RetrogeneDB ID: retro_mmus_1039

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:76935162..76935828(+)
• Located in intron of: ENSMUSG00000021596

Retrocopy information

• Ensembl ID: ENSMUSG00000090119
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Chmp2a
• Ensembl ID: ENSMUSG00000033916
• Aliases: Chmp2a, 1500016L11Rik
• Description: charged multivesicular body protein 2A [Source:MGI Symbol;Acc:MGI:1916203]

Sequence

>retro_mmus_1039
ATGGACCTGTTGTTTGGGCACCAGAAGATGCCAGAGGAACTACTTCAGGAAAACCAGGGGGCCCTGAACCAAGCTATGAG
AGAGCTGGACATGGAATGACAGAAACTAGAGACCCAGGAAAATAAAATAATTGCAGACATCAAAAAGATGGCAAAGCAAG
GCCAGGTGGATGCTGTTCAAATCATGGCAAAAGACCTGGTGCACACCCAGAGATATGTGCACAAGTTTGTGTTGATGCAG
GCCAACATCCAGGCTGTGTCTCTTAAGATACAGACTCTAAAATCCAACAACTCAATGTCACAAGCCATGAAGGGTGTTAC
TAAGGCCATGGGCACCATGAACAGACAGCTGAAATTACCCCAGATCCAGAAGATCATGATGGAGTTTGAACGGTAGGCAG
AGATCATGGACATGAAAGAAGAAATGATGAATGACACAATTGATGATGCCATGGGTGATGAGGAAGATGAAGAGGAGAGT
GATGCTATTGTGTCCCAGGTACTAGATGAGGTGGGACTGAGCCTCACAGATGAGCTGTCAAACCTTCCCTCCACTGGAGG
CTCACTCAGTGTGGCTGCTGGTGGAAAGAAAGCAGAGGCTACAGCCTCAGCCCTGGCTGATGCTGATGCAGACCTGGAAG
AGAGGCTCAAGAACCTTCCCAAGGAC

Alignment

ORF - retro_mmus_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVRIMAKDLVRTR
          MDLLFG..K.PEELL..NQ.ALN.AMRELD.E.QKLETQE.KIIADIKKMAKQGQ.DAV.IMAKDLV.T.
Retrocopy MDLLFGHQKMPEELLQENQGALNQAMRELDME*QKLETQENKIIADIKKMAKQGQVDAVQIMAKDLVHTQ

Parental  RYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKE
          RYV.KFVLM.ANIQAVSLKIQTLKSNNSM.QAMKGVTKAMGTMNRQLKLPQIQKIMMEFER.AEIMDMKE
Retrocopy RYVHKFVLMQANIQAVSLKIQTLKSNNSMSQAMKGVTKAMGTMNRQLKLPQIQKIMMEFER*AEIMDMKE

Parental  EMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA
          EMMND.IDDAMGDEEDEEESDA.VSQVLDE.GLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA
Retrocopy EMMNDTIDDAMGDEEDEEESDAIVSQVLDEVGLSLTDELSNLPSTGGSLSVAAGGKKAEATASALADADA

Parental  DLEERLKNLRRD
          DLEERLKNL..D
Retrocopy DLEERLKNLPKD

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	0.09 RPM	50.72 RPM
SRP007412_cerebellum	0.09 RPM	73.21 RPM
SRP007412_heart	0.06 RPM	56.35 RPM
SRP007412_kidney	0.06 RPM	81.73 RPM
SRP007412_liver	0.11 RPM	68.95 RPM
SRP007412_testis	0.96 RPM	61.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1039 was not detected

EST

No EST(s) were mapped for retro_mmus_1039 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_31160	374 libraries	582 libraries	113 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_1039 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_1039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1039 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013531	1 retrocopy	retro_meug_1308,
Mus musculus	ENSMUSG00000033916	1 retrocopy	retro_mmus_1039 ,
Otolemur garnettii	ENSOGAG00000005628	2 retrocopies	retro_ogar_1870, retro_ogar_2753,
Pongo abelii	ENSPPYG00000010511	1 retrocopy	retro_pabe_196,