RetrogeneDB ID: retro_mmus_1707

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:36610195..36610603(+)
• Located in intron of: ENSMUSG00000024483

Retrocopy information

• Ensembl ID: ENSMUSG00000085172
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psma4
• Ensembl ID: ENSMUSG00000032301
• Aliases: Psma4, C9
• Description: proteasome (prosome, macropain) subunit, alpha type 4 [Source:MGI Symbol;Acc:MGI:1347060]

Sequence

>retro_mmus_1707
CATCTGATGACTAACGAGCTAAGGCTCATTGCTCAATGGTACTTATTACAGTATCAGGAGCCAATTCCCTGTGAGCAGTT
GGTTACAGCACTGTGTGATATCAAACAGGCGTATACACAGTTTGGAGGCAAATGTCCCTTTGGTGTTTCTTTGCTGTATA
TTGGCTGGGATAAGCACTATGGCTTTCAGCTCTATCAGAGTGACCCAAGTGGAAACTACGGGGGATGGAAAGCCACATGC
ATTGGGAACAACAGTGCTGCGGCTGTGTCAATGTTGAAACAAGACTACAAAGAAGGAGAAATGACTCTGAAGTCAGCACT
TGCTCTGGCTGTTAAGGTGCTAAATAAGACAATGGATGTTAGTAAACTGTCAGCTGAAAAAGTGGAAATCGCCACACTAA
CAAGAGAG

Alignment

ORF - retro_mmus_1707 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.32 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPS
          ...TNELRLIAQ.YLLQYQEPIPCEQLVTALCDIKQAYTQFGGK.PFGVSLLYIGWDKHYGFQLYQSDPS
Retrocopy HLMTNELRLIAQWYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKCPFGVSLLYIGWDKHYGFQLYQSDPS

Parental  GNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRE
          GNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRE
Retrocopy GNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRE

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	40.56 RPM
SRP007412_cerebellum	0.00 RPM	40.03 RPM
SRP007412_heart	0.06 RPM	55.57 RPM
SRP007412_kidney	0.23 RPM	82.39 RPM
SRP007412_liver	0.14 RPM	81.27 RPM
SRP007412_testis	0.14 RPM	43.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1707 was not detected

EST

No EST(s) were mapped for retro_mmus_1707 retrocopy.

TSS

No TSS is located nearby retro_mmus_1707 retrocopy 5' end.

Lab

retro_mmus_1707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707 ,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,