RetrogeneDB ID: retro_mmus_1952

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:87526143..87526401(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082908
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srp9
• Ensembl ID: ENSMUSG00000026511
• Aliases: Srp9, 9kDa
• Description: signal recognition particle 9 [Source:MGI Symbol;Acc:MGI:1350930]

Sequence

>retro_mmus_1952
ATGCCTCAGTTCCAGACCTGGGAGGAGTTCAGCCGGGCGGCCGAGAAGCTCTACCTGGCGGACCCCATGAAGGTACGGGT
GGTTCTCAAATACAGGCATGTTGATGGGAATTTGTGTATCAAAGTAACGGATGATCTAGTTTGTTTGGTGTACAGAACAG
ACCAAGCGCAAGACGTAAAGAAGATTGAGAAATTCCACAGTCAGTTAATGCGACTTATGGTGGCCAAGGAATCCCGCAAT
GTCACTATGGAAACAGAA

Alignment

ORF - retro_mmus_1952 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM
          MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM
Retrocopy MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM

Parental  RLMVAKESRNVTMETE
          RLMVAKESRNVTMETE
Retrocopy RLMVAKESRNVTMETE

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	0.42 RPM	29.81 RPM
SRP007412_cerebellum	2.30 RPM	24.62 RPM
SRP007412_heart	0.09 RPM	19.55 RPM
SRP007412_kidney	2.08 RPM	19.62 RPM
SRP007412_liver	2.21 RPM	26.82 RPM
SRP007412_testis	5.99 RPM	29.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1952 was not detected

EST

No EST(s) were mapped for retro_mmus_1952 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_89694	530 libraries	397 libraries	67 libraries	30 libraries	48 libraries

The graphical summary, for retro_mmus_1952 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_1952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Mus musculus	ENSMUSG00000026511	1 retrocopy	retro_mmus_1952 ,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,