RetrogeneDB ID: retro_mmus_2017

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:24592904..24594513(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wwp1
• Ensembl ID: ENSMUSG00000041058
• Aliases: Wwp1, 8030445B08Rik, AIP5, SDRP1, Tiul1
• Description: WW domain containing E3 ubiquitin protein ligase 1 [Source:MGI Symbol;Acc:MGI:1861728]

Sequence

>retro_mmus_2017
ATGCCTCCAGGTTGGGAAAGAAGAGTTGGTGATTGTGGAAGAGTTTATTATGTGGATCATAACACCAGAACAAGAACCTG
GCAGCGACCTACTATAGAATCTGTTCGAAATTTTGAACAGTGAAAATCTCAGCGGAATCAATTGCAGGGAGCTATGCAAC
AATTCAACCAAGATACCTCTATTTGGCTTCAGTGGTAGCTTCAGAAAATGACCCCTATGGTCCCTTACCACCAGGCTGGG
AAAAAAGAGTGGATTCAACAGACAGACTTTACTTTGTGAATCATAATACAAAAACAACCCAGTGGGAAGATCCAAGAACT
CAAGGCTTACCAAATGAAGAAGCCCTGCCAGAAGGCTGGGAAATTAGGTATACTCGGGAAGGTGTTAGTACTTTGTTGAT
CATAACACGAGAACAACAACATTCAAAGATCCTGGGAAGTCATTGGTAACTAAAGGTGGTCCACAGATTGCTTATGAACG
CAGCTTTAGGTGGAAGCTTGCTCACTTCCGTTACTTGTGCCAGTCTAATGCACTACCCAGTCATGTAAAGATCAATGTGT
CCGACAGACATTATTTGAAGATTCCTTCCAACAGATTATGGCATTAAAACCATATGACTCGAGGAGGCGGTTATATGTAA
TATCTAGAGGAGAAGAAGGTCTTGATTATGGTGGCCTTGCAAGAAAATGGTTTTTCTTGCTTTCCCATGAAGTTTTGAAT
CCAGTATATTGCTTATTTGAGTATGCAAGCAAGAATAACTATTGTTTACAGATAAATCCAGCATCAACTATAAATCCTGA
CCATCTTTCATACTTCTGTTTTATTGATCGCTTTATTGCAATGGCACTGTTCCATGGAAAGTTTATTGATACTGGTTTCT
CTTTACCATTCTACAAACGTATGCTAAGCAAAAAACGTACTATTAAGGATTTGGAATCTATTGATACTGAATTTTACAAC
TCTCTAATCTGGATAAGAGATAACAATATTGAAGAATGTGGCTTAGAAATGTACTTTTCTGTAGACATGGAGATTCTGGG
AAGTTACTTCACATGATTTAAAGTTGGGAGGTTCCAATATCCTGGTGACAGAAGAAAACAAAGATGAATGTATTGGTTTA
ATGACAGAATGGCGCTTTTCTCGAGGAGTACAAGAACAGACCAAAGCTTTCCTTGATGGGTGTAATGAAGTTGTTCCCCT
TCAGTGGCTACAGTACTTTGATGAAAAAGAATTGGAGGTTATGCTGTGTGGCATGCAAGAGGTTGACTTGGCAGACTGGC
AGAGAAATACTGTTTATCGACATTATACAAGAAACAGCAAGCAAATTATTTGGTTTTGGCAGTTTGTGAAAGAGACTGAT
AGTGAAGTGCGAATGCCACTCTTGCAGCTTGTCACTGGAACCTGTCGCTTGCCTCTGGGAGGATTTGCTGAGCTCATGGG
AAGTAATGGGCCTCAAAAGTTCTGTATTGAAAAAGTTGGCAAAGACACCTGGTTACCAAGAAGCCAGACATGTTTTAATC
GCTTGGATCTCCCACCATATAAGAGTTATGAACAACTAAAGGAAAAACTTGTTTTTGCAACAGAAGAGACAGAGGGATTT
GGACAAGAA

Alignment

ORF - retro_mmus_2017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LPPGWERRVDDRGRVYYVDHNTRTTTWQRPTMESVRNFEQWQSQRNQLQGAMQQFNQ-RYLYSASMLAAE
          .PPGWERRV.D.GRVYYVDHNTRT.TWQRPT.ESVRNFEQ..SQRNQLQGAMQQFNQ.RYLY.AS..A.E
Retrocopy MPPGWERRVGDCGRVYYVDHNTRTRTWQRPTIESVRNFEQ*KSQRNQLQGAMQQFNQ<RYLYLASVVASE

Parental  NDPYGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQGLPNEEPLPEGWEIRYTREGVR-YFVDHNTR
          NDPYGPLPPGWEKRVDSTDR.YFVNHNTKTTQWEDPRTQGLPNEE.LPEGWEIRYTREGV..YFVDHNTR
Retrocopy NDPYGPLPPGWEKRVDSTDRLYFVNHNTKTTQWEDPRTQGLPNEEALPEGWEIRYTREGVS<YFVDHNTR

Parental  TTTFKDPRNGKSSVTKGGPQIAYERSFRWKLAHFRYLCQSNALPSHVKINVS-RQTLFEDSFQQIMALKP
          TTTFKDP..GKS.VTKGGPQIAYERSFRWKLAHFRYLCQSNALPSHVKINVS.RQTLFEDSFQQIMALKP
Retrocopy TTTFKDP--GKSLVTKGGPQIAYERSFRWKLAHFRYLCQSNALPSHVKINVS<RQTLFEDSFQQIMALKP

Parental  YDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCF
          YD.RRRLYVI.RGEEGLDYGGLAR.WFFLLSHEVLNP.YCLFEYA.KNNYCLQINPASTINPDHLSYFCF
Retrocopy YDSRRRLYVISRGEEGLDYGGLARKWFFLLSHEVLNPVYCLFEYASKNNYCLQINPASTINPDHLSYFCF

Parental  IGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDME
          I.RFIAMALFHGKFIDTGFSLPFYKRMLSKK.TIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDME
Retrocopy IDRFIAMALFHGKFIDTGFSLPFYKRMLSKKRTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDME

Parental  IL-GK-VTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKEL
          IL.GK.VTSHDLKLGGSNILVTEENKDE.IGLMTEWRFSRGVQEQTKAFLDG.NEVVPLQWLQYFDEKEL
Retrocopy IL<GK<VTSHDLKLGGSNILVTEENKDECIGLMTEWRFSRGVQEQTKAFLDGCNEVVPLQWLQYFDEKEL

Parental  EVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGS
          EVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETD.EVRM.LLQ.VTGTCRLPLGGFAELMGS
Retrocopy EVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDSEVRMPLLQLVTGTCRLPLGGFAELMGS

Parental  NGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE
          NGPQKFCIEKVGKDTWLPRS.TCFNRLDLPPYKSYEQLKEKL.FA.EETEGFGQE
Retrocopy NGPQKFCIEKVGKDTWLPRSQTCFNRLDLPPYKSYEQLKEKLVFATEETEGFGQE

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	1.31 RPM	49.74 RPM
SRP007412_cerebellum	0.65 RPM	57.36 RPM
SRP007412_heart	0.03 RPM	72.32 RPM
SRP007412_kidney	0.46 RPM	135.86 RPM
SRP007412_liver	0.25 RPM	99.68 RPM
SRP007412_testis	0.41 RPM	33.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2017 was not detected

EST

No EST(s) were mapped for retro_mmus_2017 retrocopy.

TSS

No TSS is located nearby retro_mmus_2017 retrocopy 5' end.

Lab

retro_mmus_2017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2017 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000123124	1 retrocopy	retro_hsap_2680,
Macaca mulatta	ENSMMUG00000006305	1 retrocopy	retro_mmul_1418,
Mustela putorius furo	ENSMPUG00000010807	1 retrocopy	retro_mputfur_963,
Mus musculus	ENSMUSG00000041058	1 retrocopy	retro_mmus_2017 ,
Nomascus leucogenys	ENSNLEG00000001517	1 retrocopy	retro_nleu_1183,
Pongo abelii	ENSPPYG00000018724	1 retrocopy	retro_pabe_2299,
Pan troglodytes	ENSPTRG00000020395	1 retrocopy	retro_ptro_1807,