RetrogeneDB ID: retro_mmus_1859

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:20586076..20586757(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000047168
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gstk1
• Ensembl ID: ENSMUSG00000029864
• Aliases: Gstk1, 0610025I19Rik, AW260476, DsbA-L
• Description: glutathione S-transferase kappa 1 [Source:MGI Symbol;Acc:MGI:1923513]

Sequence

>retro_mmus_1859
ATGGGGCAGGTGCCGAGCATTCTGGAACTGTTGTACGAAGTGCTGTCCCTGTACTCCTGGCTGGGCTTTGAGGTCCTATG
CAGATACCAACGCCTCTGGAATACAAGCTGCAGTTGCGGCCCCGCTGTAATCATTGGGATCATGAAAGACAGTGGAAACC
AACCACCAGCTCTGGTTCCCCGAAAAGGCCAGTGCATACTCAAAGAGATTCCTCTCCTGAAGCAGCTCTTTCAGGTTCCC
ATCAGCATACCCAAGAATTTCTTTGGTGAGATTGTTAAGAAGGGAAGTGTAAATGTCACGTGTTTCCTCACCACTGTGAG
CATGGAGCAACCAGAGATGCTGGGGAAGGTGTCCAGAGAGCTATGGATGCATGTTTGGTCTCGAGATGAAGATATCACGG
AGTCCCAGAACATTCTGGCTGCAGCAAAGAAGGCTGGAACGTTCACAGTGGAAGCCCAACACTTTCTGGAGAAGATCTCC
ACAGAACAGGTGAAGAACAAACTCAGGGAGACCACTGAGGCAGCCTCCAAACATGGGGCTTTTGGGCTGCCCACCACGGT
TGCCCATGTGGATGGTAAAACCTACATGTCGCCATGTGGATCTGACCGTATAGAGTTGCTAGCTTACCTGCTGGGATACA
AATGGATGGGCCCTGTGCCCCCAACCCTGAATGCCAGACTT

Alignment

ORF - retro_mmus_1859 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGPAPRILELFYDVLSPYSWLGFEVLCRYQHLWNIKLQLRPTLIAGIMKDSGNQPPAMVPRKGQYIFKEI
          MG..P.ILEL.Y.VLS.YSWLGFEVLCRYQ.LWN......P..I.GIMKDSGNQPPA.VPRKGQ.I.KEI
Retrocopy MGQVPSILELLYEVLSLYSWLGFEVLCRYQRLWNTSCSCGPAVIIGIMKDSGNQPPALVPRKGQCILKEI

Parental  PLLKQFFQVPLNIPKDFFGETVKKGSINAMRFLTTVSMEQPEMLEKVSREIWMRVWSRDEDITEYQSILA
          PLLKQ.FQVP..IPK.FFGE.VKKGS.N...FLTTVSMEQPEML.KVSRE.WM.VWSRDEDITE.Q.ILA
Retrocopy PLLKQLFQVPISIPKNFFGEIVKKGSVNVTCFLTTVSMEQPEMLGKVSRELWMHVWSRDEDITESQNILA

Parental  AAVKAGMSTAQAQHFLEKISTQQVKNKLIENTDAACKYGAFGLPTTVAHVDGKTYML-FGSDRLELLAYL
          AA.KAG..T..AQHFLEKIST.QVKNKL.E.T.AA.K.GAFGLPTTVAHVDGKTYM...GSDR.ELLAYL
Retrocopy AAKKAGTFTVEAQHFLEKISTEQVKNKLRETTEAASKHGAFGLPTTVAHVDGKTYMSPCGSDRIELLAYL

Parental  LGEKWMGPVPPTANARL
          LG.KWMGPVPPT.NARL
Retrocopy LGYKWMGPVPPTLNARL

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	0.09 RPM	6.59 RPM
SRP007412_cerebellum	0.04 RPM	6.69 RPM
SRP007412_heart	0.06 RPM	37.92 RPM
SRP007412_kidney	0.06 RPM	49.13 RPM
SRP007412_liver	0.00 RPM	103.14 RPM
SRP007412_testis	0.05 RPM	2.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1859 was not detected

EST

No EST(s) were mapped for retro_mmus_1859 retrocopy.

TSS

No TSS is located nearby retro_mmus_1859 retrocopy 5' end.

Lab

retro_mmus_1859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1859 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
Felis catus	ENSFCAG00000007274	1 retrocopy	retro_fcat_807,
Mustela putorius furo	ENSMPUG00000000713	1 retrocopy	retro_mputfur_1401,
Mus musculus	ENSMUSG00000029864	1 retrocopy	retro_mmus_1859 ,
Rattus norvegicus	ENSRNOG00000016484	1 retrocopy	retro_rnor_1598,
Sus scrofa	ENSSSCG00000016466	1 retrocopy	retro_sscr_1071,