RetrogeneDB ID: retro_mmus_3664

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:94774975..94775378(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081418
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psmb1
• Ensembl ID: ENSMUSG00000014769
• Aliases: Psmb1, AA409053, C81484, Lmpc5
• Description: proteasome (prosome, macropain) subunit, beta type 1 [Source:MGI Symbol;Acc:MGI:104884]

Sequence

>retro_mmus_3664
AACAAGGCCATGAGAACGGGGGCAGTTGCCGCAATGCTGTCTACCATCCCGTGCTCACGGCGCTTCTTCCCTTACTATGT
TTACAACATCATTGGAGGACTTGATGAAGAAGGAAAGGGAGCTGTATACAGCTTTGACCCAGTGGGCTCTTACCAGAGAG
ACTCTGTCAAGGCAGGAGCTTCAGCAAGTGCCACGCTACAGCCTCTGCTGCACAACCAGACTGGTTTCAGACGTATGCAA
AGTGTGGAGCATGTCCCCCAGGATCCTGGACAGAGCTATGAGGCTGGTGAAAGATGTCTTCATTTCTGCAGCCGAGAGGG
ATGTGTATACTGGAGATGCCCTCAGGATCTGCATCGTGACCAAAGAGGGCATCAGGGAGGAAACTGTTCCCCTGCGGAAA
GAC

Alignment

ORF - retro_mmus_3664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 55.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLL
          NKAM.TGA.AAMLSTI..SRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDS.KAG.SASA.LQPLL
Retrocopy NKAMRTGAVAAMLSTIPCSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSVKAGASASATLQPLL

Parental  DNQVGFKNMQNVEHV-PLTLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVPLRKD
          .NQ.GF..MQ.VEHV.P..LDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVPLRKD
Retrocopy HNQTGFRRMQSVEHV>PRILDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVPLRKD

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	0.47 RPM	84.95 RPM
SRP007412_cerebellum	0.09 RPM	64.87 RPM
SRP007412_heart	0.09 RPM	54.54 RPM
SRP007412_kidney	0.12 RPM	64.12 RPM
SRP007412_liver	0.05 RPM	84.06 RPM
SRP007412_testis	0.05 RPM	32.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3664 was not detected

EST

No EST(s) were mapped for retro_mmus_3664 retrocopy.

TSS

No TSS is located nearby retro_mmus_3664 retrocopy 5' end.

Lab

retro_mmus_3664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3664 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664 ,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,