RetrogeneDB ID: retro_mmus_3032

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:62683431..62684160(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plin3
• Ensembl ID: ENSMUSG00000024197
• Aliases: Plin3, 1300012C15Rik, M6prbp1, Tip47
• Description: perilipin 3 [Source:MGI Symbol;Acc:MGI:1914155]

Sequence

>retro_mmus_3032
GTCATGGGTTCCTGTGTGGGACAGATGGTGGTTAGCAGAATGGGCAGGGTGCTGGTGAAATCATAAGTCTGGGAAGACAA
TTGCCTGCCCCTGAAAGACGCAGAGGTAGCCCTGATTGCCACATCCCCGGAGGACTCAGACATGGCCTTGCTGCAGGGGA
AGTGAGAAGAGCAGAACTACTTTGTATAGTTGGGTTCGCTATCAGAGAGGCTTCGTAATCATGCCTATGAGCACTCACTC
TGCAAGATGTGCAATGCCAGGCAGAGGGCGCAGGAGAGAGTACAGCAGCTCACACATGTGCTCAGCCTGATGGAATACAT
GAAACAGGGCATGGGCCAGAGCATGAGGGAGGGGTAGGAGAAGCTGCGCCAGATGTGGCTCAGCTGGAACCAGAAGACCC
CACAGTTTGCTGAAAAGAACCCAGCTAAGCCAGAGCAGGTAGATACCCTGACACTCAGCATGTTCACAGACATTGCGCAG
CAGCTGCAGAACATGTGTGTGGCCCTGAGGGCCAGCACTGAGAATCTGCCCAGCCATGTCAGGGAGCAGGCACAGCAGGC
CTGCAGCCAGGTGGATGAACTTTAGACTACCTTCTCCAGCATCGACTCCTTTAAGGACCTCACAGCCAGCATTCTCGCCC
AAACGTAGCAGCACATAGCCAGATCCCTGGAGACCCTCGACCACACTGTGGAGTACATGGCCTAAAATACTCCAGTCATG
TGGCTCCTG

Alignment

ORF - retro_mmus_3032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.78 %
• Parental protein coverage: 55.61 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMGSRVGQMVISGVDRVLVKSEAWADNRLPLTEAELALIATPPEDSDMASLQQQRQEQNYFVRLGSLSER
          VMGS.VGQMV.S...RVLVKS..W.DN.LPL..AE.ALIAT.PEDSDMA.LQ....EQNYFV.LGSLSER
Retrocopy VMGSCVGQMVVSRMGRVLVKS*VWEDNCLPLKDAEVALIATSPEDSDMALLQGK*EEQNYFV*LGSLSER

Parental  LRNHAYEHSLGKLQNARQKAQETLQQLTSVLGLMESVKQGVDQRLGEGQEKLHQMWLSWNQKTPQDAEKD
          LRNHAYEHSL.K..NARQ.AQE..QQLT.VL.LME..KQG..Q...EG.EKL.QMWLSWNQKTPQ.AEK.
Retrocopy LRNHAYEHSLCKMCNARQRAQERVQQLTHVLSLMEYMKQGMGQSMREG*EKLRQMWLSWNQKTPQFAEKN

Parental  PAKPEQVEARALSMFRDITQQLQSMCVALGASIQGLPSHVREQAQQARSQVNDLQATFSGIHSFQDLSAG
          PAKPEQV....LSMF.DI.QQLQ.MCVAL.AS...LPSHVREQAQQA.SQV..L..TFS.I.SF.DL.A.
Retrocopy PAKPEQVDTLTLSMFTDIAQQLQNMCVALRASTENLPSHVREQAQQACSQVDEL*TTFSSIDSFKDLTAS

Parental  VLAQTRERIARAREALDNTVEYVAQNTPAMWLV
          .LAQT...IAR..E.LD.TVEY.A.NTP.MWL.
Retrocopy ILAQT*QHIARSLETLDHTVEYMA*NTPVMWLL

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	10.98 RPM
SRP007412_cerebellum	0.00 RPM	14.63 RPM
SRP007412_heart	0.00 RPM	130.09 RPM
SRP007412_kidney	0.00 RPM	73.34 RPM
SRP007412_liver	0.00 RPM	31.76 RPM
SRP007412_testis	0.27 RPM	23.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3032 was not detected

EST

No EST(s) were mapped for retro_mmus_3032 retrocopy.

TSS

No TSS is located nearby retro_mmus_3032 retrocopy 5' end.

Lab

retro_mmus_3032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3032 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024197	1 retrocopy	retro_mmus_3032 ,
Rattus norvegicus	ENSRNOG00000048834	1 retrocopy	retro_rnor_2083,