RetrogeneDB ID: retro_rnor_2133

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:24520120..24520641(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046387
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eef1e1
• Ensembl ID: ENSRNOG00000016390
• Aliases: None
• Description: eukaryotic translation elongation factor 1 epsilon-1 [Source:RefSeq peptide;Acc:NP_001099576]

Sequence

>retro_rnor_2133
ATGGCAGTGGTCTCGGAGTTGAGGCTACTAGAGAAGAGTCTGGGACTGAAGCCAGGGAGTAAGCACAGTGCTCAGGATGA
GGGACAGATTCCAGTCCTACAAACAAACAATGGGCCAAGTCTAATGGGATTGGGTACCATGGAGACCCATCTAGTCAAGC
ATGTCAGAAAGGAGCACTTTCGGGGGAGCACAACAGAAGAAAAGGTAATAGTTCAACAGTGGTTAGAGTTCAGGATCACT
TGGGTAGGTGGTCACTCCAGTAAACACGACACCCAGGCTCTGCTCAAGGGTCTTAATTCCTATCTTGAAGATAAAGTCTA
CCTTGGAGGACATAACATTACCATGACAGATATCCTATGGTACCATGGGCTCTACCACTTTATAGTTGGCCTGACAGTTC
AAGAAAAGGAGAACTATCTCGATGTGTCTCCTGGTTTTGTCACATTCAACATTACCCAGACATCAGGCAGCATCTGTCTA
GTGTTGTCTTCATCAAGAACAGACTGTATGCTAACTCCCAC

Alignment

ORF - retro_rnor_2133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAELRLLEKSLGLKPGNKYSAQGERQVPVLQTNNGPSLMGLSTIATHLVKEANKEHLLGSTAEEKAL
          MA...ELRLLEKSLGLKPG.K.SAQ.E.Q.PVLQTNNGPSLMGL.T..THLVK...KEH..GST.EEK..
Retrocopy MAVVSELRLLEKSLGLKPGSKHSAQDEGQIPVLQTNNGPSLMGLGTMETHLVKHVRKEHFRGSTTEEKVI

Parental  VQQWLEFRITRVDGHSSKEDTQTLLKDLNSYLEDKVYLAGHNTTLADILLYYGLHRFIVDLTVQEKEKYL
          VQQWLEFRIT.V.GHSSK.DTQ.LLK.LNSYLEDKVYL.GHN.T..DIL.Y.GL..FIV.LTVQEKE.YL
Retrocopy VQQWLEFRITWVGGHSSKHDTQALLKGLNSYLEDKVYLGGHNITMTDILWYHGLYHFIVGLTVQEKENYL

Parental  NVS-RWFCHIQHYPDIRQHLSSVVFIKNRLYANSH
          .VS..WFCHIQHYPDIRQHLSSVVFIKNRLYANSH
Retrocopy DVS<SWFCHIQHYPDIRQHLSSVVFIKNRLYANSH

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	21.28 RPM
SRP017611_kidney	0.00 RPM	21.49 RPM
SRP017611_liver	0.00 RPM	7.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2133 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017318	1 retrocopy	retro_amel_636,
Dasypus novemcinctus	ENSDNOG00000019203	1 retrocopy	retro_dnov_1550,
Erinaceus europaeus	ENSEEUG00000006156	1 retrocopy	retro_eeur_87,
Felis catus	ENSFCAG00000011622	1 retrocopy	retro_fcat_1075,
Macropus eugenii	ENSMEUG00000008960	1 retrocopy	retro_meug_1883,
Microcebus murinus	ENSMICG00000012636	1 retrocopy	retro_mmur_1404,
Myotis lucifugus	ENSMLUG00000007715	1 retrocopy	retro_mluc_1474,
Mustela putorius furo	ENSMPUG00000000588	1 retrocopy	retro_mputfur_486,
Pteropus vampyrus	ENSPVAG00000012305	2 retrocopies	retro_pvam_1374, retro_pvam_190,
Rattus norvegicus	ENSRNOG00000016390	5 retrocopies	retro_rnor_1682, retro_rnor_2013, retro_rnor_2132, retro_rnor_2133 , retro_rnor_785,