RetrogeneDB ID: retro_mmus_1459

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:38476584..38477526(+)
• Located in intron of: ENSMUSG00000075122

Retrocopy information

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

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_1459
GGGGCCTCCCGCAGCGACGGGGAGAACGTGTTTGCTGGGCAGCCAAAGATCTATGCCTACATGAGTCCTAACAAGTGCTC
TGGAATGCGCTCTCCACTTCAGGAAGAGAACTCGGTTGCCCATCACGAGGTCAAATGCCCGGGGAAACCATTAGCTGGAA
TCTACAGGAAGCGAGAAAAGGAACGCCAGGAACGTTATCCGAAGCGCTGTGAAGTCAGATGAACAGAAGAGCAAAGACAC
CAGGAGAGGTCCCCTGGCGCCTTTTTCAAACCAAAAATCCGAAGCAGCAGAACCTCCAAAAACTCCACCCCCATCATGTG
ACTCTACCAATGTAGCAGTCGCTAAGCAAACCCTGAAAAAGCCCCTCAAGGGCAAGCAGGCCCCTCAGAAAAAGTCTCAA
GGGAAAACCCAGCAGAATAGAAAATTCACCGATTTCTACCCTGTGCGGAGGAGCTCCTGGAAGAGCAAAGCTGAGCTGCA
GTCTGAAGAAAGGAAGAAAATAGACGAGCTGACTGAGAGCGGGAAGGAAGAAGGCATGAAGATCCATCTAATTGATGGCA
AAGGCAGGGGCGGGATCGCTACCAAGCTGTTTTCCCGGAGGATACTTTGTGGTAGAATACCATGGGAACCTCATTGAAAT
TACCGATGCCAAGAAGCGGGAGGCTCTTGTACGCACAGGACCCCTCCACAGGCTGCTACATGTACTATTTTCAGTATCTG
AGCAAAACCTACTGCGTGGATGCCACTCAAGAAACGAACTGCCTGGGGAGACTCATCAATCACAGTAAGTGTGGGAACTG
CCAGACCAAACTGCACGACATCGACGGCGTGCCTCACCTCATCCTCATCGCCACCCGAGACATCGCAGCTGGGGAGGAGC
TCCTGTACGACTATGGGGACCGAAGCAAGGCCTCCATCGAAGCCTACCCCTGGATGAAGCAC

Alignment

ORF - retro_mmus_1459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRPRSDGENVFAGQSKIYAYMSPNKCSAMRSPLQEENSVAHHEVKCPGKPLAGIYRKREEKRNTGNVIRS
          G..RSDGENVFAGQ.KIYAYMSPNKCS.MRSPLQEENSVAHHEVKCPGKPLAGIYRKRE..R......R.
Retrocopy GASRSDGENVFAGQPKIYAYMSPNKCSGMRSPLQEENSVAHHEVKCPGKPLAGIYRKREKERQERYPKRC

Parental  AVK-SDEQKSKDTRRG-PLAPFPNQKSEAAEPPKTPPPSCDSTNVAVAKQALKKSLKGKQAPRKKSQGKT
          .V....EQ.......G.P.........E....P...PPSCDSTNVAVAKQ.LKK.LKGKQAP.KKSQGKT
Retrocopy EVR*TEEQRHQERSPG>PFSNQKSEAAEPPKTP---PPSCDSTNVAVAKQTLKKPLKGKQAPQKKSQGKT

Parental  QQNRKLTDFYPVRRSSRKSKAELQSEERKKIDELIESGKEEGMKIDLIDGKGRGVIATKQFSR-GDFVVE
          QQNRK.TDFYPVRRSS.KSKAELQSEERKKIDEL.ESGKEEGMKI.LIDGKGRG.IATK.FSR.G.FVVE
Retrocopy QQNRKFTDFYPVRRSSWKSKAELQSEERKKIDELTESGKEEGMKIHLIDGKGRGGIATKLFSR>GYFVVE

Parental  YHGDLIEITDAKKREA-LYAQDPSTGCYMYYFQYLSKTYCVDATQETNRLGRLINHSKCGNCQTKLHDID
          YHG.LIEITDAKKREA.LYAQDPSTGCYMYYFQYLSKTYCVDATQETN.LGRLINHSKCGNCQTKLHDID
Retrocopy YHGNLIEITDAKKREA>LYAQDPSTGCYMYYFQYLSKTYCVDATQETNCLGRLINHSKCGNCQTKLHDID

Parental  GVPHLILIASRDIAAGEELLYDYGDRSKASIEAYPWLKH
          GVPHLILIA.RDIAAGEELLYDYGDRSKASIEAYPW.KH
Retrocopy GVPHLILIATRDIAAGEELLYDYGDRSKASIEAYPWMKH

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	0.05 RPM	32.47 RPM
SRP007412_cerebellum	0.09 RPM	33.48 RPM
SRP007412_heart	0.12 RPM	156.02 RPM
SRP007412_kidney	0.12 RPM	93.32 RPM
SRP007412_liver	0.08 RPM	30.26 RPM
SRP007412_testis	0.05 RPM	31.29 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1459 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	16:38476319..38477263
ENCFF001YIJ	POLR2A	16:38475479..38476041
ENCFF001YKA	POLR2A	16:38475727..38477028

EST

No EST(s) were mapped for retro_mmus_1459 retrocopy.

TSS

No TSS is located nearby retro_mmus_1459 retrocopy 5' end.

Lab

retro_mmus_1459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1459 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,