RetrogeneDB ID: retro_mmus_2417

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:146581359..146582309(+)
• Located in intron of: ENSMUSG00000096958

Retrocopy information

• Ensembl ID: ENSMUSG00000083038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppp2r5a
• Ensembl ID: ENSMUSG00000026626
• Aliases: Ppp2r5a, PR61alpha
• Description: protein phosphatase 2, regulatory subunit B (B56), alpha isoform [Source:MGI Symbol;Acc:MGI:2388479]

Sequence

>retro_mmus_2417
TTCTTGGAGAGTGCTGATTTCCAGCCCAGCATTGCAAAGCGATACATTGATCAGAAGTTGTCCAACTGCTCCTGGAGCTT
TTTGATAGTGAAGATCCACGGGAGCGCGACTTCCTGAAGACCGTCCTAAATCAGATTTATGGCAAGTTCCTTGGCCTGAG
AGCGTTCATCAGAAAGCAGATTAACAACATTTTCCTCAGGTTTATATATGAAACGGAACATTTCAGTGGTGTGGCTGAGC
TCCTTGAAATATTGGGAAGTATCATCAATGGCTTTGCATTGCCAGTGAAAGCAGAGCATAAGCAGTTTCTAATGAAGGTT
TTTATTCCTATGCATACTGCAAAAGGATTGGCCTTGTTTTATGCACAGCTGGCGTACTGTGTTGTGCAGTTCCTGGAGAA
AGCCACAACGCTGACAGAGCCGGTGATCAGAGGACTGCTGAAATTTCGGCCAAAAACATGCAGTCAGAAAGAGGTGATGT
TTTAGGAAAAATTGAAGATGTCTTAGATGTCATTGAACCAACACAATTCAAAAAAATTGAAGAGCTGCTTTTTAAGCAGA
TATCCAAGTGTGTCTCCAGCTCATTTCCAGGTTGCAGAAAGAGCACTGTAATTCTGGAATAATGAATATATTCTTAGTTT
GATTGAAGAGAATATAGATAAAATCCTGCCAATCATGTTTGCCAGCTTGTATAAAATTTCCAAAGAACACTGGAATCAGC
CTACTGTAGCACTGGTGTACAATGTGCTGAAAACCCTCATGGAGATGAACGGCAAGCTTTTTGACAACCTTACTAGTTCC
TACAAAGCCGAAAGACAGAGAGAGAAGAAGAAAGAACTGGAACGGGAAGAGTTATGGAAAAAGCTAGAAGAGCTGCAGCT
GAAGAAGGCTCTAGAGAAACAGAACAATGCTTAAAACATGCACAGTATTCAGAGCAGTACCAGTGCCAAA

Alignment

ORF - retro_mmus_2417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.47 %
• Parental protein coverage: 65.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLESPDFQPSIAKRYIDQKF-VQQLLELFDSEDPRERDFLKTVLHRIYGKFLGLRAFIRKQINNIFLRFI
          FLES.DFQPSIAKRYIDQK..VQ.LLELFDSEDPRERDFLKTVL..IYGKFLGLRAFIRKQINNIFLRFI
Retrocopy FLESADFQPSIAKRYIDQKL<VQLLLELFDSEDPRERDFLKTVLNQIYGKFLGLRAFIRKQINNIFLRFI

Parental  YETEHFNGVAELLEILGSIINGFALPLKAEHKQFLMKVLIPMHTAKGLALFHAQLAYCVVQFLEKDTTLT
          YETEHF.GVAELLEILGSIINGFALP.KAEHKQFLMKV.IPMHTAKGLALF.AQLAYCVVQFLEK.TTLT
Retrocopy YETEHFSGVAELLEILGSIINGFALPVKAEHKQFLMKVFIPMHTAKGLALFYAQLAYCVVQFLEKATTLT

Parental  EPVIRGLLKFWPKTCSQKEVMF-LGEIEEILDVIEPTQF-KKIEEPLFKQISKCVSSSHFQVAERALYFW
          EPVIRGLLKF.PKTCSQKEVMF.LG.IE..LDVIEPTQF.KK............VS..HFQVAERAL.FW
Retrocopy EPVIRGLLKFRPKTCSQKEVMF<LGKIEDVLDVIEPTQF>KKLKSCFLSRYPS-VSPAHFQVAERAL*FW

Parental  NNEYILSLIEENIDKILPIMFASLYKISKEHWNQTIVALVYNVLKTLMEMNGKLFDDLTSSYKAERQREK
          NNEYILSLIEENIDKILPIMFASLYKISKEHWNQ..VALVYNVLKTLMEMNGKLFD.LTSSYKAERQREK
Retrocopy NNEYILSLIEENIDKILPIMFASLYKISKEHWNQPTVALVYNVLKTLMEMNGKLFDNLTSSYKAERQREK

Parental  KKELEREELWKKLEELQLKKALEKQNNAYNMHSIRSSTSAK
          KKELEREELWKKLEELQLKKALEKQNNA.NMHSI.SSTSAK
Retrocopy KKELEREELWKKLEELQLKKALEKQNNA*NMHSIQSSTSAK

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	59.72 RPM
SRP007412_cerebellum	0.00 RPM	30.39 RPM
SRP007412_heart	0.00 RPM	71.32 RPM
SRP007412_kidney	0.00 RPM	81.29 RPM
SRP007412_liver	0.00 RPM	112.81 RPM
SRP007412_testis	0.00 RPM	15.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2417 was not detected

EST

No EST(s) were mapped for retro_mmus_2417 retrocopy.

TSS

No TSS is located nearby retro_mmus_2417 retrocopy 5' end.

Lab

retro_mmus_2417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2417 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009549	1 retrocopy	retro_mluc_1768,
Mus musculus	ENSMUSG00000026626	5 retrocopies	retro_mmus_2410, retro_mmus_2415, retro_mmus_2417 , retro_mmus_2421, retro_mmus_3390,
Pteropus vampyrus	ENSPVAG00000010468	1 retrocopy	retro_pvam_1209,
Rattus norvegicus	ENSRNOG00000000068	1 retrocopy	retro_rnor_2107,
Tarsius syrichta	ENSTSYG00000013786	1 retrocopy	retro_tsyr_1135,
Vicugna pacos	ENSVPAG00000011662	1 retrocopy	retro_vpac_63,