RetrogeneDB ID: retro_rnor_2118

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:245035893..245036334(-)
• Located in intron of: ENSRNOG00000001808

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nsmce2
• Ensembl ID: ENSRNOG00000003964
• Aliases: Nsmce2, RGD1305156
• Description: E3 SUMO-protein ligase NSE2 [Source:UniProtKB/Swiss-Prot;Acc:Q4V8A0]

Sequence

>retro_rnor_2118
ATGCCAGGACGTTCCAGTACAAATTCAGGTTCTACTCGTTGTATATCCTACAGTGGTGTAGAGTCAGCTCCCTCCTCCTT
AAAAAACTTCCAGTCCTGTATCAGCTCTGGAATGGGCACAGTTTCTAGTGTTGCCTTGGACTTTGTGGAGACACAAACTG
AAGTGAGTAGTGAGTACAGTGTGGACAAGGCCATGGTTGAATTTGCTAAGATGGATGGAGAACTATAAACCATTATGTTT
AGGCTGTCCAGTCTAAAATAAATCGTGTAAAAGAAGAACGTCCAGAAAATACCAGATTTAAAATTACTGGTGGAGAAGAA
ATTTTTGGCTTTACAGGATAAGAACTCTGGCGCTGACTTTAAAGAGAATGAAAAGTTGATGCAGTTTAAGCAGTAGCTGT
GGGAGCTGAAAAAGCAATATGGTATTCATGCAGACAGAGAA

Alignment

ORF - retro_rnor_2118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.23 %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGRSSTNSGSTRYISFSGVESALSSLKTFQSCISSGMDTVSSVALDLVETQTEVSSEYSMDKAMVEFAK
          MPGRSSTNSGSTR.IS.SGVESA.SSLK.FQSCISSGM.TVSSVALD.VETQTEVSSEYS.DKAMVEFAK
Retrocopy MPGRSSTNSGSTRCISYSGVESAPSSLKNFQSCISSGMGTVSSVALDFVETQTEVSSEYSVDKAMVEFAK

Parental  MDRELNHYVKAVQSTINHVKEERPEKVPDLKLLVEKKFLALQDKNSDADFKENEKFVQFKQQLRELKKQY
          MD.EL........S....V......K.PDLKLLVEKKFLALQDKNS.ADFKENEK..QFKQ.L.ELKKQY
Retrocopy MDGEL*TIMFRLSSLK*IV*KKNVQKIPDLKLLVEKKFLALQDKNSGADFKENEKLMQFKQ*LWELKKQY

Parental  GIHADRE
          GIHADRE
Retrocopy GIHADRE

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	0.86 RPM	9.56 RPM
SRP017611_kidney	0.28 RPM	12.91 RPM
SRP017611_liver	0.81 RPM	7.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2118 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118 , retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,