RetrogeneDB ID: retro_mmus_3516

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:121416130..121416419(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083699
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2w
• Ensembl ID: ENSMUSG00000025939
• Aliases: Ube2w, 6130401J04Rik
• Description: ubiquitin-conjugating enzyme E2W (putative) [Source:MGI Symbol;Acc:MGI:1914049]

Sequence

>retro_mmus_3516
GATGGCTTCATCATGGTGTCAATGCGGAAACAACTGCAAAAAGAACTGTTGGCTTTGAAGAATTACCCACCTCCAGGAAT
GACTTTAAATGAAAAGAGCATTTAGAATTCAATTATGCAGTGTATCCTAGACATGGAAGTTTCACCGGGAAGATTATATG
AAGGGGAAAAAATTCAACTTTTGTTTTAATTTAATAGCCGTACCCTTTGAGTCTCCTCAGGTCATGTTTACTGGTGAAAA
GTTCACATTTATCCTCATGTGTATATCAATGGTCATTATCTGTTTATCC

Alignment

ORF - retro_mmus_3516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 53.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DGFIMASMQKRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSR-YP
          DGFIM.SM.K.LQKELLAL.N.PPPGMTLNEKS..NSI.Q.I.DME..PG.LYEGEK.QLLF.F.SR.YP
Retrocopy DGFIMVSMRKQLQKELLALKNYPPPGMTLNEKSI*NSIMQCILDMEVSPGRLYEGEKIQLLF*FNSR<YP

Parental  -FDSPQVMFTGE-NIPIHPHVYSNGH-ICLS
          .F.SPQVMFTGE....I.PHVY.NGH.ICLS
Retrocopy <FESPQVMFTGE<KVHIYPHVYINGH>ICLS

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	42.85 RPM
SRP007412_cerebellum	0.00 RPM	22.62 RPM
SRP007412_heart	0.00 RPM	9.43 RPM
SRP007412_kidney	0.00 RPM	22.21 RPM
SRP007412_liver	0.00 RPM	14.06 RPM
SRP007412_testis	0.09 RPM	36.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3516 was not detected

EST

No EST(s) were mapped for retro_mmus_3516 retrocopy.

TSS

No TSS is located nearby retro_mmus_3516 retrocopy 5' end.

Lab

retro_mmus_3516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Mus musculus	ENSMUSG00000025939	1 retrocopy	retro_mmus_3516 ,
Ornithorhynchus anatinus	ENSOANG00000008597	1 retrocopy	retro_oana_106,
Oryctolagus cuniculus	ENSOCUG00000010245	1 retrocopy	retro_ocun_1189,
Otolemur garnettii	ENSOGAG00000027181	2 retrocopies	retro_ogar_460, retro_ogar_766,
Procavia capensis	ENSPCAG00000012043	2 retrocopies	retro_pcap_128, retro_pcap_278,