RetrogeneDB ID: retro_mmus_2926

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:42879395..42880002(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000092191
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppm1a
• Ensembl ID: ENSMUSG00000021096
• Aliases: Ppm1a, 2310003C21Rik, 2900017D14Rik, AI427932, AU017636, MMPa-2, MPPa-1
• Description: protein phosphatase 1A, magnesium dependent, alpha isoform [Source:MGI Symbol;Acc:MGI:99878]

Sequence

>retro_mmus_2926
ATTCAGAATGCAGGGGGCTCGATGATGATTCAGCGTGTCAATGGCTCTCTGGCTGGGGATTTCGATTACAAATGTGTCCA
TCGCAAAGGTCCCACAGAGCAGCCTGTCTCACCAAGCCCGAAGTCCATGATATTGAAAGGTCTGAAGAAGAATATCAGTT
GATCATTCTTGCATATGATGGTATCTGGGACGTCACTGGAAACGAAGAGCTCTGTGACTTTGTGAGATCCAGACTTGAAG
TCACTTATGACCATGAGGAAGTTTGTGATGAAGCAGTAGACACCTGTTTGTATAAGGAAAGTCGAGACACCGTAAGTGCG
ATTTTGATCTGTTTTCCAAATGCACCTAAAGCCTCAGCAGAAGCGGGGAAGAAGGAGGCGGGGCTGAGCGAGTACCTGGA
AAGCAGAGGAGAAGAAATCATAAGAAGCAGGGGGAAGGCGTCCCTGATTTAGTCCACGTGATGTGCACGGTAGCCATTGA
GCACATCCGCAGCCTCCCACCAGGGGGTGAATTGGCAAGCAAGCAGAAAGTAATTGAAGCCATTTACAATAGACTAAATA
CTTACAAAAATGACGACAATGATTCTACATCAACTGATGACATGTGG

Alignment

ORF - retro_mmus_2926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IQRVNGSLAVSRA----LGDFDYKCVHGKGPTEQLVSP-EPEVHDIERSEEDDQFIILACDGIWDVMGNE
          IQ...GS....R......GDFDYKCVH.KGPTEQ.VSP..PEVHDIERSEE..Q.IILA.DGIWDV.GNE
Retrocopy IQNAGGSMMIQRVNGSLAGDFDYKCVHRKGPTEQPVSP<KPEVHDIERSEEEYQLIILAYDGIWDVTGNE

Parental  ELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPSAPKVSAEAVKKEAELDKYLESRVEE
          ELCDFVRSRLEVT.D.E.VC.E.VDTCLYK.SRD..S.ILICFP.APK.SAEA.KKEA.L..YLESR.EE
Retrocopy ELCDFVRSRLEVTYDHEEVCDEAVDTCLYKESRDTVSAILICFPNAPKASAEAGKKEAGLSEYLESRGEE

Parental  II-KKQVEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPYKNDDTDSASTDDMW
          II.KKQ.EGVPDLVHVM.T.A.E.I.SLPPGGELASK..VIEA.YNRLN.YKNDD.DS.STDDMW
Retrocopy II<KKQGEGVPDLVHVMCTVAIEHIRSLPPGGELASKQKVIEAIYNRLNTYKNDDNDSTSTDDMW

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	146.81 RPM
SRP007412_cerebellum	0.00 RPM	124.75 RPM
SRP007412_heart	0.00 RPM	115.21 RPM
SRP007412_kidney	0.00 RPM	104.35 RPM
SRP007412_liver	0.00 RPM	126.41 RPM
SRP007412_testis	0.59 RPM	332.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2926 was not detected

EST

No EST(s) were mapped for retro_mmus_2926 retrocopy.

TSS

No TSS is located nearby retro_mmus_2926 retrocopy 5' end.

Lab

retro_mmus_2926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2926 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021096	2 retrocopies	retro_mmus_2925, retro_mmus_2926 ,
Mus musculus	ENSMUSG00000061130	1 retrocopy	retro_mmus_468,
Otolemur garnettii	ENSOGAG00000003689	1 retrocopy	retro_ogar_1834,
Drosophila melanogaster	FBgn0035425	1 retrocopy	retro_dmel_64,
Drosophila melanogaster	FBgn0086361	1 retrocopy	retro_dmel_66,