RetrogeneDB ID: retro_mmus_2868

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:117472995..117473309(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2m
• Ensembl ID: ENSMUSG00000005575
• Aliases: Ube2m, 2510040H03Rik, UBC12, Ubc-rs2
• Description: ubiquitin-conjugating enzyme E2M [Source:MGI Symbol;Acc:MGI:108278]

Sequence

>retro_mmus_2868
GACATCAGCTTCTCAGACCCATACGACCTCCTCAACTTCAAGCTGGTGATCTGTCCTGATGAAGGCTTCTACAAGAGTGG
CAAGTTTGTATTCAGCTTTAGGTGGGACAGGGTTACCCACACGACTCTCCTAAGGTGATGTGTGAAACAATGGTTTATCA
TCCCAATCTTGACCTGGAGGGCAACGTCTGCCTCAATGTCCTCAGAGAGGACTGGAAGCCAGTCCTTAAGATAAACTCCA
TAATTTATGGCCTGCACCATCTCTTCTTGGAGCCCAACCCCGAGGTTCCACTGAACAAGGAGGCTGCTGGGGTA

Alignment

ORF - retro_mmus_2868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 57.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFK-VGQGYPHDPPKVKCETMVYHPNIDLEGNVCLNILR
          DISFSDP.DLLNFKLVICPDEGFYKSGKFVFSF..VGQGYPHD.PKV.CETMVYHPN.DLEGNVCLN.LR
Retrocopy DISFSDPYDLLNFKLVICPDEGFYKSGKFVFSFR<VGQGYPHDSPKVMCETMVYHPNLDLEGNVCLNVLR

Parental  EDWKPVLTINSIIYGLQYLFLEPNPEDPLNKEAAEV
          EDWKPVL.INSIIYGL..LFLEPNPE.PLNKEAA.V
Retrocopy EDWKPVLKINSIIYGLHHLFLEPNPEVPLNKEAAGV

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	0.02 RPM	76.28 RPM
SRP007412_cerebellum	0.04 RPM	88.80 RPM
SRP007412_heart	0.03 RPM	100.46 RPM
SRP007412_kidney	0.00 RPM	77.23 RPM
SRP007412_liver	0.00 RPM	33.62 RPM
SRP007412_testis	0.00 RPM	160.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2868 was not detected

EST

No EST(s) were mapped for retro_mmus_2868 retrocopy.

TSS

No TSS is located nearby retro_mmus_2868 retrocopy 5' end.

Lab

retro_mmus_2868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2868 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130725	1 retrocopy	retro_hsap_1677,
Gorilla gorilla	ENSGGOG00000013357	1 retrocopy	retro_ggor_27,
Mus musculus	ENSMUSG00000005575	1 retrocopy	retro_mmus_2868 ,
Mus musculus	ENSMUSG00000034343	3 retrocopies	retro_mmus_2161, retro_mmus_255, retro_mmus_845,