RetrogeneDB ID: retro_rnor_2343

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:27915323..27915759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2e1
• Ensembl ID: ENSRNOG00000008794
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:MGI Symbol;Acc:MGI:107411]

Sequence

>retro_rnor_2343
TCAAAGCTCCTATACACCATTGCTAAGAAGGAACTGGCTGACATCACTTTAGAACCTCCACTAAATTCCAGCACCAGTCC
CAAAGGTCACATCTCTGAATAGAGATCAACCATTCTTGGGCTTCCAAGATCTGTTTATGAGGGTGGTGTCTTCTACCTCA
ATATCAGTTTTACACTACGATATTCTTTCTAGTCTCCAAAAGTTACATTTTTTTACAAGAATTTATCACTGTACTATCAA
TAGCCAATGAGTTATTTGCTTATACATATTGAAAGACAACTGGAGTCTGTCACTCCCTATCTCAAACGTCTTCTTTTTCT
GCTCACTCCTTATAGAATGCAATCCTGCTGACTCTTTTGTTGGAATTATTGCCACCCACTGTATGACAAACATAGCAGAA
CATGGCAGAATGCCTAGGCAGTGAACCAAGAGATAC

Alignment

ORF - retro_rnor_2343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.21 %
• Parental protein coverage: 96.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPP
          SKLL.T.AK...KELADITL.PP.N.S..PKG..I.E.RSTILG.P.SVYEGGVF.L.I.FT..Y.F..P
Retrocopy SKLLYTIAK---KELADITLEPPLNSSTSPKG-HISE*RSTILGLPRSVYEGGVFYLNISFTLRYSF*SP

Parental  KVTFR-TRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEH
          KVTF..TRIYHC.INSQ.VICL.ILKDNWS..L.IS.V....CSLL..CNPAD..VG.IAT..MTN.AEH
Retrocopy KVTFF>TRIYHCTINSQ*VICLYILKDNWSLSLPISNVFF-FCSLLIECNPADSFVGIIATHCMTNIAEH

Parental  DRMARQWTKRY
          .RM.RQ.TKRY
Retrocopy GRMPRQ*TKRY

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	49.54 RPM
SRP017611_kidney	0.00 RPM	37.05 RPM
SRP017611_liver	0.00 RPM	15.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2343 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Dipodomys ordii	ENSDORG00000015441	1 retrocopy	retro_dord_785,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Gorilla gorilla	ENSGGOG00000008393	1 retrocopy	retro_ggor_76,
Loxodonta africana	ENSLAFG00000004150	1 retrocopy	retro_lafr_320,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Otolemur garnettii	ENSOGAG00000007527	3 retrocopies	retro_ogar_2029, retro_ogar_2566, retro_ogar_626,
Pan troglodytes	ENSPTRG00000014693	1 retrocopy	retro_ptro_68,
Pteropus vampyrus	ENSPVAG00000001773	1 retrocopy	retro_pvam_1451,
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,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,