RetrogeneDB ID: retro_mmus_3478

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:78785756..78786781(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082912
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Setd8
• Ensembl ID: ENSMUSG00000049327
• Aliases: Setd8, 2410195B05Rik, AA617402, AW536475, PR-SET7
• Description: SET domain containing (lysine methyltransferase) 8 [Source:MGI Symbol;Acc:MGI:1915206]

Sequence

>retro_mmus_3478
ATGGGCAAAGCAGGTGCTGTGGGGCACTGCAGGCCCTTTTCAGGAGCGCCATGGCGGCGCTGATGGCGGAGGTGGTGGCA
GTAGCAGAGGTGGCGGCAGAGTTGGTGGCCGGGTCGAGGTGAGGGCGAGGGTGCTGGCCGCGCAGTCATGGGCCTAGCCG
GTCTGCAGGAGAACATATTTACTGGGCAGTCAAAGATCTATGCCTACAGGAGGCCGAACAAGTGCTCTGCAATGTGCTCT
CCACTTCAGGAAGAGAACTCGGTTGCCCATCAAGAGGTCAAATGCCTGGGGAAACCATTAGCTGGAATCTACAGGAAGCG
AGAAGAAAAGGAACGCCGGGAACGTTATCTGAAGCACTGTGAAGTCAGATGAACAGAAGAGCAAAGACAACAGGAGTGGT
CCCCTGCCGCCTTTTCCAAACCAAAAATCTGAAGCAGCAGAACCTCCAAATTCTCCCCCCCCCATCATGTGATTCTACCA
ATGTAGCAGTCGCTGCTAAGCAAGCCCTGAAAGAGCCCCTCAAGGGCAAGCAGGCCCCTCGGAAAAAGTCTCAAGGGAAA
ACCCAGCAGAATAGAAAACTCACCGATTTCTACCCTGTGTGGTGGAGCTCCTGGAAGAGCAAAGCTGAGCTGCAGTCTGA
AGAAAGGGAGAAAATAGACAGCTGATTGAGAGGGGAAGGAAGAAGGCATGAAGATCGATCTAATTGATGTCAAAGGCAGG
GGTGTGATCACTACCAAGGAGTTCTCCCGGGGAGACTTTTGGTAGAATACCATGGGGATCTCATTGAAATCACTGATGCC
AAGAAGCGGGAGGCTCTGTATGCACAGGACCCCTCCACGGGCTGCTACATGTACTATTTTCAGTATCTGAGCAAAACCTA
CTGCGTGGATGCCACTCAAGAAACGAACCACCTGGGGAGACTCATCAGTCACAGTAAGTGTGGGAACTGCCAGACCAAAC
TGCACGACATTGATGGCGTGCCTAGCCTCATCGTCATCACCACCTGAGACATCGAGACATCGCAG

Alignment

ORF - retro_mmus_3478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.8 %
• Parental protein coverage: 93.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGEAGAVGRRRPFPGAPRRRWWRRQQQQQRRRQRWWPGRGEGEGAGRAAMGLAGLQENVFAGQSKIYAYM
          MG.AGAVG..RPF.GAP.RR.WRR..Q.QR.RQ.WWPGRGEGEGAGRA.MGLAGLQEN.F.GQSKIYAY.
Retrocopy MGKAGAVGHCRPFSGAPWRR*WRRWWQ*QRWRQSWWPGRGEGEGAGRAVMGLAGLQENIFTGQSKIYAYR

Parental  SPNKCSAMRSPLQEENSVAHHEVKCPGKPLAGIYRKREEKR-NTGNVIRSAVKSDEQKSKDT-RRGPLAP
          .PNKCSAM.SPLQEENSVAH.EVKC.GKPLAGIYRKREEK....G..............K.T.R.GPL.P
Retrocopy RPNKCSAMCSPLQEENSVAHQEVKCLGKPLAGIYRKREEKE<TPGTLSEAL*SQMNRRAKTT<RSGPLPP

Parental  FPNQKSEAAEPPKT-PPPSCDSTNVAV-AKQALKKSLKGKQAPRKKSQGKTQQNRKLTDFYPVRRSSRKS
          FPNQKSEAAEPP......SCDSTNVAV.AKQALK..LKGKQAPRKKSQGKTQQNRKLTDFYPV..SS.KS
Retrocopy FPNQKSEAAEPPNS>XXXSCDSTNVAVAAKQALKEPLKGKQAPRKKSQGKTQQNRKLTDFYPVWWSSWKS

Parental  KAELQSEERKKID-ELIE-SGKEEGMKIDLIDGKGRGVIATKQFSRGDF-VVEYHGDLIEITDAKKREAL
          KAELQSEER.KID..LIE..GKEEGMKIDLID.KGRGVI.TK.FSRGDF..VEYHGDLIEITDAKKREAL
Retrocopy KAELQSEEREKID<QLIE<EGKEEGMKIDLIDVKGRGVITTKEFSRGDF<LVEYHGDLIEITDAKKREAL

Parental  YAQDPSTGCYMYYFQYLSKTYCVDATQETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGE
          YAQDPSTGCYMYYFQYLSKTYCVDATQETN.LGRLI.HSKCGNCQTKLHDIDGVP.LI.I...DI....
Retrocopy YAQDPSTGCYMYYFQYLSKTYCVDATQETNHLGRLISHSKCGNCQTKLHDIDGVPSLIVITT*DIETSQ

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	32.47 RPM
SRP007412_cerebellum	0.00 RPM	33.48 RPM
SRP007412_heart	0.00 RPM	156.02 RPM
SRP007412_kidney	0.08 RPM	93.32 RPM
SRP007412_liver	0.00 RPM	30.26 RPM
SRP007412_testis	0.00 RPM	31.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3478 was not detected

EST

No EST(s) were mapped for retro_mmus_3478 retrocopy.

TSS

No TSS is located nearby retro_mmus_3478 retrocopy 5' end.

Lab

retro_mmus_3478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478 ,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,