RetrogeneDB ID: retro_mmus_979

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:110858567..110858894(-)
• Located in intron of: ENSMUSG00000021271

Retrocopy information

• Ensembl ID: ENSMUSG00000091498
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mpc1
• Ensembl ID: ENSMUSG00000023861
• Aliases: Mpc1, 0610006G08Rik, 3830411I18Rik, Brp44l
• Description: mitochondrial pyruvate carrier 1 [Source:MGI Symbol;Acc:MGI:1915240]

Sequence

>retro_mmus_979
ATGGCTGGAGCGCTGGTGCGCAAAGCGGCGGACTATGTCCAGAGCAAGGACTTCCGGGACTATCTCATGAGTACGCACTT
CTGGGGCCCAGTTGCCAACTGGGGTCTCCCCATTGCTGCTATCAATGACATGAAGAAATCTCCAGAGATTATCAGTGGGC
GGATGACTTTCGCCCTCTGTTGCTATTCTCTGACATTCATGAGATTTGCCTACAAGGTACAACCTCGAAACTGGCTTTTG
TTTGCATGCCATGTAACAAACGAAGTAGCTCAGCTCATTCAGGGAGGACGACTTATCAACTACGAGATGAGTAAGCGGCC
ATCTGCA

Alignment

ORF - retro_mmus_979 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFA
          MAGALVRKAADYV.SKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFA
Retrocopy MAGALVRKAADYVQSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFA

Parental  YKVQPRNWLLFACHVTNEVAQLIQGGRLINYEMSKRPSA
          YKVQPRNWLLFACHVTNEVAQLIQGGRLINYEMSKRPSA
Retrocopy YKVQPRNWLLFACHVTNEVAQLIQGGRLINYEMSKRPSA

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	2.10 RPM	13.25 RPM
SRP007412_cerebellum	2.21 RPM	14.63 RPM
SRP007412_heart	5.60 RPM	32.25 RPM
SRP007412_kidney	5.24 RPM	22.75 RPM
SRP007412_liver	5.08 RPM	19.01 RPM
SRP007412_testis	0.18 RPM	2.29 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_979 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	12:110858828..110858964
ENCFF001YKA	POLR2A	12:110858728..110859081

EST

No EST(s) were mapped for retro_mmus_979 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_21396	593 libraries	190 libraries	241 libraries	36 libraries	12 libraries

The graphical summary, for retro_mmus_979 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_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_979 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027879	1 retrocopy	retro_btau_43,
Callithrix jacchus	ENSCJAG00000012552	2 retrocopies	retro_cjac_2102, retro_cjac_4053,
Dasypus novemcinctus	ENSDNOG00000001205	1 retrocopy	retro_dnov_2139,
Homo sapiens	ENSG00000060762	1 retrocopy	retro_hsap_4675,
Myotis lucifugus	ENSMLUG00000000583	1 retrocopy	retro_mluc_28,
Mus musculus	ENSMUSG00000023861	3 retrocopies	retro_mmus_2037, retro_mmus_3420, retro_mmus_979 ,
Ornithorhynchus anatinus	ENSOANG00000004153	1 retrocopy	retro_oana_45,
Pongo abelii	ENSPPYG00000017166	1 retrocopy	retro_pabe_17,
Rattus norvegicus	ENSRNOG00000012415	3 retrocopies	retro_rnor_1111, retro_rnor_2632, retro_rnor_296,
Tursiops truncatus	ENSTTRG00000004456	1 retrocopy	retro_ttru_663,