RetrogeneDB ID: retro_mmus_701

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:30528404..30528973(+)
• Located in intron of: ENSMUSG00000060923

Retrocopy information

• Ensembl ID: ENSMUSG00000081712
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psmd14
• Ensembl ID: ENSMUSG00000026914
• Aliases: Psmd14, 2610312C03Rik, 3200001M20Rik, AA986732, Pad1, Poh1, rpm11
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:MGI Symbol;Acc:MGI:1913284]

Sequence

>retro_mmus_701
GTGATTGATGTGTTTGCTATGCCACAGTCATGAACTGGTGTCAGTGTAGAAGCAGTTGATCCAGTGTTCCAAGACAAAAT
GTTGTGTATGCTGAGACAAACAGGAAGGCCAGAGATGGTTGTTGGTTAGTATCAGAGTTTCCCTGGCTTTGGCTGTTAGC
TTTCTGGTGTGCATGTCAACACTCAGCAGAGCTCTGAAGCCTTGTCAGAGAGAGCTGTGGCAGTGGTTGTGGATCCCATT
CAGAGTGTAAAAGGAAAGGTTGTTATTGATGCCTGTTACTGATCAATGCTAATATGATGGTCTTAGGACATGAACCAAGA
CAAATTACTTCAAATCTGGGCCACTTAAACAAGCCATCCATCCAGGCATTAGTTCACAGATTAAACAGACATTATTACTC
CATCAATATTAATTACCGGAAAAATGAACTGGGACAGAAGATGCTGTTAAATTTGCATAAGAAGAGTTGGATGGAAGGAT
TGGCACTTCAGGACTACAGTGAACACTGTAAAGACAATGAATCAGTGGTAAAAGAGATGTTGAAATTAGCCTAGAATTAT
AATAAGGCT

Alignment

ORF - retro_mmus_701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSE
          VIDVFAMPQS.TGVSVEAVDPVFQ.KML.ML.QTGRPEMVVG.Y.S.PGFGC.LSGV..NTQQS.EALSE
Retrocopy VIDVFAMPQS*TGVSVEAVDPVFQDKMLCMLRQTGRPEMVVG*YQSFPGFGC*LSGVHVNTQQSSEALSE

Parental  RAVAVVVDPIQSVKGKVVIDA-FRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINY
          RAVAVVVDPIQSVKGKVVIDA...LINANMMVLGHEPRQ.TSNLGHLNKPSIQAL.H.LNRHYYSI.INY
Retrocopy RAVAVVVDPIQSVKGKVVIDA<LLLINANMMVLGHEPRQITSNLGHLNKPSIQALVHRLNRHYYSININY

Parental  RKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKA
          RKNEL.QKMLLNLHKKSWMEGL.LQDYSEHCK.NESVVKEML.LA.NYNKA
Retrocopy RKNELGQKMLLNLHKKSWMEGLALQDYSEHCKDNESVVKEMLKLA*NYNKA

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	0.14 RPM	56.91 RPM
SRP007412_cerebellum	0.26 RPM	49.41 RPM
SRP007412_heart	0.50 RPM	29.67 RPM
SRP007412_kidney	0.46 RPM	43.64 RPM
SRP007412_liver	0.00 RPM	38.40 RPM
SRP007412_testis	0.14 RPM	24.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_701 was not detected

EST

No EST(s) were mapped for retro_mmus_701 retrocopy.

TSS

No TSS is located nearby retro_mmus_701 retrocopy 5' end.

Lab

retro_mmus_701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701 ,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,