RetrogeneDB ID: retro_mmus_3074

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:107199204..107200102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000086261
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pwp1
• Ensembl ID: ENSMUSG00000001785
• Aliases: Pwp1, 2310058A11Rik, 2610205J09Rik, AI098170, AL022879, AV083409, AW550690
• Description: PWP1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914735]

Sequence

>retro_mmus_3074
GAAGTGAAATGTCTCATTGCTGAAGCAAAAGGAAAATTACAAGAAGGATGTGGTAGTGAGGAAGAGGAGGCAAGCAGTCC
TTCCAAAGATGGCATGCAGAGTGCCCAGACCCAGGATGGGGATCCACAAGATGACTGTATGCTAGATGAGCTGGCCGAGT
ACGACTTAGATAATTATGACAAAGAGGACAACCCAAATACTGAGACCATTGGCGAATCTCTATTGGCTTTACGGCATATG
GTAGTAGTGATCAGGATCCATAGGTCACCCTGGAAGACATGGAACAACATGAGCATGAAGATTTCTAGATTAAGCCGACT
AACAACATTGTTTGTGGCCATGCTGAACAAAGGCGGTGCAATTTAGAGGTACACACTTACAATCAAGGAGTCTTTCTATG
CCCACCTGACATACTCCTGTCTGCCTACCCTCTGAGTGTGGAATAGCTGAAATTTGATCCTAGCCCAGATCTGTCTACTG
GAAATTACATTGCTGTGGGAAACATGACCCCTGTTGCTGAGGTGTGGGACCTGGATATTGTGGACTCTATAGAGCCAGTC
TTCACAATGGGAAGCAAGCTTTCTAAAAAGAAGAAAAGAAGAATAGTTCCTCAGCAGAAGAACATATTGATGCTGTCCTT
GATGTTTCCTGGAGTAAGACAGTCAGAAATGTGCTGGCAAGTGCATCAGTAGATAACACTGTAATTCCCTGGGATCTGTC
TGTGGGGAAGCCAGCAACCAGGTTTACTGAGCTTACAGACAAGGTTCAAACTCTGCAGTTTCATCCATTTGAAGCACAGA
CACTGATTTCTGGACCCTATGACAAATCAGTGGCTCTGTATGACTGCAGAGATCCTAGCCAGAACCACCACCTATGGTGG
TTCAGTGGGCCGATCGAG

Alignment

ORF - retro_mmus_3074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.59 %
• Parental protein coverage: 61.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EAKGKLQEEGGSEEEEAGNPSEDGMQSGPTQAPPRESLEDGDPQDDRTLDDDELAGYDLDNYDEEDNPDA
          E.K....E..G...E..G...E....S............DGDPQDD..LD..ELA.YDLDNYD.EDNP..
Retrocopy EVKCLIAEAKGKLQEGCGSEEEEA-SSPSKDGMQSAQTQDGDPQDDCMLD--ELAEYDLDNYDKEDNPNT

Parental  ETIGESLL-GLTVYGSNDQDPYVTLKDTEQYEHEDFLIKPTDNLIVCGRAEQEQCNLEVHVYNQEE-ESF
          ETIGESLL.G.T.YGS.DQDP.VTL.D.EQ.EHEDF.IKPT.N.IVCG.A..EQ......V......ESF
Retrocopy ETIGESLL<GFTAYGSSDQDP*VTLEDMEQHEHEDF*IKPTNN-IVCGHA--EQRRCNLEVHTYNQ>ESF

Parental  YVH-HDILLSAYPLSVEWLNFDPSPDASTGNYIAVGNMTPVIEVWDLDIVDSLEPVFTLGSKLSKKKKKK
          Y.H..DILLSAYPLSVE.L.FDPSPD.STGNYIAVGNMTPV.EVWDLDIVDS.EPVFT.GSKLS..KKKK
Retrocopy YAH<PDILLSAYPLSVE*LKFDPSPDLSTGNYIAVGNMTPVAEVWDLDIVDSIEPVFTMGSKLS--KKKK

Parental  G-KKSSSAEGHTDAVLDLSWNKTVRNVLASASADSTVVLWDLSVGKSVARLTAHTDKVQTLQFHPFEAQT
          ..K.SSSAE.H.DAVLD.SW.KTVRNVLASAS.D.TV..WDLSVGK...R.T..TDKVQTLQFHPFEAQT
Retrocopy R<KNSSSAEEHIDAVLDVSWSKTVRNVLASASVDNTVIPWDLSVGKPATRFTELTDKVQTLQFHPFEAQT

Parental  LISGSYDKSVALYDCRDPSQNHRQWRFSGQIE
          LISG.YDKSVALYDCRDPSQNH..W.FSG.IE
Retrocopy LISGPYDKSVALYDCRDPSQNHHLWWFSGPIE

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	17.43 RPM
SRP007412_cerebellum	0.00 RPM	14.16 RPM
SRP007412_heart	0.00 RPM	16.44 RPM
SRP007412_kidney	0.00 RPM	15.23 RPM
SRP007412_liver	0.00 RPM	12.12 RPM
SRP007412_testis	0.23 RPM	12.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3074 was not detected

EST

No EST(s) were mapped for retro_mmus_3074 retrocopy.

TSS

No TSS is located nearby retro_mmus_3074 retrocopy 5' end.

Lab

retro_mmus_3074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3074 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000015544	1 retrocopy	retro_mmul_688,
Macaca mulatta	ENSMMUG00000031574	1 retrocopy	retro_mmul_687,
Mus musculus	ENSMUSG00000001785	2 retrocopies	retro_mmus_1600, retro_mmus_3074 ,
Otolemur garnettii	ENSOGAG00000011940	2 retrocopies	retro_ogar_2999, retro_ogar_3444,
Rattus norvegicus	ENSRNOG00000005350	1 retrocopy	retro_rnor_646,
Tursiops truncatus	ENSTTRG00000011036	1 retrocopy	retro_ttru_540,