RetrogeneDB ID: retro_mmus_3247

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:15644523..15646091(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmd2
• Ensembl ID: ENSMUSG00000006998
• Aliases: Psmd2, 9430095H01Rik, AA407121, TEG-190, Tex190
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 [Source:MGI Symbol;Acc:MGI:1096584]

Sequence

>retro_mmus_3247
TTTGATCAAGATTAACTGCTGACTGATCATGGCAACAAATGTCTTTACAAGAACAAGGACCATGGGATGTTATGTGCTGC
TGTGTCTCTTGGCATGATTCTGCTGTGGGATGTGGATGGTGGCCTCACCCAGATTGACAAGTATCTGTATTCCTCTGAGG
ACATCAAGTCAGGAGCTCTCCTTGTCTGTGGTATCATGAATTTTGGGGTCCGGAATGACTGTGATCCTGCCCTGGCACTG
CTTTCAGACTATGTTCTCCATAACAGCAATACCATGAAACTTGGCTCCATCTTTGGGCTAGGTTTGGCCTATGCTAACTC
TAATTGGGAGGATGTTCTAACACTGCTGCTACCTGTAATGGGAGATTCCAAGTCCAGCGTGGAGGTAGCAGGTGTGACGG
CTCTAGCTGTGGGATGATAGCAGTGGGATCTTACAATGCAGATGTCACTTCCACCATCCTTCAAACCATCTTGGAGAAAT
CTGAGACTGAGCTCAAAGATACCTATGCTTGCTGGCTTCCTCTTGGCCTGGGCCTCAATCACTTGGGGAAGGGTGAAGCT
ATTGAGGCCATCCTGGCTGCCTTGGAGGTCGTGTCAGAGCCACTCCGCAGTTTTGCCAGCATTCTGGTGGATGTATGTGC
CTTTGCAGGCTCCGGGAATGTGCTGACGGTTCAGCAGCTCCTCCACGTCTGTAGTGAGCACTTTGACTCCAAGGAAAAGG
AAGAAGACAAAGACAAGAAGGTAAAGAAGGACAAGGGCGAGAAGGACGTCCCTGCTGCCATGGGAGCACGTCAGGGAGCA
GCTGTTCTGGGGATTGCACTTACTGCTCTGGGGGAAGAGATTGGTGCAGAGATGGCATTGTGAACTTTTGGTCACTTGCT
GAGATATGAGGAGCCCACCCTCCGTCAGGCTGTAGCTTTAGCACTGGCAGTAATCTCTGTTTCAAATCCATGACTTAACA
TCCTGGATACTCTAAGCAAATTGTCTCATGATGCTGATCCAGAAGTTTCCTATAACTACATCTTTGCTATAGGCATGGTG
GGCAGTACTACCAATAATGCCCGTCTGGCTGCAATGTTGTGCCAGTTAGCTCAATATCATGCCAAGGACCCCAATAACTT
CTTCATGGTGCACTTGGCACAGGGCCTGAACACATTTAGGGAAGAGCATACTTACCCTCTGCCCCATCACAGTGATCGGC
AGCTCATGAGTCAAGTAGCTGTGGCAGGACTACTCACGGTGCTTGTTTCTTTCCTGGATGTTCGAAACATCATCCTAGGC
AAATCTCACTATGTATTGTGTGGGCTGGTGGCCACCATGCAGCCTCGGATGCTGGTTACATTTGATGAGGAGTTGTGACC
ATTGCCAGTTTCTGTCCATGTGGGTCAGGCAGTGGATGTGGTGGGCCAGGCTGGGAAGCCAAAAACGATCACGGAGTTCC
AGACTGATACAACTCCAGTGTTGTTGGCTCATGGGGTGCGGGCAGAGTTGGCCACTGAGGAGCTTCTTCCTGTCACCCCC
ATTCTGGAAGGCTTTGCTATTATTCGGAAGAACTCCAACTATGATCTT

Alignment

ORF - retro_mmus_3247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.67 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLWDVDGGLTQIDKYLYSSEDYIKSGALLACGIVNSG
          F.QD.LLTD.GNK.LYKNKDHGML.AA.SLGMILLWDVDGGLTQIDKYLYSSED.IKSGALL.CGI.N.G
Retrocopy FDQD*LLTDHGNKCLYKNKDHGMLCAAVSLGMILLWDVDGGLTQIDKYLYSSED-IKSGALLVCGIMNFG

Parental  VRNECDPALALLSDYVLHNSNTMRLGSIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAGVTALA-CG
          VRN.CDPALALLSDYVLHNSNTM.LGSIFGLGLAYA.SN.EDVLTLLLPVMGDSKSS.EVAGVTALA.CG
Retrocopy VRNDCDPALALLSDYVLHNSNTMKLGSIFGLGLAYANSNWEDVLTLLLPVMGDSKSSVEVAGVTALA<CG

Parental  MIAVGSCNGDVTSTILQTIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANT
          MIAVGS.N.DVTSTILQTI.EKSETELKDTYA.WLPLGLGLNHLGKGEAIEAILAALEVVSEP.RSFA..
Retrocopy MIAVGSYNADVTSTILQTILEKSETELKDTYACWLPLGLGLNHLGKGEAIEAILAALEVVSEPLRSFASI

Parental  LVDVCAYAGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALIAMG
          LVDVCA.AGSGNVL.VQQLLH.CSEHFDSKEKEEDKDKK.KKDK..K..PA.MGA.QG.AVLGIAL.A.G
Retrocopy LVDVCAFAGSGNVLTVQQLLHVCSEHFDSKEKEEDKDKKVKKDKGEKDVPAAMGARQGAAVLGIALTALG

Parental  EEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPEVSYNSIFAMGMVG
          EEIGAEMAL.TFGHLLRY.EPTLR.AV.LALA.ISVSNP.LNILDTLSK.SHDADPEVSYN.IFA.GMVG
Retrocopy EEIGAEMAL*TFGHLLRYEEPTLRQAVALALAVISVSNP*LNILDTLSKLSHDADPEVSYNYIFAIGMVG

Parental  SGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGL-THLGKGTLTLCP-YHSDRQLMSQVAVAGLLTVLV
          S.TNNARLAAML.QLAQYHAKDPNN.FMV.LAQGL.THLGK..LTLCP..HSDRQLMSQVAVAGLLTVLV
Retrocopy STTNNARLAAMLCQLAQYHAKDPNNFFMVHLAQGL>THLGKSILTLCP<HHSDRQLMSQVAVAGLLTVLV

Parental  SFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPLPVSVRVGQAVDVVGQAGKPKTITGFQTHTTP
          SFLDVRNIILGKSHYVL.GLVA.MQPRMLVTFDEEL.PLPVSV.VGQAVDVVGQAGKPKTIT.FQT.TTP
Retrocopy SFLDVRNIILGKSHYVLCGLVATMQPRMLVTFDEEL*PLPVSVHVGQAVDVVGQAGKPKTITEFQTDTTP

Parental  VLLAHGERAELATEEFLPVTPILEGFVILRKNPNYDL
          VLLAHG.RAELATEE.LPVTPILEGF.I.RKN.NYDL
Retrocopy VLLAHGVRAELATEELLPVTPILEGFAIIRKNSNYDL

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	180.57 RPM
SRP007412_cerebellum	0.04 RPM	190.14 RPM
SRP007412_heart	0.06 RPM	209.23 RPM
SRP007412_kidney	0.02 RPM	187.70 RPM
SRP007412_liver	0.03 RPM	167.07 RPM
SRP007412_testis	0.46 RPM	434.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3247 was not detected

EST

No EST(s) were mapped for retro_mmus_3247 retrocopy.

TSS

No TSS is located nearby retro_mmus_3247 retrocopy 5' end.

Lab

retro_mmus_3247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3247 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175166	1 retrocopy	retro_hsap_531,
Gorilla gorilla	ENSGGOG00000027136	1 retrocopy	retro_ggor_486,
Mus musculus	ENSMUSG00000006998	2 retrocopies	retro_mmus_209, retro_mmus_3247 ,
Nomascus leucogenys	ENSNLEG00000006305	1 retrocopy	retro_nleu_1786,
Pongo abelii	ENSPPYG00000014354	1 retrocopy	retro_pabe_218,
Pan troglodytes	ENSPTRG00000015689	1 retrocopy	retro_ptro_397,