RetrogeneDB ID: retro_mmus_3384

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:116040592..116041063(-)
• Located in intron of: ENSMUSG00000056880

Retrocopy information

• Ensembl ID: ENSMUSG00000080848
• Aliases: Gm9385, EG668829
• Status: KNOWN_PSEUDOGENE

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_3384
ATGAAGGTCGAGCTGTGCAGTTTCAGCGGGTACAAGATCTACCCGGGACACGGGCGGCGCTACGCCAGGACCGACGGGAA
GGTTTTCCAGTTTCTTAATGCAAAATGTGAGTCAGCATTCCTTTCCAAAAGGAATCCTCGGCAGATAAACTGGACTGTCC
TCTACAGAAGGAAACACAAGAAAGGGCAGTCGGAAGAAATTCAAAAGAAAAGAACCCGCCGTGCAGTCAAATTCCAACGA
GCCATCACTGGTGCATCTCTTGCTGATATAATGGCCAAGAGGAATCAGAAACCAGAGGTTAGGAAAGCCCAGTGAGAGCA
GGCTATCAGGGCTGCCAAGGAAGCAAAAAAGGCTAAGCAGGCATCAAAGAAGACAGCAATGGCTGCTGCCAAGGCCCCCA
CAAAGGCAGCACCTAAACAAAAGATTGTGAAGCCTGTGAAGGTCTCTGCCCCCAGAGTTGGTGGGAAACGC

Alignment

ORF - retro_mmus_3384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK
          MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK
Retrocopy MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKK

Parental  RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQREQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQ
          RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQ.EQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQ
Retrocopy RTRRAVKFQRAITGASLADIMAKRNQKPEVRKAQ*EQAIRAAKEAKKAKQASKKTAMAAAKAPTKAAPKQ

Parental  KIVKPVKVSAPRVGGKR
          KIVKPVKVSAPRVGGKR
Retrocopy KIVKPVKVSAPRVGGKR

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	0.16 RPM	83.94 RPM
SRP007412_cerebellum	0.04 RPM	81.85 RPM
SRP007412_heart	0.25 RPM	59.33 RPM
SRP007412_kidney	0.15 RPM	59.77 RPM
SRP007412_liver	0.05 RPM	60.76 RPM
SRP007412_testis	0.09 RPM	67.05 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3384 was not detected

EST

No EST(s) were mapped for retro_mmus_3384 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_147473	246 libraries	418 libraries	396 libraries	10 libraries	2 libraries

The graphical summary, for retro_mmus_3384 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3384 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,