RetrogeneDB ID: retro_mmus_3365

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:92334551..92335079(-)
• Located in intron of: ENSMUSG00000074139

Retrocopy information

• Ensembl ID: ENSMUSG00000082623
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ubald1
• Ensembl ID: ENSMUSG00000039568
• Aliases: None
• Description: UBA-like domain containing 1 [Source:MGI Symbol;Acc:MGI:1916255]

Sequence

>retro_mmus_3365
ATGTCATTGAACATGGACCGGCTCAAACACCAGGTCATGATCAACCAGTTCATGCTGATAACAGGCTAAGCAGCCGATCA
GGCAAAGCAACTGCTGCAAGCAGCCCAGTAGCAGTTCGAGACACCCCTCAGTGCCCTTTTCCAGGAGACCAACATCCCCT
ACAGCCACCACCACCAGATGATGTTCACTCCGGCCAACACCCCTGCCACGCCCCCCAACTTCCCTGATGTTCTCACCATG
TTCTCCTATCCTAAGACCTCTGAAAGCATCTATGGTGGTGGCAGCAGCTGCAGCCCAATGGCCACTTTGGTCACGTCACC
CCCACTGCACTTCCCCCATGCCACTGGCAGCTTTGCAACACCCAGCAGGCCAACTGCAGCCTCGCCCCCAGGAGGCCCAC
AGCACCACCAGTCGCAGCCGCCCCTGTGGACACGAGCACCCCCTTCGCCAACTTCAGACTGGCCTTCCCTGGCTCCCCAA
CGGGTCACCTTAGAAACAAGGGCCCACTCTGCCATTGAGGCAGAGAGA

Alignment

ORF - retro_mmus_3365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVNMDELKHQVMINQFVLTAGCAADQAKQLLQAAHWQFETALSTFFQETNIPYSHHHQMMCTPANTPAT
          MS.NMD.LKHQVMINQF.L..G.AADQAKQLLQAA..QFET.LS..FQETNIPYSHHHQMM.TPANTPAT
Retrocopy MSLNMDRLKHQVMINQFMLITG*AADQAKQLLQAAQ*QFETPLSALFQETNIPYSHHHQMMFTPANTPAT

Parental  PPNFPDALTMFSRLKASESFHGGGGSSSPMATSATSPPPHFPHATGSFATPSWPTAASPPGGPQQHQPQP
          PPNFPD.LTMFS..K.SES..GGG.S.SPMAT..TSPP.HFPHATGSFATPS.PTAASPPGGPQ.HQ.QP
Retrocopy PPNFPDVLTMFSYPKTSESIYGGGSSCSPMATLVTSPPLHFPHATGSFATPSRPTAASPPGGPQHHQSQP

Parental  PLWTPAPPSPTSDWPPLAPQQATSEPRAHPAMEAER
          PLWT.APPSPTSDWP.LAPQ..T.E.RAH.A.EAER
Retrocopy PLWTRAPPSPTSDWPSLAPQRVTLETRAHSAIEAER

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	67.87 RPM
SRP007412_cerebellum	0.00 RPM	47.03 RPM
SRP007412_heart	0.00 RPM	28.42 RPM
SRP007412_kidney	0.00 RPM	27.58 RPM
SRP007412_liver	0.00 RPM	15.18 RPM
SRP007412_testis	0.05 RPM	70.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3365 was not detected

EST

No EST(s) were mapped for retro_mmus_3365 retrocopy.

TSS

No TSS is located nearby retro_mmus_3365 retrocopy 5' end.

Lab

retro_mmus_3365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3365 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
Mustela putorius furo	ENSMPUG00000014980	1 retrocopy	retro_mputfur_206,
Mus musculus	ENSMUSG00000039568	1 retrocopy	retro_mmus_3365 ,
Mus musculus	ENSMUSG00000050628	1 retrocopy	retro_mmus_241,