RetrogeneDB ID: retro_mmus_204

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:141256567..141257158(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095238
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Gstm4
• Ensembl ID: ENSMUSG00000027890
• Aliases: Gstm4, 1110004G14Rik, GSTM7-7, Gstb-4, Gstb4
• Description: glutathione S-transferase, mu 4 [Source:MGI Symbol;Acc:MGI:95862]

Sequence

>retro_mmus_204
ATGCCTATGACACTGTGTTACTGGGATATTCATGGGCTGGCTCACGCTATTTGGCTGCTCCTGGAATATACAGACTCATG
CTATGAGGAGAAGAGATACACCATGAGAGACCCTCCCAAATATGACAGAAGCCAATGGCTGAGTGAATTCAAACTGGGCC
TGGAATTTTTCAATTTGCCTTACTTAATTGATGGGTCACACAAAATCACCCAGAGCAATGCCATCCTGCGCTATACTGCC
CGAAAGAACAACCTGTGTGGGGAGACAGAAGAGAAGAGTCGTGTGGAAATTCTGAAGAACCAGGTTATGGATGTCTCCAG
TCAACTGGGTAGAGTCTGTTACAGCCCAGACTTTGAGAAACTGAAGGCAGAATACTTGGTGCAGCTCTCCTCACAGTTCC
TGGGCAAGCGGACATGGTTTGTTAGTGAAAAGATTACTTTCGTAGATTTCCTTGCTTACGATATCCTGGACAGGCACCTT
ATATTCGAACCCACGTGCCTGGATGCCTTCCTAAACCTGAAGGACTTTGTGGCCTGCGTTGAGGAACTGAAGAAGATGTC
TGATTACATGAAGACCAGCTACTTCCTCTGA

Alignment

ORF - retro_mmus_204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.21 %
• Parental protein coverage: 60.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTGSSYEEKRYTMGDAPDYDRSQWLSEKFKLGLDFPNLPYLIDGSHKI
          MPMTL.YWDI.GLAHAI.LLLEYT.S.YEEKRYTM.D.P.YDRSQWLSE.FKLGL.F.NLPYLIDGSHKI
Retrocopy MPMTLCYWDIHGLAHAIWLLLEYTDSCYEEKRYTMRDPPKYDRSQWLSE-FKLGLEFFNLPYLIDGSHKI

Parental  TQSNAILRYIARKHNLCGETEEEKIRVDILENQAMDVSNQLARVCYSPDFEKLKVEYLEQL
          TQSNAILRY.ARK.NLCGET.EEK.RV.IL.NQ.MDVS.QL.RVCYSPDFEKLK.EYL.QL
Retrocopy TQSNAILRYTARKNNLCGET-EEKSRVEILKNQVMDVSSQLGRVCYSPDFEKLKAEYLVQL

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	5.12 RPM
SRP007412_cerebellum	0.00 RPM	3.00 RPM
SRP007412_heart	0.00 RPM	7.78 RPM
SRP007412_kidney	0.00 RPM	9.16 RPM
SRP007412_liver	0.00 RPM	44.70 RPM
SRP007412_testis	0.00 RPM	5.72 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_204 was not detected

EST

No EST(s) were mapped for retro_mmus_204 retrocopy.

TSS

No TSS is located nearby retro_mmus_204 retrocopy 5' end.

Lab

retro_mmus_204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Canis familiaris	ENSCAFG00000019812	2 retrocopies	retro_cfam_1766, retro_cfam_2062,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
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,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,