RetrogeneDB ID: retro_mmus_2479

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:90543644..90544370(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Usp46
• Ensembl ID: ENSMUSG00000054814
• Aliases: None
• Description: ubiquitin specific peptidase 46 [Source:MGI Symbol;Acc:MGI:1916977]

Sequence

>retro_mmus_2479
TGTACCATGGGTGCCAATGCTTCAGCATTAGAGAAAGAGATTGGCTCAGAATAGTTTCTGGTCAATGAGCATTATTTTAG
ATTAGAGAATTTTGGGAATACCTGCTACTGCAACTCAGTTCTTCAAGCAATTATTTTTGTCCATTTCAGGAAAAAATTCT
AGCATACAAAAGTCAGCCCAGATAAAAGGAGAACCTTCTCACCTGTCTGGCATACCTCTTCCACAGCCTAACTACTCAGA
AGAGGAAGGTCAGTGTGATCCTGCCCAAGGAGTTCATCACAAGATTTCAGAAAGAAATTGAGTTGTTTGACAACTACAAT
AAGATGTCCATAAATTTTAAAATTACCTACTCAGTACAATTGCTGGTATTTCTAAGAAGAAAGAAAACGGGAGAAGCAAA
ATAACCTATTACATAAAGGGGACGTGGACAGCGAGGATAAAAATAGCATACCAGACCCAACAAGAGTCCATGAGATTTTT
CAGGGAACATTAACTAATGAAATCTGGTTTCTTACTTATGAAACTATAAACAGCAAAGATGAAGATTTTTTTTTAGACCT
TTCTGTTGACGTGGAATGAAACACATCAGTTACTCAATGCTTAAGAGGGTTCAGTAACACAGAGCAAGTCTTAATGAGGT
TTTGTCTAACCTTACTGTCAAGAAAGTAAAGGGCACACTCAGGAAGAGTAGCAGCCTTACCTCTGTACTCTAGCATGCTG
ATAAGG

Alignment

ORF - retro_mmus_2479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.6 %
• Parental protein coverage: 67.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CNMGTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQAL-YFCRPFRENVLAYKAQQKKKENLLT
          C.MG.NASALEK.IG.E.F..NEHYF.L.NFGNTCYCNSVLQA..YFC.PF.E..LAYK.Q...KENLLT
Retrocopy CTMGANASALEKEIGSE*FLVNEHYFRLENFGNTCYCNSVLQAI<YFC-PFQEKILAYKSQPR*KENLLT

Parental  CLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDAHEFLNYLLNTIADILQEEKK-QEKQNG
          CLA.LFHS..TQK.KV.VI.PK.FI.R..KE..LFDNY..........Y............KK..EKQN.
Retrocopy CLAYLFHSLTTQKRKVSVILPKEFITRFQKEIELFDNYNKMSINFKITYSVQLL--VFLRRKK>REKQNN

Parental  KLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSSKDE-DFLDLSVDVEQNTSITHCLRDFS
          .L..G.......N..P..T.VHEIFQGTLTNE...L..ET..SKDE....DLSVDVE.NTS.T.CLR.FS
Retrocopy LLHKGDVDSEDKNSIPDPTRVHEIFQGTLTNEIWFLTYETINSKDEXXXXDLSVDVE*NTSVTQCLRGFS

Parental  NTETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLK
          NTE.........C.T..S........RV..LP........
Retrocopy NTEQVLMR---FCLTLLSRK*RAHSGRVAALPLYSSMLIR

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	117.59 RPM
SRP007412_cerebellum	0.00 RPM	117.54 RPM
SRP007412_heart	0.00 RPM	27.27 RPM
SRP007412_kidney	0.00 RPM	33.19 RPM
SRP007412_liver	0.00 RPM	10.32 RPM
SRP007412_testis	0.00 RPM	26.07 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2479 was not detected

EST

No EST(s) were mapped for retro_mmus_2479 retrocopy.

TSS

No TSS is located nearby retro_mmus_2479 retrocopy 5' end.

Lab

retro_mmus_2479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2479 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028560	1 retrocopy	retro_mmus_2136,
Mus musculus	ENSMUSG00000054814	1 retrocopy	retro_mmus_2479 ,
Oryctolagus cuniculus	ENSOCUG00000017031	1 retrocopy	retro_ocun_1012,