RetrogeneDB ID: retro_mmus_874

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:69981296..69982019(+)
• Located in intron of: ENSMUSG00000021067

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ppp2r2a
• Ensembl ID: ENSMUSG00000022052
• Aliases: Ppp2r2a, 2410004D02Rik, mKIAA1541
• Description: protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform [Source:MGI Symbol;Acc:MGI:1919228]

Sequence

>retro_mmus_874
CAACACCCCAGTGAGAACAAAATCCAGTCTCATAGCAGAGGAGAATACAATGTTTACAGCACCTTCCAGAGCCATGAGCC
AGAATTTGACTACTTGAAAAGCTTAGAAATAGAAGGGAAGATCAACAAAATTAGGTGGTTACCCCAGAAAAATGCTGCCC
AGTTTTTATTGTCTACCAATGATAAAACAATAAAATTATGGAAAATCAGTGAAAGAGACAAAAGACCAGAAGGCTATAAC
TTGAAAGAGGAAGATGGAAGATATAGAGATCCTACTACAGTCACTACGCTACGGGTGCCAGTATTTAGGCCCATGGATCT
AATGGTGGAAGCCAGTCCACAGAGAATATTTGCCAACACCCACACTTATCACATCAACTCAATTTCTATCAATAGTGATT
ATGAAACCTACTTATCAGCAGATGATTTGTGAATTATCTCTGGCATCTGGAAATTACAGACTGGAGTTTTAATATTGTGG
CTATCAAGCCTGGCAATATGGAAAAGCTCACAGAGGTGCTCACAGCTGCCGAATTTCACCCCAACAGCTGTAACACATTT
GTGTACAGCAGCAGTAAAGGAACCATTCGGTTATGTGACATGAGGGCATCTGCGCTCTGTGACAGGCATTCTAAACTGTT
TGAAGAACGTGAAGATCCCAGCAACAGGTCATTTTTTTTCTGAAATCATCTCCTCTATTTCTGATGTAAAATTCAGCCAT
AGT

Alignment

ORF - retro_mmus_874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.18 %
• Parental protein coverage: 53.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQEQENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKIS
          Q...ENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIE.KINKIRWLPQKNAAQFLLSTNDKTIKLWKIS
Retrocopy QHPSENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEGKINKIRWLPQKNAAQFLLSTNDKTIKLWKIS

Parental  ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSA
          ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASP.RIFAN.HTYHINSISINSDYETYLSA
Retrocopy ERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPQRIFANTHTYHINSISINSDYETYLSA

Parental  DDLRI-NLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR
          DDL.I..LWHLEITD.SFNIV.IKP.NME.LTEV.TAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR
Retrocopy DDL*I<YLWHLEITDWSFNIVAIKPGNMEKLTEVLTAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDR

Parental  HSKLFEEPEDPSNRS-FFSEIISSISDVKFSHS
          HSKLFEE.EDPSNRS....EIISSISDVKFSHS
Retrocopy HSKLFEEREDPSNRS>XXXEIISSISDVKFSHS

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	0.61 RPM	80.67 RPM
SRP007412_cerebellum	0.43 RPM	52.37 RPM
SRP007412_heart	0.53 RPM	41.50 RPM
SRP007412_kidney	0.54 RPM	35.46 RPM
SRP007412_liver	0.36 RPM	19.63 RPM
SRP007412_testis	0.37 RPM	34.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_874 was not detected

EST

No EST(s) were mapped for retro_mmus_874 retrocopy.

TSS

No TSS is located nearby retro_mmus_874 retrocopy 5' end.

Lab

retro_mmus_874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_874 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019205	1 retrocopy	retro_ecab_305,
Monodelphis domestica	ENSMODG00000016691	1 retrocopy	retro_mdom_529,
Mus musculus	ENSMUSG00000022052	1 retrocopy	retro_mmus_874 ,