RetrogeneDB ID: retro_mmus_1784

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:63898576..63899028(-)
• Located in intron of: ENSMUSG00000040560

Retrocopy information

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

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_1784
TCCACTGCTGCTTATCAGGACAGGGGCTGAGAGCTGGGAACGGGGCCTCACGGCTCTGCTGGCCCTGTGCAGCTGCCTTT
CTCGCCTTAGGTCTTCAGTGGAGGTCCTGTATCGGCAGCTGCTGGAGAAGATTTTTCCATCATTGCTTCAAACACTCGGC
TGAGTGAAGGATTTTCAATTCATACCCGAGATAGCCCCAAATGTTACAAAGGAACAGAGAGAACAGTAATTGGCTGCAGT
GGTTTTCATGGAGATTGTCTCACTTTGGCAAAGATTATTGAAGCAAGATTAAAGATGTACAAGCATTGCAATAACAAGGC
CATGACAACCGGGGCGATCGCCACAATGCTGTCTACCATCCTGTACCAGCACGCTTCTTCCCTTACTATGTTTACAACAT
CACTGGAGGATTCCATGAAGGAAAGGGAGCTGTGTACAGCTCTGACCCAGTG

Alignment

ORF - retro_mmus_1784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 63.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STAAYRDVERELGMGPHGSAGPVQLRFSPYAFNGGTVLAIAGEDFSIVASDTRLSEGFSIHTRDSPKCYK
          STAAY.D...ELG.GPHGSAGPVQL.FSP..F.GG.V.A.AGEDFSI.AS.TRLSEGFSIHTRDSPKCYK
Retrocopy STAAYQDRG*ELGTGPHGSAGPVQLPFSP*VFSGGPVSAAAGEDFSIIASNTRLSEGFSIHTRDSPKCYK

Parental  LTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSR-RFFPYYVYNIIGGLD
          .T..TVIGCSGFHGDCLTL.KIIEARLKMYKH.NNKAMTTGAIA.MLSTILY...RFFPYYVYNI.GG..
Retrocopy GTERTVIGCSGFHGDCLTLAKIIEARLKMYKHCNNKAMTTGAIATMLSTILYQH<RFFPYYVYNITGGF-

Parental  EEGKGAVYSFDPV
          .EGKGAVYS.DPV
Retrocopy HEGKGAVYSSDPV

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	84.95 RPM
SRP007412_cerebellum	0.00 RPM	64.87 RPM
SRP007412_heart	0.00 RPM	54.54 RPM
SRP007412_kidney	0.02 RPM	64.12 RPM
SRP007412_liver	0.00 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_1784 was not detected

EST

No EST(s) were mapped for retro_mmus_1784 retrocopy.

TSS

No TSS is located nearby retro_mmus_1784 retrocopy 5' end.

Lab

retro_mmus_1784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1784 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,