RetrogeneDB ID: retro_mmus_3721

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:157612691..157612971(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081222
• 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_3721
ACAGCAAGGGAAGGTCACAAGGAGCAACGGAAGCGCCTCAAGCTGGAGGAGTGGATTTTAGAACAGCTCATGCGACTCTA
TGACTGTCAGGAGGAGGAACTCCCAGAGCCCAGGATAGATGTGGATGAACTTTTGGACACAGAACAAGGAAAGCGATGAT
ACCCGGGCTGCTAGAGTCAAGGAGCTGTTAGTTGACTGTTACAAACCCACTGAGGCCTTCATCTCTGGCCTGCTGGACAA
GATCCAGGGCATGCAAAAGCTGAGCACATCCCAGAAGAAG

Alignment

ORF - retro_mmus_3721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.51 %
• Parental protein coverage: 55.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVKYDRKELRKRLVLEEWIVEQLGQLYGCEEEEMPDVEIDIDDLLDA-NSEEE--RASKLQEALVDCYKP
          T.....KE.RKRL.LEEWI.EQL..LY.C.EEE.P...ID.D.LLD..N.E....RA....E.LVDCYKP
Retrocopy TAREGHKEQRKRLKLEEWILEQLMRLYDCQEEELPEPRIDVDELLDT>NKESDDTRAARVKELLVDCYKP

Parental  TEEFIRELLSRIRGMRKLSPPQKK
          TE.FI..LL..I.GM.KLS..QKK
Retrocopy TEAFISGLLDKIQGMQKLSTSQKK

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	8.92 RPM
SRP007412_cerebellum	0.00 RPM	4.99 RPM
SRP007412_heart	0.00 RPM	83.58 RPM
SRP007412_kidney	0.00 RPM	17.29 RPM
SRP007412_liver	0.05 RPM	0.19 RPM
SRP007412_testis	0.00 RPM	1.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3721 was not detected

EST

No EST(s) were mapped for retro_mmus_3721 retrocopy.

TSS

No TSS is located nearby retro_mmus_3721 retrocopy 5' end.

Lab

retro_mmus_3721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3721 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,