RetrogeneDB ID: retro_mmus_2835

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:70429669..70429981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc5a6
• Ensembl ID: ENSMUSG00000006641
• Aliases: Slc5a6, E430023I20
• Description: solute carrier family 5 (sodium-dependent vitamin transporter), member 6 [Source:MGI Symbol;Acc:MGI:2660847]

Sequence

>retro_mmus_2835
AGTTCCCACTCGGAGAGAGCTGCTGTGCTCTCCTGCTATGCAGTGTTCCCTTGCCAGCAAGTGGCCCTCTGCATGAGCTG
CCTCATTGGTCTGTTCATGTTTGCCTATTATAACATGTATAGCATGAGCACCGAGCTGAAGCAAGCAGCCCCTGACCAGT
TAGTCCTCTATTTTGTGATGGACCTCCTGAAAGACATGCCAGGGCTGCCTGGGTTCTTCGTTGCCTGTCTCTTCAGTGGA
TCTCTCAGCACCATATCCTCTGCATTCAATTCACTGGCAACTGTCACAATGGAAGACCTGATCCAGCCCTGG

Alignment

ORF - retro_mmus_2835 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.42 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQHGLISGINSCYAVFPCQQVALCMSCLIGLVMFAYYNMYSMSPELKQAAPDQLVLYFVMDLLKDMPGLP
          S.H.......SCYAVFPCQQVALCMSCLIGL.MFAYYNMYSMS.ELKQAAPDQLVLYFVMDLLKDMPGLP
Retrocopy SSHSERAAVLSCYAVFPCQQVALCMSCLIGLFMFAYYNMYSMSTELKQAAPDQLVLYFVMDLLKDMPGLP

Parental  GLFVACLFSGSLSTISSAFNSLATVTMEDLIQPW
          G.FVACLFSGSLSTISSAFNSLATVTMEDLIQPW
Retrocopy GFFVACLFSGSLSTISSAFNSLATVTMEDLIQPW

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	23.18 RPM
SRP007412_cerebellum	0.00 RPM	28.01 RPM
SRP007412_heart	0.03 RPM	13.20 RPM
SRP007412_kidney	0.00 RPM	33.17 RPM
SRP007412_liver	0.00 RPM	20.13 RPM
SRP007412_testis	0.00 RPM	2.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2835 was not detected

EST

No EST(s) were mapped for retro_mmus_2835 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_124195	1029 libraries	26 libraries	12 libraries	4 libraries	1 library

The graphical summary, for retro_mmus_2835 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_2835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000006641	2 retrocopies	retro_mmus_2835 , retro_mmus_2836,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200,