RetrogeneDB ID: retro_mmus_1600

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:93331633..93332477(+)
• Located in intron of: None

Retrocopy information

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

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_1600
CTTCAGAGTGCCCAGACCTAGGCATGGCATAGGGAGCCCCTGAAGGATGGGGATTGACAAGATGACTGTATGCTAGATGA
TGATGAGCTGGCCGAGTATAACTTAGGTAATTTTGGTGAAGGGGACAAGCTAGATACTGAGACCATTGGCGAATCTCTGT
TGGGTCTTACGGTCTATGGTAGTAATGATCAGGATCCATATGTCACCCTGGAAGGCATGGAACAATATGAGCATGAAGAT
TTCTAGATTAAGCCGACTAACAACCTTATTGTTTGTGGCCATGCTGAGCAAAAGCAGTGCAATTTAGACATACACATTTA
CAATGAAGAAGAGGAGTTTTTCTATGTCCACCTGACATACTCCTGTCTGCATACCCTCTGAGTGTGGAATACCTGAATTT
TGATCCTAGCCCAGATATGTCTACTGGAAATTACACTGCTGTGGGAAACATGACCCCTGTTGCTGAGGTGTGGGACCTGG
ATATTGTCTATAGAGTGCCAGTCTTCACAATGGGAAGCAAGCTTTCTAAAAAAGGAAGAAAGGGAAGAATAGTTCCTCAG
CAGAAGAACATACTGATGCTGTCCTTGATGTTTCCTGGAATAAGACAGTCAGAAATGTGCTGGCAAGTGCATCCGCAGAT
AGCATTGTAATTCTCTGGGATCTGTCTGTGGGGAAGTCAGCAACCAGGCTTACTGAACATACAGACAAGGTTCAGACTCT
GCAGTTTCATCCATTTGAAGCACAGATACTGATTTCTGGGTCCTATGACAAATCTGTGGCTCTATATGACAGCAGAGATC
CTATCCAGAACAACCGCCTAAGGCGGTTCAGTGGGCAGATCGAG

Alignment

ORF - retro_mmus_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.32 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQSGPTQAPPRESLEDGDPQDDRTLDDDELAGYDLDNYDEEDNPDAETIGESLLGLTVYGSNDQDPYVTL
          .QS..T.A..RE.L.DGD.QDD..LDDDELA.Y.L.N..E.D..D.ETIGESLLGLTVYGSNDQDPYVTL
Retrocopy LQSAQT*AWHREPLKDGD*QDDCMLDDDELAEYNLGNFGEGDKLDTETIGESLLGLTVYGSNDQDPYVTL

Parental  KDTEQYEHEDFLIKPTDNLIVCGRAEQEQCNLEVHVYNQEEESFYVH-HDILLSAYPLSVEWLNFDPSPD
          ...EQYEHEDF.IKPT.NLIVCG.AEQ.QCNL..H.YN.EEE.FYVH..DILLSAYPLSVE.LNFDPSPD
Retrocopy EGMEQYEHEDF*IKPTNNLIVCGHAEQKQCNLDIHIYNEEEEFFYVH<PDILLSAYPLSVEYLNFDPSPD

Parental  ASTGNYIAVGNMTPVIEVWDLDIVDSLEPVFTLGSKLSKKKKKKGK-KSSSAEGHTDAVLDLSWNKTVRN
          .STGNY.AVGNMTPV.EVWDLDIV....PVFT.GSKLS.KK..KG...SSSAE.HTDAVLD.SWNKTVRN
Retrocopy MSTGNYTAVGNMTPVAEVWDLDIVYRV-PVFTMGSKLS-KKGRKGR<NSSSAEEHTDAVLDVSWNKTVRN

Parental  VLASASADSTVVLWDLSVGKSVARLTAHTDKVQTLQFHPFEAQTLISGSYDKSVALYDCRDPSQNHRQWR
          VLASASADS.V.LWDLSVGKS..RLT.HTDKVQTLQFHPFEAQ.LISGSYDKSVALYD.RDP.QN.R..R
Retrocopy VLASASADSIVILWDLSVGKSATRLTEHTDKVQTLQFHPFEAQILISGSYDKSVALYDSRDPIQNNRLRR

Parental  FSGQIE
          FSGQIE
Retrocopy FSGQIE

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	0.03 RPM	16.44 RPM
SRP007412_kidney	0.00 RPM	15.23 RPM
SRP007412_liver	0.00 RPM	12.12 RPM
SRP007412_testis	0.00 RPM	12.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1600 was not detected

EST

No EST(s) were mapped for retro_mmus_1600 retrocopy.

TSS

No TSS is located nearby retro_mmus_1600 retrocopy 5' end.

Lab

retro_mmus_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1600 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,