RetrogeneDB ID: retro_mmus_2709

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:147325954..147326334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mgst3
• Ensembl ID: ENSMUSG00000026688
• Aliases: None
• Description: microsomal glutathione S-transferase 3 [Source:MGI Symbol;Acc:MGI:1913697]

Sequence

>retro_mmus_2709
ATGGCTGTCCTTTCTAAGGAATATGGATTTGTGCTTCTCACTGGTGCTGCCAGCTTTGATATGGTGCTCCACCTAGCCAT
CAACGTGGGCAAAGCCTGCAAGAAGAACAAGGTAGAGTACCCTGTCACTTACAGCACAGATCCTGAAAGTGGGCATATGT
TCAGCTGCATTCAGCGCGTCCACCAGAACGTGTTGGAGGTACACCCTCCCTCCCTGTTTTTCCTAACGGTGGGAGGTGTT
TACTACCCCCGTATAGCTTCTGGCCTGGGCTTGGCCTTGATTTCTTGGACGAGTTCTTTACACATATGGAGACCCTAGCA
AGCGGTATCGAGGAGCCACGGGGCTCTCTTGCCCTCTTTACTCTGATGGGCACCGCCATG

Alignment

ORF - retro_mmus_2709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 84.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVLSKEYGFVLLTGAASFVMVLHLAINVGKARKKYKVEYPVMYSTDPENGHMFNCIQRAHQNTLEVYPP
          MAVLSKEYGFVLLTGAASF.MVLHLAINVGKA.KK.KVEYPV.YSTDPE.GHMF.CIQR.HQN.LEV.PP
Retrocopy MAVLSKEYGFVLLTGAASFDMVLHLAINVGKACKKNKVEYPVTYSTDPESGHMFSCIQRVHQNVLEVHPP

Parental  FLFFLTVGGVYHPRIASGLGLAWI-IGRVLYAYGYYTGDPSKRYRGAV-GSLALFALMGTTV
          .LFFLTVGGVY.PRIASGLGLA.I..GRVLY.YG....DPSKRYRGA..GSLALF.LMGT..
Retrocopy SLFFLTVGGVYYPRIASGLGLALI>LGRVLYTYG----DPSKRYRGAT>GSLALFTLMGTAM

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	39.09 RPM
SRP007412_cerebellum	0.00 RPM	30.18 RPM
SRP007412_heart	0.00 RPM	88.85 RPM
SRP007412_kidney	0.00 RPM	49.86 RPM
SRP007412_liver	0.00 RPM	5.41 RPM
SRP007412_testis	0.00 RPM	2.61 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2709 was not detected

EST

No EST(s) were mapped for retro_mmus_2709 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_112064	214 libraries	178 libraries	363 libraries	134 libraries	183 libraries

The graphical summary, for retro_mmus_2709 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_2709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709 ,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385, retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,