RetrogeneDB ID: retro_mmus_189

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:19028231..19028654(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000060811
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_189
ATGACGGTCTCCACAGGAGTTCCTCATAATTTTCGCTTGTTGGAAGAACTTGAAGAAGGACAAAAAGGAGTAGGTGATAG
TACTGTTAGCTGGGGCCTTGAAGATGATGGAGACATGACACCTACATGGTGGACAGGCATGATTATTGGGCCACCAAGGA
CAAACTATGAAAACAGAATATATAGCCTGAAAGTAGAATGTGGATCTAAATACCCAGAAGTTCCTCCATCAGTTAGATTT
ATAACAAAAATTAATATGAATGGGATCAATAATTCCAGTGGAATGGTGGATGCACAGAGCATACCAGTATTAGCAAAATG
GCAAAATTTCTATAGAATTAAAGTCATACCTCAAGAGCTAAGATGTCTTATGAGGTCCAAAGAAAATATGAAGCCACCAG
AAGGACAGATGTACAACAACTAA

Alignment

ORF - retro_mmus_189 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECG
          M.VSTGV..P.NFRLLEELEEGQKGVGD.TVSWGLEDD.DMT.T.WTGMIIGPPRTNYENRIYSLKVECG
Retrocopy MTVSTGV--PHNFRLLEELEEGQKGVGDSTVSWGLEDDGDMTPTWWTGMIIGPPRTNYENRIYSLKVECG

Parental  SKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVILQELRRLMMSKENMKLPQPPEG
          SKYPE.PPSVRF.TKINMNGINNSSGMVDA.SIPVLAKWQN.Y.IKVI.QELR.LM.SKENMK...PPEG
Retrocopy SKYPEVPPSVRFITKINMNGINNSSGMVDAQSIPVLAKWQNFYRIKVIPQELRCLMRSKENMK---PPEG

Parental  QTYNN
          Q.YNN
Retrocopy QMYNN

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	23.48 RPM
SRP007412_cerebellum	0.00 RPM	18.80 RPM
SRP007412_heart	0.00 RPM	3.89 RPM
SRP007412_kidney	0.00 RPM	6.70 RPM
SRP007412_liver	0.00 RPM	5.24 RPM
SRP007412_testis	0.05 RPM	3.98 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_189 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	16:19023620..19028712

EST

No EST(s) were mapped for retro_mmus_189 retrocopy.

TSS

No TSS is located nearby retro_mmus_189 retrocopy 5' end.

Lab

retro_mmus_189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_189 has 0 orthologous retrocopies within eutheria group .

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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,