATTCTCAAG

Alignment

ORF - retro_mmus_3152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVPPVQVSPLIKFGRYSALIIGMAYGAKRYSYLKPRAEEERRIAAEEKKRLDELKRIERELAEAQDDSIL
          MVP.VQVSPLIKFGRYSALI.GMA.GAKRYSYLKP.AEEERRIAAEEKKRLDELKRIERELAEAQDDSIL
Retrocopy MVPLVQVSPLIKFGRYSALILGMA*GAKRYSYLKPLAEEERRIAAEEKKRLDELKRIERELAEAQDDSIL

Parental  K
          K
Retrocopy K

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	0.07 RPM	58.85 RPM
SRP007412_cerebellum	0.17 RPM	61.05 RPM
SRP007412_heart	0.37 RPM	401.11 RPM
SRP007412_kidney	0.10 RPM	172.28 RPM
SRP007412_liver	0.19 RPM	137.80 RPM
SRP007412_testis	0.09 RPM	27.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3152 was not detected

EST

No EST(s) were mapped for retro_mmus_3152 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_144963	315 libraries	295 libraries	433 libraries	25 libraries	4 libraries

The graphical summary, for retro_mmus_3152 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_3152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016722	2 retrocopies	retro_amel_1171, retro_amel_1761,
Bos taurus	ENSBTAG00000017496	2 retrocopies	retro_btau_1222, retro_btau_219,
Canis familiaris	ENSCAFG00000023527	1 retrocopy	retro_cfam_62,
Callithrix jacchus	ENSCJAG00000001989	1 retrocopy	retro_cjac_352,
Cavia porcellus	ENSCPOG00000008678	1 retrocopy	retro_cpor_98,
Felis catus	ENSFCAG00000029708	1 retrocopy	retro_fcat_268,
Mustela putorius furo	ENSMPUG00000011414	1 retrocopy	retro_mputfur_494,
Mus musculus	ENSMUSG00000050856	1 retrocopy	retro_mmus_3152 ,
Otolemur garnettii	ENSOGAG00000012271	1 retrocopy	retro_ogar_1292,
Rattus norvegicus	ENSRNOG00000000064	1 retrocopy	retro_rnor_697,
Tursiops truncatus	ENSTTRG00000002962	1 retrocopy	retro_ttru_1938,