RetrogeneDB ID: retro_mmus_3578

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:13927286..13928384(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082736
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mkrn2
• Ensembl ID: ENSMUSG00000000439
• Aliases: Mkrn2, 2610002L04Rik, C81377
• Description: makorin, ring finger protein, 2 [Source:MGI Symbol;Acc:MGI:1914277]

Sequence

>retro_mmus_3578
AGATATGATCATACAAAACCCCCAGCTGCAGCAGGTGGTGCTGTGGGTCCTGCATCCCACCCTTCACCCTCCTCAGGCCT
GCATAGTCCTCACCCTTATCCCGACATTGCCATATCTGTTATGAGGACACATTTGAATGAACCTGGAAAGCAGGAGAAGA
CAATGCTGGTGCTCACAGACAGCAATCTCACTGGTCTAGCTGAAGACAAGACTCCTCCAAGCACAGAGACTAGTCCAGGT
GGCTGTAGTGACCCTCAGACCAGCCCAGAGATGAAGCCCCATTTCTACCTAAATGCCATCAGAACTGGCCTGATGCTCCT
ACAGGAGGCCAGCAACTCCTGCAGCAATGAGCAGCAGTTGTGCTCCTATGCTGCCGCTGGGGAGTGCCAGTTTGAAGATG
CCTGTGTCTACCTGCATGGGGACATGTGTGAGATCTGCAGGCTTCAAATCCTCCACCCCTTTGACCCAAGAGCCAAGGAA
AGCTCATGAGAAGATGTGCAGGTCGACATTTGAACATGAGATGGAAAAGGCTTCGTCCAGGTAAGCCAGGACGAAGTGTG
CAGCATCTGTATGGAGGTGATCCTGGAGAAAGCATCTGCTTCTGAAAGGAGGTTTGGATTCTCTCCAACTGCAGCCACAC
CTACTGCCTGTCCTGCATCTGTCAATGAAGATGTGCCAAGCAGTTTGAAAACCCTATCATAAAGTCTTGTCCAGAGGGCC
GTGTGATAGCAAAGTTTGTAACTCCAAGTGTGTACTGGGTAGAAGATCAGAATAAAAAGAATGAATTAGTTGAAGTTTTC
AAACAGGGAATGGGGGTAAAAGGCATGTAAATACTTTGAACAAGGCAAGGAGACCTGCCCCTTTGGAAACAAGTGCCTTT
ACCACCACCATGCTTACCCTGATGGGCAGTTGGCAGAGCCAGAGAAACCTCAGAAGCAGCTAAGCTCTGAAGGCGCTGTG
AGGTTCTTTAACTCAGTGCGGCTTTGGGATTTTAACGAGAACCAAGAAACCCGGCAAGTTCCCAGCACTGATGATGTGGA
TGTGATGGAGCTAGGAGATCTCTTCATGCACCTTTCTGGAGTAGAGACATCAGAACCC

Alignment

ORF - retro_mmus_3578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.64 %
• Parental protein coverage: 87.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RYDHTKPPAAAGGAVGPAPNPSPSSGLHSPHPSPDIATSVMRTHSNEPGKREKKTLVLRDRNLTGLAEDK
          RYDHTKPPAAAGGAVGPA..PSPSSGLHSPHP.PDIA.SVMRTH.NEPGK.EK..LVL.D.NLTGLAEDK
Retrocopy RYDHTKPPAAAGGAVGPASHPSPSSGLHSPHPYPDIAISVMRTHLNEPGKQEKTMLVLTDSNLTGLAEDK

Parental  TPPSKVNNPGGCSDPQTSPEMKPHSYLDAIRTGLDDL-EASSSYSNEPQLCPYAAAGECRFGDACVYLHG
          TPPS....PGGCSDPQTSPEMKPH.YL.AIRTGL..L.EAS.S.SNE.QLC.YAAAGEC.F.DACVYLHG
Retrocopy TPPSTETSPGGCSDPQTSPEMKPHFYLNAIRTGLMLLQEASNSCSNEQQLCSYAAAGECQFEDACVYLHG

Parental  DMCEICRLQVLHPFDP-EQRKAHEKMCMSTFEHEME-KAFAFQASQDKVCSICMEVILEKASASERRFG-
          DMCEICRLQ.LHPFDP.E.RKAHEKMC.STFEHEME.K.F..Q.SQD.VCSICMEVILEKASASERRFG.
Retrocopy DMCEICRLQILHPFDP>EPRKAHEKMCRSTFEHEME<KGFV-QVSQDEVCSICMEVILEKASASERRFG<

Parental  ILSNCSHTYCLSCIRQWRCAKQFENPIIKSCPECRVISEFVIPSVYWVEDQNKKNELIEAFKQGMGKK-A
          ILSNCSHTYCLSCI.Q.RCAKQFENPIIKSCPE.RVI..FV.PSVYWVEDQNKKNEL.E.FKQGMG.K.A
Retrocopy ILSNCSHTYCLSCICQ*RCAKQFENPIIKSCPEGRVIAKFVTPSVYWVEDQNKKNELVEVFKQGMGVK>A

Parental  CKYFEQGKGTCPFGSKCLYRH-AYPDGRLAEPEKPRKQLSSEGTVRFFNSVRLWDFIENRETRQVPSTDD
          CKYFEQGK.TCPFG.KCLY.H.AYPDG.LAEPEKP.KQLSSEG.VRFFNSVRLWDF.EN.ETRQVPSTDD
Retrocopy CKYFEQGKETCPFGNKCLYHHHAYPDGQLAEPEKPQKQLSSEGAVRFFNSVRLWDFNENQETRQVPSTDD

Parental  VDVTELGDLFMHLSGVESSEP
          VDV.ELGDLFMHLSGVE.SEP
Retrocopy VDVMELGDLFMHLSGVETSEP

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	20.19 RPM
SRP007412_cerebellum	0.00 RPM	19.76 RPM
SRP007412_heart	0.00 RPM	26.99 RPM
SRP007412_kidney	0.00 RPM	18.23 RPM
SRP007412_liver	0.00 RPM	9.99 RPM
SRP007412_testis	0.05 RPM	62.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3578 was not detected

EST

No EST(s) were mapped for retro_mmus_3578 retrocopy.

TSS

No TSS is located nearby retro_mmus_3578 retrocopy 5' end.

Lab

retro_mmus_3578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3578 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016733	1 retrocopy	retro_cjac_2362,
Mus musculus	ENSMUSG00000000439	2 retrocopies	retro_mmus_3578 , retro_mmus_544,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Otolemur garnettii	ENSOGAG00000003255	1 retrocopy	retro_ogar_3196,
Pteropus vampyrus	ENSPVAG00000005822	1 retrocopy	retro_pvam_1177,