RetrogeneDB ID: retro_mmus_3360

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:78936586..78936783(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdc42se1
• Ensembl ID: ENSMUSG00000046722
• Aliases: Cdc42se1, 1300002M12Rik, AW558204, Cdcse1, SCIP1, Spec1
• Description: CDC42 small effector 1 [Source:MGI Symbol;Acc:MGI:1889510]

Sequence

>retro_mmus_3360
ATGAGTGAGTTTTGGCACAAACTGGGCTGCTGCGTGGTCGAGAAGCCTCAGCCAAAGAAAAAGAGAAGATGGACTGACCG
AACCATGCTGGGGAGCCAATGAGCTTTGTCCACCTGACTCACATCGGCTAGGAGGAGATGGGGGCTGAAGATGGACTTGC
CATAACAGGTGCAAGAGCAGATGAGATCCAAGAGAAA

Alignment

ORF - retro_mmus_3360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.12 %
• Parental protein coverage: 82.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSEFWHKLGCCVVEKPQPKKKRRRIDRTMI-GEPMNFVHLTHIGSGEMGAGDGLAMTGAVQEQMRSK
          MSEFWHKLGCCVVEKPQPKKKRR..DRTM..GEPM.FVHLTHIG..EMGA.DGLA.TGA.......K
Retrocopy MSEFWHKLGCCVVEKPQPKKKRRWTDRTML<GEPMSFVHLTHIG*EEMGAEDGLAITGARADEIQEK

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	46.63 RPM
SRP007412_cerebellum	0.00 RPM	56.84 RPM
SRP007412_heart	0.00 RPM	22.66 RPM
SRP007412_kidney	0.00 RPM	81.25 RPM
SRP007412_liver	0.00 RPM	21.90 RPM
SRP007412_testis	0.00 RPM	78.90 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3360 was not detected

EST

No EST(s) were mapped for retro_mmus_3360 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_153543	577 libraries	449 libraries	46 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_3360 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_3360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015363	1 retrocopy	retro_btau_894,
Dipodomys ordii	ENSDORG00000007370	1 retrocopy	retro_dord_322,
Echinops telfairi	ENSETEG00000019984	1 retrocopy	retro_etel_1111,
Mus musculus	ENSMUSG00000046722	1 retrocopy	retro_mmus_3360 ,
Tursiops truncatus	ENSTTRG00000007000	1 retrocopy	retro_ttru_549,