RetrogeneDB ID: retro_mmus_491

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:138984003..138984437(-)
• Located in intron of: ENSMUSG00000056268

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gstm5
• Ensembl ID: ENSMUSG00000004032
• Aliases: None
• Description: glutathione S-transferase, mu 5 [Source:MGI Symbol;Acc:MGI:1309466]

Sequence

>retro_mmus_491
ATCTGCATGCTCCTGGAGTGCACTGATGACAGCTATGAGCAGAAATAGGCATGTGTGGGGATGCTCCTGACTACCTTCAG
AGTCAATGGCTGGACAGGAAATTCAAGCTTGGTCCGGATTTCCCTAACCATTCAACTTCACAGATGAGATAAGGATCACC
TGGAGTAATGCAGTCTTGAGCTACCTCACTGGTAAGCACAACACGTGTGGTGACACTAAAGAAGAAAAGACAGGAGTGGG
CATCAGGAGAAAGCGAATCATGGACTTCCATTCACAACTTGTATGGCTCTGCTACAGCAGGGGCCTGAAAGTCTGACGCC
ACAGTGCTAGGAATAGCTACCTACGCAACTTAAACACACGTTGTCGTTACTCCTGGGGAAATTCCACAGTTTACAAGGGG
AAAGCTCACCTTTGTGGATTTTCTCACTTATGAA

Alignment

ORF - retro_mmus_491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.95 %
• Parental protein coverage: 65.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IRMLLEFTDTSYEE-KRYICGEAPDYDRSQWLDVKFKLDLD-FPNLPYLMDGKNKITQSNAILRYIARKH
          I.MLLE.TD.SYE......CG.APDY..SQWLD.KFKL..D.FP..P........IT.SNA.L.Y...KH
Retrocopy ICMLLECTDDSYEQ<EIGMCGDAPDYLQSQWLDRKFKLGPD<FP*-PFNFTDEIRITWSNAVLSYLTGKH

Parental  NMCGDTEEEKIRVDIMENQIMDFRMQLVRLCYN-SNHENLKPQYLEQLPAQLKQ-FSLFLGKFTWFAGE-
          N.CGDT.EEK..V.I....IMDF..QLV.LCY.....E.L.PQ..E.LP.QLK...SL.LGKF....GE.
Retrocopy NTCGDTKEEKTGVGIRRKRIMDFHSQLVWLCYS<QGPESLTPQC*E*LPTQLKHTLSLLLGKFHSLQGE<

Parental  KLTFVDFLTYD
          KLTFVDFLTY.
Retrocopy KLTFVDFLTYE

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	85.39 RPM
SRP007412_cerebellum	0.00 RPM	46.03 RPM
SRP007412_heart	0.00 RPM	24.84 RPM
SRP007412_kidney	0.02 RPM	66.55 RPM
SRP007412_liver	0.03 RPM	9.67 RPM
SRP007412_testis	0.09 RPM	970.81 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_491 was not detected

EST

No EST(s) were mapped for retro_mmus_491 retrocopy.

TSS

No TSS is located nearby retro_mmus_491 retrocopy 5' end.

Lab

retro_mmus_491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_491 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_963

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
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,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,