RetrogeneDB ID: retro_rnor_2924

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:59407591..59408060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif4h
• Ensembl ID: ENSRNOG00000001454
• Aliases: Eif4h, Wbscr1
• Description: Eukaryotic translation initiation factor 4H [Source:UniProtKB/Swiss-Prot;Acc:Q5XI72]

Sequence

>retro_rnor_2924
GACATTAATACCTATGATGATCAGGCCTAGAGCAGCATGAGTGGCTATAGAGAGTCCCATGACAGTGCTGGTGGTCATGG
GTCCAGAAGCCTGAAGGAGCTATCCACAGAGCCCCATCTACATAGCTTACATAGGAAATCTCCCTTTTAACACAAATCAG
GGTGACACAGATCTTATTTTTAAGGATCTCAGCATTCAGAGTGTATGGCTAATCAGACACAAAGACACAGACAAATTTAA
AGAGTTCTGCTGTGTAAAATTTGATGAGGTGGATTTCCTGAAGGAGGCTCTGACTTATGATGGAGCATGCTTTTGTGACC
GGTCACTTTGCGTAGCAGAATGCAAAAAGCAAGATAAAGGTGGCTTTAGATTCAGGAAAGGCAGACCTGATGACAGAGGA
ATGGGTGACTCTTGAGAATGTAGAATTGGATGATATTCCTGGGATGACTTCAACTCTGGCTACAGGGAT

Alignment

ORF - retro_rnor_2924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.7 %
• Parental protein coverage: 63.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFDTYDDRAYSSFGGGRGSRGSAGGHGSRSQKELPTEPP-YTAYVGNLPFNTVQGDIDAIFKDLSIRSVR
          D..TYDD.A.SS..G.R.S..SAGGHGSRS.KEL.TEP..Y.AY.GNLPFNT.QGD.D.IFKDLSI.SV.
Retrocopy DINTYDDQA*SSMSGYRESHDSAGGHGSRSLKELSTEPH>YIAYIGNLPFNTNQGDTDLIFKDLSIQSVW

Parental  LVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGMGGS
          L.R.KDTDKFK.FC.V.FDEVD.LKEALTYDGA...DRSL.V..AE..KQDKGGF.FRKG.PDDRGMG.S
Retrocopy LIRHKDTDKFKEFCCVKFDEVDFLKEALTYDGACFCDRSLCV--AECKKQDKGGFRFRKGRPDDRGMGDS

Parental  REPRGGWDSRDDFSSGYRD
          .E.R.G..S.DDF.SGYRD
Retrocopy *ECRIG*YSWDDFNSGYRD

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	281.98 RPM
SRP017611_kidney	0.00 RPM	197.48 RPM
SRP017611_liver	0.00 RPM	93.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2924 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2924 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2924 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924 ,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,