RetrogeneDB ID: retro_mmus_3473

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:75155958..75156270(+)
• Located in intron of: ENSMUSG00000073094

Retrocopy information

• Ensembl ID: ENSMUSG00000082244
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3473
GCTGATGACGATGGCCCGGTGAGATGGCAAGGGAAGGTCACCATCAAGTACGACCGCAAGGAGCTATGGAAGCGCCTCAA
CCTGGAGGAGTGGATTTTAGAACAGCTCACGCGACTCTATGACTGCCAGGAGGACGAGATCCCGGAGCTTGAGATAGATG
TGGATGAACTTTTAGACATGGAAAGTGATGATACCCGGGCTGCTAGAGTCAAGGAGCTGTTAGTTGACTGTTACAAACCC
ACTGAGGCCTTCATCTCTGGCCTGCTGGACAAGATCTGGGGCATGCAGAAGCTGAGCACACCCCAGAAGAAG

Alignment

ORF - retro_mmus_3473 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.19 %
• Parental protein coverage: 70.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADDDGPVRRQGKVTVKYDRKELRKRLNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDTRAARV
          ADDDGPVR.QGKVT.KYDRKEL.KRLNLEEWILEQLTRLYDCQE.EIPELEIDVDELLDMESDDTRAARV
Retrocopy ADDDGPVRWQGKVTIKYDRKELWKRLNLEEWILEQLTRLYDCQEDEIPELEIDVDELLDMESDDTRAARV

Parental  KELLVDCYKPTEAFISGLLDKIRGMQKLSTPQKK
          KELLVDCYKPTEAFISGLLDKI.GMQKLSTPQKK
Retrocopy KELLVDCYKPTEAFISGLLDKIWGMQKLSTPQKK

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	4.72 RPM
SRP007412_cerebellum	0.00 RPM	4.43 RPM
SRP007412_heart	0.00 RPM	11.52 RPM
SRP007412_kidney	0.02 RPM	9.76 RPM
SRP007412_liver	0.00 RPM	6.36 RPM
SRP007412_testis	0.09 RPM	27.86 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_3473 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	X:75155572..75155917
ENCFF001YKA	POLR2A	X:75155682..75155737

EST

No EST(s) were mapped for retro_mmus_3473 retrocopy.

TSS

No TSS is located nearby retro_mmus_3473 retrocopy 5' end.

Lab

retro_mmus_3473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3473 has 0 orthologous retrocopies within eutheria group .

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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,