RetrogeneDB ID: retro_mmus_2048

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:77255993..77256423(-)
• Located in intron of: ENSMUSG00000042272

Retrocopy information

• Ensembl ID: ENSMUSG00000084087
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2v2
• Ensembl ID: ENSMUSG00000022674
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 variant 2 [Source:MGI Symbol;Acc:MGI:1917870]

Sequence

>retro_mmus_2048
ATGGCGGTCTCCACAGGAGTTAAAGTTACTCATAATTTTAGCTTGTTGGAAGAACTTGAAGAAGGACAGAAAGGAGTAGG
TGATGGTACTGTTAGCTGGGGCCTTGAAGATGATGAAGACATGATACAAGGTGGGCAGGCATGTTGATTGGGCCACCAAG
GACAAACTATGAAAACAGAATGTATAGCCTGAAAGTAAAATGTGGATCTAAATACCCATAAGACCCCACATCAGTTAGAT
TTGTAACAAAAATTAATATGAATGGGATCAATAATTTCAGTGGAATGGTGGATGCATGGAGCATACCAGTATTAGCAAAA
TGGCAAAATTCCTATAGCATTAAAGTCATACTTCAAGAGCTAAGACATCTTATGATGTCCCAAGAAAATATGAAGCTTCC
AAGGCACCACAAGGACAGACATACAACAAC

Alignment

ORF - retro_mmus_2048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTL-TRWTGMIIGPPRTNYENRIYSLKVEC
          MAVSTGVKV..NF.LLEELEEGQKGVGDGTVSWGLE.D......TRW.GM.IGPPRTNYENR.YSLKV.C
Retrocopy MAVSTGVKVTHNFSLLEELEEGQKGVGDGTVSWGLE-DDEDMI<TRWAGMLIGPPRTNYENRMYSLKVKC

Parental  GSKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVILQELRRLMMSKENMKLP-QPP
          GSKYP..P.SVRFVTKINMNGINN.SGMVDA.SIPVLAKWQNSYSIKVILQELR.LMMS.ENMKLP...P
Retrocopy GSKYP*DPTSVRFVTKINMNGINNFSGMVDAWSIPVLAKWQNSYSIKVILQELRHLMMSQENMKLP<KAP

Parental  EGQTYNN
          .GQTYNN
Retrocopy QGQTYNN

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	0.16 RPM	23.48 RPM
SRP007412_cerebellum	0.04 RPM	18.80 RPM
SRP007412_heart	0.00 RPM	3.89 RPM
SRP007412_kidney	0.54 RPM	6.70 RPM
SRP007412_liver	0.03 RPM	5.24 RPM
SRP007412_testis	0.09 RPM	3.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2048 was not detected

EST

No EST(s) were mapped for retro_mmus_2048 retrocopy.

TSS

No TSS is located nearby retro_mmus_2048 retrocopy 5' end.

Lab

retro_mmus_2048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2048 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032182	1 retrocopy	retro_cjac_814,
Loxodonta africana	ENSLAFG00000017749	1 retrocopy	retro_lafr_1168,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mus musculus	ENSMUSG00000022674	4 retrocopies	retro_mmus_1385, retro_mmus_189, retro_mmus_2048 , retro_mmus_2770,
Mus musculus	ENSMUSG00000090213	2 retrocopies	retro_mmus_2219, retro_mmus_3132,
Nomascus leucogenys	ENSNLEG00000013382	1 retrocopy	retro_nleu_1671,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Procavia capensis	ENSPCAG00000000293	1 retrocopy	retro_pcap_138,
Rattus norvegicus	ENSRNOG00000001829	1 retrocopy	retro_rnor_1181,
Sus scrofa	ENSSSCG00000022190	1 retrocopy	retro_sscr_524,
Tursiops truncatus	ENSTTRG00000008325	1 retrocopy	retro_ttru_1623,