RetrogeneDB ID: retro_mmus_2089

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:130803503..130803982(-)
• Located in intron of: ENSMUSG00000027309

Retrocopy information

• Ensembl ID: ENSMUSG00000089662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppp1r14c
• Ensembl ID: ENSMUSG00000040653
• Aliases: Ppp1r14c, 6330514J04Rik, KEPI
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14c [Source:MGI Symbol;Acc:MGI:1923392]

Sequence

>retro_mmus_2089
ATGTCGGTGGTGACTGGCGGTGGTGAGGCGGTGGGTGGCAGTGCGAGTGTCTTCTTCCAGATTCCCTGCGGTGGCACTGG
CGGCAGCCCAGGATCTAGCAGCAGCTCCGGCTCCTCGAGGGAGGACTCAGTGCCGGTGACTATGGTGGCCACCGCTGGGC
AAGTGCAACAGCAGCAGCGACACCACCAGCAGGGAAAAGTGACAGTGAAATATGACCATAAGGAGCTTCGTAAGCGGTTG
GTGCTGGAAGAATGGATCGTGGAGCAGCTGGGTCAGCTGTATGGCTGCAAGGAAGAAGAAATGCCAGACGTAGAAATTGA
CATTGATGATCTTCTTGATGCCAACCGCAAGGAGGAAAGAGCTTCGAAATTACAGGAAGCTCTCGTAGTCTGCTATAAAC
CAACAGAGGAATTCATCAGAGAGCTGCTCTCCCGAATAAGAGCATGAGGAAGCTGAACCCTCCGCAGAAGAAGAGCGTA

Alignment

ORF - retro_mmus_2089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVVTGGGEAAGGGGGGGARVFFQSPRGGTGGSPGSSSSSGSSREDSAPVTTVAAAGQVQQQQRRHQQGK
          MSVVTGGGEA.....GG.A.VFFQ.P.GGTGGSPGSSSSSGSSREDS.PVT.VA.AGQVQQQQR.HQQGK
Retrocopy MSVVTGGGEAV----GGSASVFFQIPCGGTGGSPGSSSSSGSSREDSVPVTMVATAGQVQQQQRHHQQGK

Parental  VTVKYDRKELRKRLVLEEWIVEQLGQLYGCEEEEMPDVEIDIDDLLDANSEEERASKLQEALVDCYKPTE
          VTVKYD.KELRKRLVLEEWIVEQLGQLYGC.EEEMPDVEIDIDDLLDAN..EERASKLQEALV.CYKPTE
Retrocopy VTVKYDHKELRKRLVLEEWIVEQLGQLYGCKEEEMPDVEIDIDDLLDANRKEERASKLQEALVVCYKPTE

Parental  EFIRELLSRIR-GMRKLSPPQKKSV
          EFIRELLSRIR..MRKL.PPQKKSV
Retrocopy EFIRELLSRIR<SMRKLNPPQKKSV

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	0.42 RPM	8.92 RPM
SRP007412_cerebellum	0.39 RPM	4.99 RPM
SRP007412_heart	1.00 RPM	83.58 RPM
SRP007412_kidney	0.71 RPM	17.29 RPM
SRP007412_liver	0.60 RPM	0.19 RPM
SRP007412_testis	1.78 RPM	1.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2089 was not detected

EST

No EST(s) were mapped for retro_mmus_2089 retrocopy.

TSS

No TSS is located nearby retro_mmus_2089 retrocopy 5' end.

Lab

retro_mmus_2089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2089 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026586	2 retrocopies	retro_btau_161, retro_btau_571,
Dasypus novemcinctus	ENSDNOG00000017261	2 retrocopies	retro_dnov_1661, retro_dnov_80,
Myotis lucifugus	ENSMLUG00000023245	2 retrocopies	retro_mluc_1095, retro_mluc_499,
Mus musculus	ENSMUSG00000040653	2 retrocopies	retro_mmus_2089 , retro_mmus_3721,
Mus musculus	ENSMUSG00000056612	5 retrocopies	retro_mmus_1045, retro_mmus_2245, retro_mmus_2624, retro_mmus_30, retro_mmus_3473,
Pongo abelii	ENSPPYG00000017102	4 retrocopies	retro_pabe_1880, retro_pabe_2079, retro_pabe_3001, retro_pabe_3232,
Tarsius syrichta	ENSTSYG00000002873	1 retrocopy	retro_tsyr_245,