RetrogeneDB ID: retro_mmus_1624

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:21964131..21964423(-)
• Located in intron of: ENSMUSG00000053347

Retrocopy information

• Ensembl ID: ENSMUSG00000086004
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl20
• Ensembl ID: ENSMUSG00000029066
• Aliases: Mrpl20, 2610008D01Rik, 4930425I20Rik
• Description: mitochondrial ribosomal protein L20 [Source:MGI Symbol;Acc:MGI:2137221]

Sequence

>retro_mmus_1624
TGTACGAAGTCCCACAGACTTAAGAAGCAGAACTTTGAGGACCCTCTGGATTAATCCAATTACAGCTGCCTCCCAGGAGC
ATGGCTTACAGTACCCCGAATTCACTGTCAACTTAATGAAGTGCCAGGTGGAGCTCAACCGGAAAGTACCTGTGGACCTG
GCCATCTACGAACCATAGACGCTTAAATCTTTGGCTGCTTTGGCTAAGAGGAGGCAGCAGGAAGGATTTGCTGCAGCTTT
GGGGGATGGAAAGGAGCCTGAAGGTATCTTTTCCAGAGTGGTACAGTACCAC

Alignment

ORF - retro_mmus_1624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CTKARRLKKRN-LRTLWINRITAASQEHGLKYPAFIVNLIKCQVELNRKVLVDLAIYEPKTFKSLAALAK
          CTK..RLKK.N.LRTLWIN.ITAASQEHGL.YP.F.VNL.KCQVELNRKV.VDLAIYEP.T.KSLAALAK
Retrocopy CTKSHRLKKQN>LRTLWINPITAASQEHGLQYPEFTVNLMKCQVELNRKVPVDLAIYEP*TLKSLAALAK

Parental  RRQQEGFAAALGDGKEPEGIFSRVVQYH
          RRQQEGFAAALGDGKEPEGIFSRVVQYH
Retrocopy RRQQEGFAAALGDGKEPEGIFSRVVQYH

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	0.02 RPM	23.39 RPM
SRP007412_cerebellum	0.13 RPM	15.20 RPM
SRP007412_heart	0.00 RPM	14.32 RPM
SRP007412_kidney	0.06 RPM	19.23 RPM
SRP007412_liver	0.05 RPM	16.28 RPM
SRP007412_testis	0.14 RPM	26.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1624 was not detected

EST

No EST(s) were mapped for retro_mmus_1624 retrocopy.

TSS

No TSS is located nearby retro_mmus_1624 retrocopy 5' end.

Lab

retro_mmus_1624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1624 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013932	2 retrocopies	retro_amel_143, retro_amel_545,
Canis familiaris	ENSCAFG00000019259	2 retrocopies	retro_cfam_2112, retro_cfam_826,
Dasypus novemcinctus	ENSDNOG00000010105	1 retrocopy	retro_dnov_1620,
Homo sapiens	ENSG00000242485	1 retrocopy	retro_hsap_2508,
Gorilla gorilla	ENSGGOG00000027251	1 retrocopy	retro_ggor_1565,
Myotis lucifugus	ENSMLUG00000011857	1 retrocopy	retro_mluc_1423,
Monodelphis domestica	ENSMODG00000006562	2 retrocopies	retro_mdom_1424, retro_mdom_719,
Mus musculus	ENSMUSG00000029066	1 retrocopy	retro_mmus_1624 ,
Otolemur garnettii	ENSOGAG00000005968	1 retrocopy	retro_ogar_2263,
Procavia capensis	ENSPCAG00000001425	1 retrocopy	retro_pcap_238,
Tupaia belangeri	ENSTBEG00000008735	2 retrocopies	retro_tbel_2193, retro_tbel_892,