RetrogeneDB ID: retro_mmus_2685

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:109016459..109016915(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093545
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Smndc1
• Ensembl ID: ENSMUSG00000025024
• Aliases: Smndc1, 2410004J23Rik, 4933440I19Rik
• Description: survival motor neuron domain containing 1 [Source:MGI Symbol;Acc:MGI:1923729]

Sequence

>retro_mmus_2685
ATGTCAGAGGATCTAGCAAAACAGTTGGCTAGCTACAAAGCTCAACTCCAGCAAGTAGAAGCTGCTCTTTCTGGAAATGG
AGAAAATGAAGATCTATTGAAACTGAAAAAGGCTTTGAAAGAAGTAATAGAACTGACCAAAGACCTTCTGTCAACTCAGC
CTTCAGAGACGCTTGCAAGTTCAGACAGTTTTGCTTCTACTCAGCCCACTCATTCATGGAAAGTAGGGGACAAGTGCATG
GCCATGTGGAATGAAGACGGACAGTGTTACGAAGTGGAGATTGAAGAGATAGATGAAGAAAATGGCACCCCTGCAATCAC
CTTTGCTGTTTACAGCAATGCCGAAGTGACGCCATTGCTGAACCTCAAGCCTATAGAAGAAGGAAGGAAGGCGAAAGAGG
ACAGCGGCAACAAACCCATGTCAAAAAAAGAAATGATCGCCCAGCAGAGTGAATAT

Alignment

ORF - retro_mmus_2685 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKDLQEVIELTKDLLSTQPSETLASSDSFASTQPT
          MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKK.L.EVIELTKDLLSTQPSETLASSDSFASTQPT
Retrocopy MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKALKEVIELTKDLLSTQPSETLASSDSFASTQPT

Parental  HSWKVGDKCMAVWSEDGQCYEAEIEEIDEENGTAAITFAVYGNAEVTPLLNLKPVEEGRKAKEDSGNKPM
          HSWKVGDKCMA.W.EDGQCYE.EIEEIDEENGT.AITFAVY.NAEVTPLLNLKP.EEGRKAKEDSGNKPM
Retrocopy HSWKVGDKCMAMWNEDGQCYEVEIEEIDEENGTPAITFAVYSNAEVTPLLNLKPIEEGRKAKEDSGNKPM

Parental  SKKEMIAQQREY
          SKKEMIAQQ.EY
Retrocopy SKKEMIAQQSEY

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	23.43 RPM
SRP007412_cerebellum	0.00 RPM	23.19 RPM
SRP007412_heart	0.00 RPM	16.62 RPM
SRP007412_kidney	0.00 RPM	25.33 RPM
SRP007412_liver	0.00 RPM	13.57 RPM
SRP007412_testis	0.00 RPM	37.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2685 was not detected

EST

No EST(s) were mapped for retro_mmus_2685 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_108007	338 libraries	475 libraries	253 libraries	4 libraries	2 libraries

The graphical summary, for retro_mmus_2685 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_2685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2685 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000007775	2 retrocopies	retro_mmul_1972, retro_mmul_2419,
Mus musculus	ENSMUSG00000025024	1 retrocopy	retro_mmus_2685 ,
Tarsius syrichta	ENSTSYG00000006636	1 retrocopy	retro_tsyr_965,