RetrogeneDB ID: retro_mmus_2478

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:88599177..88599810(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000078480
• 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_2478
ATGAGCGGAACCCTGGGAAAGGTGCTGGGCGTGTGGACCAATACTGTTTCTAAGCAAGGCTTTTCCCTCCTAAGATTCAG
AAGTTTGGGAGAGAATCCCATTTTTTCTGCAGGTGGTATTCTGTGGACCAGTCGGCACTACAAGACAAAGCCCACTCATG
GCATCGGAAGATACAGACACTTGGTGAAAGTGCAGGAGCCCAAAAAGAAGAAAGCAAAAGTAGAACTGAGAGCCATTAAT
GTGGGGACAGATTATGAATATGGGGTTTTAAACATCCACCTGACAGCATATGACATGAGTCTGGCAGAAAGTTATGCCCA
GTATGTCCACCGCCTCTGCAACCGGCTGTCCATCAAAGTCGAGGAAAGTTATGCAATGCCTACCAAAACCATAGAAGTGA
TGCAACTACCAGACCAAGGCAACAAAATGGTCCTAGACTCCGTCCTTAGCACCCATGAGCGAGTGGTGCAGATCAGCGGT
CTGAGTGCTACATTTGCAGAGATTTTCTTGGAAGTACTCCAAAGCAATCTTCCAGAAGGAGTCAGATTGTCCGTGAGGGA
GCACACCGAAGAAGACTTCAAGGGAAGGTTCAAAGCTCGGCCCGAACTGGAAGAGTTGTTGGCCAAGTTGAAC

Alignment

ORF - retro_mmus_2478 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGTLGKVLGVWTNTVSKQGFSLLRFRSLGENPIFSAGGILWTSRHYKTKPTRGIGRYRHLVKVQEPKKK
          MSGTLGKVLGVWTNTVSKQGFSLLRFRSLGENPIFSAGGILWTSRHYKTKPT.GIGRYRHLVKVQEPKKK
Retrocopy MSGTLGKVLGVWTNTVSKQGFSLLRFRSLGENPIFSAGGILWTSRHYKTKPTHGIGRYRHLVKVQEPKKK

Parental  KAKVELRAINVGTDYEYGVLNIHLTAYDMSLAESYAQYVHRLCNRLSIKVEESYAMPTKTMEVMRLPDQG
          KAKVELRAINVGTDYEYGVLNIHLTAYDMSLAESYAQYVHRLCNRLSIKVEESYAMPTKT.EVM.LPDQG
Retrocopy KAKVELRAINVGTDYEYGVLNIHLTAYDMSLAESYAQYVHRLCNRLSIKVEESYAMPTKTIEVMQLPDQG

Parental  NKMVLDSILTTHERVVQISGLSATFAEIFLEVLQSNLPEGVRLSVREHTEEDFKGRFKARPELEELLAKL
          NKMVLDS.L.THERVVQISGLSATFAEIFLEVLQSNLPEGVRLSVREHTEEDFKGRFKARPELEELLAKL
Retrocopy NKMVLDSVLSTHERVVQISGLSATFAEIFLEVLQSNLPEGVRLSVREHTEEDFKGRFKARPELEELLAKL

Parental  N
          N
Retrocopy N

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	0.49 RPM	26.68 RPM
SRP007412_cerebellum	1.04 RPM	25.05 RPM
SRP007412_heart	0.09 RPM	26.71 RPM
SRP007412_kidney	1.25 RPM	18.19 RPM
SRP007412_liver	0.19 RPM	12.26 RPM
SRP007412_testis	0.87 RPM	12.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2478 was not detected

EST

No EST(s) were mapped for retro_mmus_2478 retrocopy.

TSS

No TSS is located nearby retro_mmus_2478 retrocopy 5' end.

Lab

retro_mmus_2478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2478 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,