RetrogeneDB ID: retro_rnor_1682

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:216157580..216157989(-)
• Located in intron of: ENSRNOG00000021155

Retrocopy information

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

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_1682
ATGGCGGCCGCCTTGGAGCTGAGGCTTCTAGAGAAGAGTCTGGGACTGAAGCCGGGGAATAAGTACAGCACTCAGGGCGA
ATGACAGGTTCCAGTCCTACAGTCAAACAATGGCCCCAGTCTAATGAGATTGAGCACCATTGCAACCCATCTGGTCAAGC
AAGCCAACAGGGAGCACTTGCTGGGGAGCACTGCAGAAGAAAAGGCACTAGTTCAGCAGTGGTTAGAGTTCAGGATCACT
CGAGTAGATGGACACACCACAAAGAAGACACCAGACTCTGCTGAAGGATCTCAACTCCTATCTGGAAGACAAAATCTACC
TTGCAGGACATAACACTACCCTGGCGGACATCCTCCTGTACTACGGGTTCCACCGCTTTATAGTTGATGAGAGTTCAAGA
AAAGGAGAA

Alignment

ORF - retro_rnor_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 78.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAAELRLLEKSLGLKPGNKYSAQGERQVPVLQTNNGPSLMGLSTIATHLVKEANKEHLLGSTAEEKAL
          MAAA.ELRLLEKSLGLKPGNKYS.QGE.QVPVLQ.NNGPSLM.LSTIATHLVK.AN.EHLLGSTAEEKAL
Retrocopy MAAALELRLLEKSLGLKPGNKYSTQGE*QVPVLQSNNGPSLMRLSTIATHLVKQANREHLLGSTAEEKAL

Parental  VQQWLEFRITRVDGHSS-KEDT-QTLLKDLNSYLEDKVYLAGHNTTLADILLYYGLHRFIVDLTVQEKE
          VQQWLEFRITRVDGH...KEDT.QTLLKDLNSYLEDK.YLAGHNTTLADILLYYG.HRFIVD......E
Retrocopy VQQWLEFRITRVDGHTT<KEDT<QTLLKDLNSYLEDKIYLAGHNTTLADILLYYGFHRFIVDESSRKGE

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	0.14 RPM	21.28 RPM
SRP017611_kidney	0.00 RPM	21.49 RPM
SRP017611_liver	0.13 RPM	7.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1682 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1682 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,