RetrogeneDB ID: retro_mmus_2888

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:4412435..4412898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Atp6v0c
• Ensembl ID: ENSMUSG00000024121
• Aliases: Atp6v0c, Atp6c, Atp6c2, Atp6l, Atpl, Atpl-rs1, PL16, VATL, Vma3
• Description: ATPase, H+ transporting, lysosomal V0 subunit C [Source:MGI Symbol;Acc:MGI:88116]

Sequence

>retro_mmus_2888
ATGGCTGACATCAAGAACAACCCCGAATATTCTTCGGTTTTCGGTGTCATGGGCGCCTCGTCCACCATGGTCTTCAGCGC
CATGGGAGCCGCCTATGGCACAGCCAAGAGCGGCACTGGCATTGCAGTCATGTCAGTCATGAGGCCAGAGCTGATCATGA
AGTCCATCATCCCAGTGGTTATGGCTGGGATCATCGCCATCTACGGCCTGGCGGTGGCAGTACTTATCGCTATCTCCCTG
ACTGATGGCATCACCCTCTACAGGTTTTCTTCAACTGGGTGCTGGCCTGAGTGTGGGGTTGAGTGGCCTGGCTGCTGGCT
TTGCCATTGGCATCGTCGGAGATGCTGGTGTTCGGGGCACTGCCCAGCAGCCTCGACTGTTCGTGGGCACGATCCTGATC
CTCATCTTTGCAAAGGTGCTTGGCCTCTACGGTCTCATCGTGGCCCTAATCCTCTCCACAAAG

Alignment

ORF - retro_mmus_2888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIKNNPEYSSFFGVMGASSAMVFSAMGAAYGTAKSGTGIAAMSVMRPELIMKSIIPVVMAGIIAIYGL
          MADIKNNPEYSS.FGVMGASS.MVFSAMGAAYGTAKSGTGIA.MSVMRPELIMKSIIPVVMAGIIAIYGL
Retrocopy MADIKNNPEYSSVFGVMGASSTMVFSAMGAAYGTAKSGTGIAVMSVMRPELIMKSIIPVVMAGIIAIYGL

Parental  VVAVLIANSLTDGITLYRSFLQLG-AGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAE
          .VAVLIA.SLTDGITLYR.F...G.AGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVG.ILILIFA.
Retrocopy AVAVLIAISLTDGITLYR-FSSTG>AGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGTILILIFAK

Parental  VLGLYGLIVALILSTK
          VLGLYGLIVALILSTK
Retrocopy VLGLYGLIVALILSTK

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	69.27 RPM
SRP007412_cerebellum	0.00 RPM	27.44 RPM
SRP007412_heart	0.16 RPM	17.87 RPM
SRP007412_kidney	0.19 RPM	24.79 RPM
SRP007412_liver	0.00 RPM	10.87 RPM
SRP007412_testis	0.00 RPM	6.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2888 was not detected

EST

No EST(s) were mapped for retro_mmus_2888 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_134521	524 libraries	255 libraries	258 libraries	26 libraries	9 libraries

The graphical summary, for retro_mmus_2888 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_2888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026428	1 retrocopy	retro_btau_1638,
Homo sapiens	ENSG00000185883	2 retrocopies	retro_hsap_1798, retro_hsap_3462,
Gorilla gorilla	ENSGGOG00000028600	2 retrocopies	retro_ggor_1323, retro_ggor_2335,
Macropus eugenii	ENSMEUG00000004597	2 retrocopies	retro_meug_1428, retro_meug_1837,
Myotis lucifugus	ENSMLUG00000026715	2 retrocopies	retro_mluc_2507, retro_mluc_294,
Monodelphis domestica	ENSMODG00000015439	5 retrocopies	retro_mdom_1669, retro_mdom_1739, retro_mdom_507, retro_mdom_84, retro_mdom_982,
Mus musculus	ENSMUSG00000024121	2 retrocopies	retro_mmus_2726, retro_mmus_2888 ,
Nomascus leucogenys	ENSNLEG00000009416	2 retrocopies	retro_nleu_1692, retro_nleu_2770,
Procavia capensis	ENSPCAG00000015060	1 retrocopy	retro_pcap_148,
Pan troglodytes	ENSPTRG00000007653	2 retrocopies	retro_ptro_1204, retro_ptro_2346,
Rattus norvegicus	ENSRNOG00000006542	1 retrocopy	retro_rnor_118,
Sarcophilus harrisii	ENSSHAG00000014251	1 retrocopy	retro_shar_194,
Ictidomys tridecemlineatus	ENSSTOG00000013420	3 retrocopies	retro_itri_119, retro_itri_387, retro_itri_691,
Drosophila melanogaster	FBgn0262736	3 retrocopies	retro_dmel_3, retro_dmel_38, retro_dmel_65,
Caenorhabditis elegans	R10E11.2	2 retrocopies	retro_cele_1, retro_cele_5,