RetrogeneDB ID: retro_mmus_3534

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:146654828..146655466(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082594
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl15
• Ensembl ID: ENSMUSG00000033845
• Aliases: Mrpl15, HSPC145, MRP-L7, Rpml7
• Description: mitochondrial ribosomal protein L15 [Source:MGI Symbol;Acc:MGI:1351639]

Sequence

>retro_mmus_3534
CCAAGGGATCAGACACGAGGTAAGAAATGTGGCAAAGGCCATAAAGTATAAAGGCAGAGAGAAACTTGGCCGAAATTGTG
CTTTGAGGGAGGGCAGACTACATTTTACATCCAAATCCCAAGTATGGATTTAATGAAGGACAATTTCAGGCACCAGTATC
ACCCTGTGATTCTCAGGAGACTACAGTAGATCATAATTTTAAGTCAAGTTAATCCAACTGTACCTATTGACTTAATCCAT
TTTGTGAGTGGGAAAGGTGTGACCATCCAACCACTTAAAGGGGATTATGGAGTCCAGCTTTTTCAAGATGGTGCTGATCC
TTTTCAAGCACAAGTTAATTTGAGGTGTAGTTAGCTTCAGAATTAGCCATTGCTGCGAATGGGGAAAACAAATGGTGGTG
GTGTTACTACTGCCTTCTATGACCCAAGGCGTCTAGAAATTCTGTGCAAGCTTGTCCCATTCCTTCTGTGAGGACAACCC
ATTCCAAAAAGAATGCTCCCTCCTGAGGTGTTCCTGCCATATTTTACTGATGCAAAAAACAGAGGGTACCTGGCTACCCT
GCCAAGTTTCCTGAAGTAAGGTTTGATCACGCCACGAAGTATGACTACTTTGTTCTTGAGATCACAAAAGATGAACTA

Alignment

ORF - retro_mmus_3534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 72.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRDRRRGRKCGRGHKGERQRGTRPRLGFEGGQTPFYIRIPKYGFNEGHSFRHQYQPLSLRRLQYLIDLGR
          PRD..RG.KCG.GHK..RQR.T.P.L.FEGGQT.FYI.IP.........FRHQY.P..LRRLQ..I.L..
Retrocopy PRDQTRGKKCGKGHKV*RQRETWPKLCFEGGQTTFYIQIPSMDLMKDN-FRHQYHPVILRRLQ*IIILSQ

Parental  VDPTQPIDLTQLVNGRGVTIQPLKRDYGVQLVEEGADTFQAKINIEVQLASELAIAAIEK-NGGVVTTAF
          V.PT.PIDL...V.G.GVTIQPLK.DYGVQL...GAD.FQA..N...............K.NGG.VTTAF
Retrocopy VNPTVPIDLIHFVSGKGVTIQPLKGDYGVQLFQDGADPFQAQVNLRCS*LQN*PLLRMGKTNGGGVTTAF

Parental  YDPRSLEILCKPIPFFLRGQPIPKRMLPPESLVPYYTDAKNRGYLAD-PAKFPEARLELAMKFGYVLPDI
          YDPR.LEILCK..PF.L.GQPIPKRMLPPE...PY.TDAKNRGYLA..PAKFPE.R...A.K..Y....I
Retrocopy YDPRRLEILCKLVPFLL*GQPIPKRMLPPEVFLPYFTDAKNRGYLAT<PAKFPEVRFDHATKYDYFVLEI

Parental  TKDEL
          TKDEL
Retrocopy TKDEL

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	18.29 RPM
SRP007412_cerebellum	0.00 RPM	15.63 RPM
SRP007412_heart	0.00 RPM	32.38 RPM
SRP007412_kidney	0.02 RPM	24.60 RPM
SRP007412_liver	0.00 RPM	42.66 RPM
SRP007412_testis	0.00 RPM	33.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3534 was not detected

EST

No EST(s) were mapped for retro_mmus_3534 retrocopy.

TSS

No TSS is located nearby retro_mmus_3534 retrocopy 5' end.

Lab

retro_mmus_3534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3534 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2785

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534 ,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,