RetrogeneDB ID: retro_mmus_30

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:23101769..23102231(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000073730
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ppp1r14b
• Ensembl ID: ENSMUSG00000056612
• Aliases: Ppp1r14b, AOM172, PHI-1, PLCB3N, Png
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:MGI Symbol;Acc:MGI:107682]

Sequence

>retro_mmus_30
ATGGCGGACAGCGGCCCCTCGGGGGGGCCAGCTTTGACTGATCCAGGCCCCGAGCCAGGCAGTGCCAACACAGGGCCCCG
AGTCTACTTCGAGAGTCCCCCTGGGACCCCAGGCGAAACCCCTGGCCCCGGGAACAACCCGGATAAAGATGACCAGGTGA
GACGGCCACATAGGCCAGATAAGATCATCGTCAAGTACGACCGCAAGGAGCTACGGAAGCGCCTCAACCTGGACGACTGG
ATCTTAGAACAGCTCACTGGTCTCTACGACTGCAAGGAAGAGGAAATCCCAGAGCTCGAGATCGATGTGGACGAACTCTT
AGACATGGAAAGCGACGATACCCGGGCTGCTAGAGTCAAGGAGCTGTTAGTTGACTGTTACAAACCCACTGAGGCCTTCA
TCAATGACCTGCTAGACAGGATCCGGGGCATGCAGAAGCTGACCATACCCCTGAAGAACTAA

Alignment

ORF - retro_mmus_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADSGPAGGAALAAPAPGPGSGSTGPRVYFQSPPGAAGEGPG---GADDDGPVR---RQGKVTVKYDRKE
          MADSGP.GG.AL..P.P.PGS..TGPRVYF.SPPG..GE.PG.....D.D..VR...R..K..VKYDRKE
Retrocopy MADSGPSGGPALTDPGPEPGSANTGPRVYFESPPGTPGETPGPGNNPDKDDQVRRPHRPDKIIVKYDRKE

Parental  LRKRLNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFISGLLDK
          LRKRLNL..WILEQLT.LYDC.EEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFI..LLD.
Retrocopy LRKRLNLDDWILEQLTGLYDCKEEEIPELEIDVDELLDMESDDTRAARVKELLVDCYKPTEAFINDLLDR

Parental  IRGMQKLSTPQK
          IRGMQKL..P.K
Retrocopy IRGMQKLTIPLK

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	0.02 RPM	4.72 RPM
SRP007412_cerebellum	0.00 RPM	4.43 RPM
SRP007412_heart	0.00 RPM	11.52 RPM
SRP007412_kidney	0.00 RPM	9.76 RPM
SRP007412_liver	0.03 RPM	6.36 RPM
SRP007412_testis	78.99 RPM	27.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_30 was not detected

EST

No EST(s) were mapped for retro_mmus_30 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_73669	1000 libraries	59 libraries	5 libraries	2 libraries	6 libraries

The graphical summary, for retro_mmus_30 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_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_30 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_41

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018019	1 retrocopy	retro_amel_934,
Felis catus	ENSFCAG00000030667	1 retrocopy	retro_fcat_1417,
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,
Otolemur garnettii	ENSOGAG00000030926	2 retrocopies	retro_ogar_3158, retro_ogar_376,
Pteropus vampyrus	ENSPVAG00000017120	1 retrocopy	retro_pvam_1095,
Rattus norvegicus	ENSRNOG00000021151	2 retrocopies	retro_rnor_1262, retro_rnor_41,