RetrogeneDB ID: retro_mmus_563

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:57601372..57601945(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl48
• Ensembl ID: ENSMUSG00000030706
• Aliases: None
• Description: mitochondrial ribosomal protein L48 [Source:MGI Symbol;Acc:MGI:1289321]

Sequence

>retro_mmus_563
GGCTTTTCCCTCCAAAGATCAGAAGTTTGGGAGAGAATCCCATTTTTTTTTTCTGCAGGTAGTATTCTGAGGACCAGTCG
TCAGTACAAGACAAAGCCCACTCATGGCATTGGAAGGTACAGACACTCGATGAAAGTGCTAGAGCCCAAAAGGAAGAAAG
CAAAAGTAGAAGTGAGAGCCATTAACTTGGGGACAGATTATGAATATGGGGTTTTAAATATCCACATGACAACTTATGAC
ATTAGTCTGGCAGAAAGTTATGCCCAGTGTGTCCACCGCTTCTGCAACTAGCTGTCCATCAAAATCGAGAAAAGTTATGG
GATGCCCATCAAAACCATAGAAGTGACGCATCTGCCAGACAACAAAATGGTCCTAGACTCAGTCCTTACCACACATGAGC
GGGTGGTTCAGATCAGCGATCTGAGTGCTACATTTGCAGAGATTTTCTTGGAAATACTCCAAAGCAATCTTCCAGAAGGA
GTCAGAATGTCAGTGAGGGAGCACACTGAAGAAGGCTTCAAGGGAAGGTTCAAAGCTTGGCCATAACTGGAAGAGTTGTT
GGCCAAGTTGAAC

Alignment

ORF - retro_mmus_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.2 %
• Parental protein coverage: 91. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GFSLLRFRSLGENPIFS-AGGILWTSRHYKTKPTRGIGRYRHLVKVQEPKKKKAKVELRAINVGTDYEYG
          GFSL.R.......P....AG.IL.TSR.YKTKPT.GIGRYRH..KV.EPK.KKAKVE.RAIN.GTDYEYG
Retrocopy GFSLQRSEVWERIPXXXXAGSILRTSRQYKTKPTHGIGRYRHSMKVLEPKRKKAKVEVRAINLGTDYEYG

Parental  VLNIHLTAYDMSLAESYAQYVHRLCNRLSIKVEESYAMPTKTMEVMRLPDQGNKMVLDSILTTHERVVQI
          VLNIH.T.YD.SLAESYAQ.VHR.CN.LSIK.E.SY.MP.KT.EV..LPD..NKMVLDS.LTTHERVVQI
Retrocopy VLNIHMTTYDISLAESYAQCVHRFCN*LSIKIEKSYGMPIKTIEVTHLPD--NKMVLDSVLTTHERVVQI

Parental  SGLSATFAEIFLEVLQSNLPEGVRLSVREHTEEDFKGRFKARPELEELLAKLN
          S.LSATFAEIFLE.LQSNLPEGVR.SVREHTEE.FKGRFKA.P.LEELLAKLN
Retrocopy SDLSATFAEIFLEILQSNLPEGVRMSVREHTEEGFKGRFKAWP*LEELLAKLN

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	26.68 RPM
SRP007412_cerebellum	0.00 RPM	25.05 RPM
SRP007412_heart	0.00 RPM	26.71 RPM
SRP007412_kidney	0.00 RPM	18.19 RPM
SRP007412_liver	0.00 RPM	12.26 RPM
SRP007412_testis	0.00 RPM	12.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_563 was not detected

EST

No EST(s) were mapped for retro_mmus_563 retrocopy.

TSS

No TSS is located nearby retro_mmus_563 retrocopy 5' end.

Lab

retro_mmus_563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005585	1 retrocopy	retro_cfam_1437,
Homo sapiens	ENSG00000175581	1 retrocopy	retro_hsap_3557,
Mustela putorius furo	ENSMPUG00000009716	1 retrocopy	retro_mputfur_38,
Mus musculus	ENSMUSG00000030706	2 retrocopies	retro_mmus_2478, retro_mmus_563 ,
Nomascus leucogenys	ENSNLEG00000017097	1 retrocopy	retro_nleu_1376,
Oryctolagus cuniculus	ENSOCUG00000009302	1 retrocopy	retro_ocun_39,
Otolemur garnettii	ENSOGAG00000004771	1 retrocopy	retro_ogar_234,
Pan troglodytes	ENSPTRG00000004049	1 retrocopy	retro_ptro_2417,
Tursiops truncatus	ENSTTRG00000005403	2 retrocopies	retro_ttru_1123, retro_ttru_297,
Vicugna pacos	ENSVPAG00000004657	1 retrocopy	retro_vpac_538,