RetrogeneDB ID: retro_rnor_2935

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:67496095..67497402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Etf1
• Ensembl ID: ENSRNOG00000019450
• Aliases: None
• Description: Eukaryotic peptide chain release factor subunit 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5U2Q7]

Sequence

>retro_rnor_2935
ATGGCGGACGACCCCAGTGCTGCGGATAGGAACATGGAGATCTGGAAGATTAAGAAGTTCATTAAGAGCTTGGAGGCGGC
CGAGGCAATGGCACGAGCATGATATCGCTGATCATTCCTCTCAAAGACCAGATTTCATGAGTTGCAAAAATGTTAGCAGG
TGAGTTTGGAACTGCATCTAACATTAAGTCACAAGTAAACCGCCTTTCAGTCCTGGGAGCCATCACATCTGTACAACAGA
GAATCAAACATTATAACAAAGTACCTCCAAATGGTCTGGTTGTTTACTGTGGAACAACTGTAACAGAAGAAGGAAAGGAA
AAGAAAGCCAACATTGACTTTGAACCTTTCAAACCAATTAACACATCATCGTATTTGTGCAACAACTTTCATACAGAGGC
TCTTACAGCGTTACTTTCAGATGACAGCAAGTTTGGTTTTATTGTGATTGACGGCAGTGGTGCTCTTTTTGGCACGCTCC
AAGGAAACACCAGAGAAGTCCTGCACAAATTCACTGTAGATCTCCCAAAGAAACACGGCAGAGGAGGTCAATCAGCCTTG
CGTTTGCCCGTTTAAGAATGGAAAAGCGACATAACTATGTTCAGAAAGTAGCAGAGACTGCTGTGAAGCTGTTTATTTCT
GGAGACAAAGTGAATGTGACTGGTTTGGTTTTAGCTGGATCAGCTGACTTTAAAACTGAACTAAGTCAATCTGACATGTC
TGACCAGAGGTTGCAATCTAAAGTTTTAAAATTAGTTGATATATCCTATGGTGGTGAAAATGGATTCAACCAAGCTATTG
AATTTTCTACTGAAGTTCTCTCCAACGTGAAGTTCATTCAAGAGAAGAAATTAATAGGGCGATACTTTGATGAAATTAGC
CAGGACACAGGCAAGTACTGTGTTGGAGTTGAAGATACACTAAAGGCTTTGGAAATGGGAGCTGTAGAGATTCTAATAGT
CTATGAAAATTATGGATATAATGAGATACGTTCTTCATCACTACAGTACAGAAGAGGAAAAAATTCTCTATTTAACTCCA
GAACAAGGAAGGATAAATCTCACTTCACAGACAAAAAGACTGGACAGGAACATGAGCTGATAGAGACCATGCCCCTCTTG
GAATGGTTTGCTAACAACTATAAAAAATTTGGAGCTACACTAGAAATTGTCACAGTTAAGTCACAAGAAGGATCACAGTT
TGTGAAAGGATTTGGTGGAATTGGAGGTATCTTGCCGTACTGAGTAGATTTCCAGGGAATGGAATACCAAGGAGGAGATG
ACGAATTTTTTTGACCTTGATGACTAC

Alignment

ORF - retro_rnor_2935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MADDPSAADRNVEIWKIKKLIKSLEAA-RGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRL
          MADDPSAADRN.EIWKIKK.IKSLEAA.RGNGTSMISLIIP.KDQIS.VAKMLA.EFGTASNIKS.VNRL
Retrocopy MADDPSAADRNMEIWKIKKFIKSLEAA<RGNGTSMISLIIPLKDQIS*VAKMLAGEFGTASNIKSQVNRL

Parental  SVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTAL
          SVLGAITSVQQR.K.YNKVPPNGLVVYCGT.VTEEGKEKK.NIDFEPFKPINTS.YLC.N.FHTEALTAL
Retrocopy SVLGAITSVQQRIKHYNKVPPNGLVVYCGTTVTEEGKEKKANIDFEPFKPINTSSYLCNN-FHTEALTAL

Parental  LSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALR-FARLRMEKRHNYVRKVAET
          LSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALR.FARLRMEKRHNYV.KVAET
Retrocopy LSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALR<FARLRMEKRHNYVQKVAET

Parental  AVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNV
          AV.LFISGDKVNV.GLVLAGSADFKTELSQSDM.DQRLQSKVLKLVDISYGGENGFNQAIE.STEVLSNV
Retrocopy AVKLFISGDKVNVTGLVLAGSADFKTELSQSDMSDQRLQSKVLKLVDISYGGENGFNQAIEFSTEVLSNV

Parental  KFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYEN-LDIMRYVLHCQGTEEEKILYLT
          KFIQEKKLIGRYFDEISQDTGKYC.GVEDTLKALEMGAVEILIVYEN..DIMRYVLH...TEEEKILYLT
Retrocopy KFIQEKKLIGRYFDEISQDTGKYCVGVEDTLKALEMGAVEILIVYEN>MDIMRYVLHHYSTEEEKILYLT

Parental  PEQ-EKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYR
          PEQ..KDKSHFTDK.TGQEHELIE.MPLLEWFANNYKKFGATLEIVT.KSQEGSQFVKGFGGIGGIL.Y.
Retrocopy PEQ<RKDKSHFTDKKTGQEHELIETMPLLEWFANNYKKFGATLEIVTVKSQEGSQFVKGFGGIGGILPY*

Parental  VDFQGMEYQGGDDE-FFDLDDY
          VDFQGMEYQGGDDE.FFDLDDY
Retrocopy VDFQGMEYQGGDDE>FFDLDDY

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	44.00 RPM
SRP017611_kidney	0.00 RPM	72.43 RPM
SRP017611_liver	0.07 RPM	54.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2935 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2935 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935 ,