RetrogeneDB ID: retro_mmus_2037

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:60098402..60098699(-)
• Located in intron of: ENSMUSG00000026987

Retrocopy information

• Ensembl ID: ENSMUSG00000087181
• 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_2037
GCGCTAATGCGGAAAACGCGAGATTATTTTAAGACCAAGGAGTTTCGGGATTATATAACCAGCACCCACTTCTGGGGTCC
TGTGGCCAACTGGGGCCTTCCGCTGGCCGCCTTTAAGGATATGAAGGCGCCTCCCGACATCATCAGTGGCCGCATGACGA
CGGCCCTCATCTTCTACTCCATGGCTTTCATGCGCTTTGCCTACCGTGTCCAGCCTCGAAACTACCTGCTGCTGGCATGC
CATTTCTCCAACGTATTGGCGCAGAGCATCCAGGCGAGCCGTTACCTGAAGCACCAA

Alignment

ORF - retro_mmus_2037 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.65 %
• Parental protein coverage: 90.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALVRKAADYVRSKDFRDYLMSTHFWGPVANWGLPIAAINDMKKSPEIISGRMTFALCCYSLTFMRFAYKV
          AL.RK..DY...K.FRDY..STHFWGPVANWGLP.AA..DMK..P.IISGRMT.AL..YS..FMRFAY.V
Retrocopy ALMRKTRDYFKTKEFRDYITSTHFWGPVANWGLPLAAFKDMKAPPDIISGRMTTALIFYSMAFMRFAYRV

Parental  QPRNWLLFACHVTNEVAQLIQGGRLINYE
          QPRN.LL.ACH..N..AQ.IQ..R.....
Retrocopy QPRNYLLLACHFSNVLAQSIQASRYLKHQ

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	0.00 RPM	13.25 RPM
SRP007412_cerebellum	0.09 RPM	14.63 RPM
SRP007412_heart	0.03 RPM	32.25 RPM
SRP007412_kidney	0.02 RPM	22.75 RPM
SRP007412_liver	0.05 RPM	19.01 RPM
SRP007412_testis	5.53 RPM	2.29 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2037 was not detected

EST

No EST(s) were mapped for retro_mmus_2037 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_87825	1056 libraries	10 libraries	2 libraries	2 libraries	2 libraries
TSS #2	TSS_87826	1058 libraries	10 libraries	1 library	1 library	2 libraries

The graphical summary, for retro_mmus_2037 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_2037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2037 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,