RetrogeneDB ID: retro_rnor_1181

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:18597154..18597585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2v2
• Ensembl ID: ENSRNOG00000001829
• Aliases: Ube2v2, MMS2
• Description: Ubiquitin-conjugating enzyme E2 variant 2 [Source:UniProtKB/Swiss-Prot;Acc:Q7M767]

Sequence

>retro_rnor_1181
GTAGTGGTCTCCACAGGAGTTAAAGTTCCTCATAATTTTCGCTAGTTGGAAGAATTTGAAGAAGGACAAAAAGGAGTAGG
TGATGGTACAGTTAGCTGGGACCTTGAAGATGATGAAGACATAACACTTACAAGGTGGACAGGCATGATTATTGGGCCAC
CAAGGACAAGCTATGAAGACAGAATATATAACCCGAAGGTAGAATGGGGATCTAAACACCCAGAAGGTCCTCCATCAGTT
AGATATGTAACAAAGATTAATATGAATGGAATCAATAGTTCTAGTGGGATGGTGGATGCACGGAGCATACGAGTATAGCA
AAATGGCAAAATTCCTATAGCATTAAAGTTGTACTTCAAGAGCTAAGACCTCTTACGATGTTCAAAGAAAATATGAAGCT
TCCACAGCCACCAGAAGGACAGATGTACAAC

Alignment

ORF - retro_rnor_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.14 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECG
          ..VSTGVKVP.NFR.LEE.EEGQKGVGDGTVSW.LEDDED.TLTRWTGMIIGPPRT.YE.RIY..KVE.G
Retrocopy VVVSTGVKVPHNFR*LEEFEEGQKGVGDGTVSWDLEDDEDITLTRWTGMIIGPPRTSYEDRIYNPKVEWG

Parental  SKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPV-LAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPE
          SK.PE.PPSVR.VTKINMNGIN.SSGMVDARSI.V..AKWQNSYSIKVVLQELR.L.M.KENMKLPQPPE
Retrocopy SKHPEGPPSVRYVTKINMNGINSSSGMVDARSIRV<IAKWQNSYSIKVVLQELRPLTMFKENMKLPQPPE

Parental  GQTYN
          GQ.YN
Retrocopy GQMYN

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
SRP017611_brain	0.00 RPM	44.43 RPM
SRP017611_kidney	0.00 RPM	22.75 RPM
SRP017611_liver	0.00 RPM	13.65 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1181 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Nomascus leucogenys	ENSNLEG00000013382	1 retrocopy	retro_nleu_1671,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Rattus norvegicus	ENSRNOG00000001829	1 retrocopy	retro_rnor_1181 ,
Rattus norvegicus	ENSRNOG00000025580	21 retrocopies	retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,