RetrogeneDB ID: retro_mmus_2692

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:116632910..116633564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gstm1
• Ensembl ID: ENSMUSG00000058135
• Aliases: Gstm1, Gstb-1, Gstb1
• Description: glutathione S-transferase, mu 1 [Source:MGI Symbol;Acc:MGI:95860]

Sequence

>retro_mmus_2692
ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCTGCATGCTCCTGGAATACACAGACTCAAG
CTATGATGAGAAGAGATGCACCATGGGTGATGCTCCCGATTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGG
GCCTGGACTTTCCCAATCTGCCTTACTTGATTGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGTGCTACCTT
GCCAGCAAGCACCACCTGGGTGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACAC
CCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGGCCATCCCTGAGA
AAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCT
TATGACATTCTTTACTAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCG
CTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCTGCTACATCGCAACACCTGTATTTTCAAAGATGGCCC
ACTGGAGTAACAAG

Alignment

ORF - retro_mmus_2692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKI
          MPMILGYWNVRGLTHPI.MLLEYTDSSYDEKR.TMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKI
Retrocopy MPMILGYWNVRGLTHPICMLLEYTDSSYDEKRCTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKI

Parental  TQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSE
          TQSNAIL.YLA.KHHL.GETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLK.IPEKMKLYSE
Retrocopy TQSNAILCYLASKHHLGGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKAIPEKMKLYSE

Parental  FLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFS
          FLGKRPWFAGDKVTYVDFLAYDIL..YRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSS.YIATP.FS
Retrocopy FLGKRPWFAGDKVTYVDFLAYDILY*YRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSCYIATPVFS

Parental  KMAHWSNK
          KMAHWSNK
Retrocopy KMAHWSNK

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	0.33 RPM	125.69 RPM
SRP007412_cerebellum	0.04 RPM	150.06 RPM
SRP007412_heart	0.59 RPM	146.59 RPM
SRP007412_kidney	0.90 RPM	304.99 RPM
SRP007412_liver	2.10 RPM	1009.62 RPM
SRP007412_testis	0.50 RPM	203.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2692 was not detected

EST

No EST(s) were mapped for retro_mmus_2692 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_108903	509 libraries	333 libraries	194 libraries	15 libraries	21 libraries

The graphical summary, for retro_mmus_2692 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_2692 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2692 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Mus musculus	ENSMUSG00000058135	1 retrocopy	retro_mmus_2692 ,