RetrogeneDB ID: retro_rnor_539

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:247159806..247160205(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2d3
• Ensembl ID: ENSRNOG00000013741
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 D3 [Source:RefSeq peptide;Acc:NP_112516]

Sequence

>retro_rnor_539
AATAATTTGGCATATGGCCTTCCGGCCCAGTGTTCTGCAGGTCCAGTTGGAGAAGATAAGTTTCCCTGGAAAGCCACAAT
TATGGGACCTAATTTCAACCCATATCAAGGTGGTGTATTCTTTCTGTTAATTTATTTTCCTAAAGACTACTCCTTCAAGT
CACCTAAGGTTGCATTTACAACAAAAATTTATCATCTAAATATTAACTGTAATGGCAGAATTTGTCTTAATACTCTAAGT
TCACAGTGGTCTCCTGGTTTATCTATTTTTAAAGTTCTCTTATGCATTTGTTCACTGCTATGTGATTGAAGTCCAGGTGG
TCCCCTAGTGCCAGAGATTGCATGAATCTCTAAAACAGATAAGTACCACAGAATATTTCAGAAACGGACTCAAGTATAC

Alignment

ORF - retro_rnor_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.63 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINS
          ..LA...PAQCSAGPVG.D.F.W.ATIMGPN..PYQGGVFFL.I.FP.DY.FK.PKVAFTT.IYH.NIN.
Retrocopy NNLAYGLPAQCSAGPVGEDKFPWKATIMGPNFNPYQGGVFFLLIYFPKDYSFKSPKVAFTTKIYHLNINC

Parental  NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKY
          NG.ICL..L.SQWSP.L.I.KVLL.ICSLLCD..P..PLVPEIA.I.KT..DKY.RI....TQ.Y
Retrocopy NGRICLNTLSSQWSPGLSIFKVLLCICSLLCD*SPGGPLVPEIA*ISKT--DKYHRIFQKRTQVY

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	133.66 RPM
SRP017611_kidney	0.00 RPM	209.77 RPM
SRP017611_liver	0.00 RPM	130.51 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_539 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_539 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1818

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Dasypus novemcinctus	ENSDNOG00000009320	30 retrocopies	retro_dnov_1061, retro_dnov_1125, retro_dnov_113, retro_dnov_114, retro_dnov_1167, retro_dnov_1193, retro_dnov_1198, retro_dnov_1257, retro_dnov_141, retro_dnov_1544, retro_dnov_1752, retro_dnov_1761, retro_dnov_1831, retro_dnov_1862, retro_dnov_1912, retro_dnov_1934, retro_dnov_1995, retro_dnov_2084, retro_dnov_2135, retro_dnov_2289, retro_dnov_2362, retro_dnov_2457, retro_dnov_2622, retro_dnov_436, retro_dnov_574, retro_dnov_750, retro_dnov_795, retro_dnov_83, retro_dnov_889, retro_dnov_917,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Ochotona princeps	ENSOPRG00000011695	9 retrocopies	retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602, retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539 , retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,