RetrogeneDB ID: retro_rnor_1508

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:90067093..90067509(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2r2
• Ensembl ID: ENSRNOG00000010727
• Aliases: None
• Description: None

Sequence

>retro_rnor_1508
GTAGATGACCCACAGAGTGGAGAGCTGCCCTCTGAAAGGTGGAATCCTACTCAGAATGTGTGGACTGTCCTGCTGAGTGT
AATCTCCCTGCTTAATGAGCCCAACACCTTTTCTCCAGCTAATGTGGATGCTTCAGTCATGTTCAGGAAATGGAGGGACA
GCGAAGAAAGGACAAGGAGTATGCTGAGATCATTAGGAAACAGGTCTCAGCCACGAAAGCTGAAGCAGAAAAGGATGGAG
TGAAATTCCCCACAACCCTGGCAGAATACTGCACCAAAACTAAAGTGCCTTCCAATGACAACAGCTCAGATTTGCTCTAT
GATGACCTGTATGACGACGACATTGATGACGAAGATGTGGAGGAAGAAGATGCCTACTGTTATGATGATGATGACGACTC
TGGAAATGAGGAGAGT

Alignment

ORF - retro_rnor_1508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 57.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDS-KGKDKEYAEIIRKQV
          VDDPQSGELPSERWNPTQNV.T.LLSVISLLNEPNTFSPANVDASVMFRKWRDS...KDKEYAEIIRKQV
Retrocopy VDDPQSGELPSERWNPTQNVWTVLLSVISLLNEPNTFSPANVDASVMFRKWRDS<RRKDKEYAEIIRKQV

Parental  SATKAEAEKDGVKVPTTLAEYCIKTKVPSNDNSSDLLYDDLYDDDIDDEDEEEEDADCY-DDDDSGNEES
          SATKAEAEKDGVK.PTTLAEYC.KTKVPSNDNSSDLLYDDLYDDDIDDED.EEEDA.CY.DDDDSGNEES
Retrocopy SATKAEAEKDGVKFPTTLAEYCTKTKVPSNDNSSDLLYDDLYDDDIDDEDVEEEDAYCYDDDDDSGNEES

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	67.08 RPM
SRP017611_kidney	0.00 RPM	54.01 RPM
SRP017611_liver	0.00 RPM	43.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1508 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1508 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211, retro_ogar_2040, retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496, retro_rnor_317, retro_rnor_970,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508 ,