RetrogeneDB ID: retro_mmus_500

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:148938064..148938376(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rpl24
• Ensembl ID: ENSMUSG00000022601
• Aliases: Zbtb11, 9230110G02Rik, ZNF-U69274
• Description: ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1915443]

Sequence

>retro_mmus_500
ATGAATGTCGAGATGTGCAGTTTCAGCGGTACAAGATCTACCCGGAACAGGGCGGCGCTCCGCCAGGACTGAAGGGAAGG
TTCTCCAGTCACTTAGTGCAAAATGTGAGTCCACATTTGTTTCCAAAAGGAATCTTTGACAGATAAACTGGACTGTCCTT
TACAGAAGAAAACACAAGGACAGTGGGAAGAAATTCAAAAGAAAAGAATCCTCCGTGCAGTCAAATTCCAACGAGCCATC
ACTGGTGCTTCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCGGAAGTTAGGAAAGCCCAGGGAGAG

Alignment

ORF - retro_mmus_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.23 %
• Parental protein coverage: 79.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSG-YKIYP-GHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQ
          M.VE.CSFSG.YKIYP.G.GRR.ART.GKV.Q.L.AKCES.F.SKRN..QINWTVLYRRKHK........
Retrocopy MNVEMCSFSG<YKIYP<GTGRRSARTEGKVLQSLSAKCESTFVSKRNL*QINWTVLYRRKHK-DSGKKFK

Parental  KK-RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQRE
          .K.R..RAVKFQRAITGASLADIMAKRNQKPEVRKAQ.E
Retrocopy RK<RILRAVKFQRAITGASLADIMAKRNQKPEVRKAQGE

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	83.94 RPM
SRP007412_cerebellum	0.00 RPM	81.85 RPM
SRP007412_heart	0.00 RPM	59.33 RPM
SRP007412_kidney	0.00 RPM	59.77 RPM
SRP007412_liver	0.00 RPM	60.76 RPM
SRP007412_testis	0.00 RPM	67.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_500 was not detected

EST

No EST(s) were mapped for retro_mmus_500 retrocopy.

TSS

No TSS is located nearby retro_mmus_500 retrocopy 5' end.

Lab

retro_mmus_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022601	13 retrocopies	retro_mmus_1398, retro_mmus_1418, retro_mmus_1555, retro_mmus_2145, retro_mmus_2429, retro_mmus_2434, retro_mmus_2870, retro_mmus_2981, retro_mmus_3208, retro_mmus_3384, retro_mmus_500 , retro_mmus_793, retro_mmus_87,