RetrogeneDB ID: retro_ocun_1614

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:3737897..3739194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026983
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSOCUG00000006650
• Aliases: ETF1, ERF1
• Description: eukaryotic translation termination factor 1 (ETF1), mRNA [Source:RefSeq mRNA;Acc:NM_001082767]

Sequence

>retro_ocun_1614
ATGGTGGACTACCCCAGTGCTGCCGACAGGAACGTGGAAATCTGGAAGATCAAGAAGCTCATTAGAGCTTGAGCGGCCCG
CGCAATGGCACCAGCATGATATCATTGATCATTCCTCCCAAAGACCAGATTTCCCGAGTGGCAAAAAAATTTGGAACTGC
ATCCAACATTAAGTCACGAGTAAACCGCCTTTCAGTCCTGAGAAGCCATTACATCTGTACAACAAAGACTCAAACTTTAT
AACAAAGCACCTCCAAATGGTCTGGTTGTTTACTGTGGAACAATTGTAACAGAAAAAGGAAAGGAAAAGAAAGTCAACAT
TGACTTTGAACCTTTCAAACCAATTAATACGTCATTGTATTTGTGTGACAACAAATTCCATACAGAGGCTCTTACAGCAC
TACTTTCAGATGATAGCAAGTTTGGCTTCATTGTAATAGATGGTAGTGGTGCACTTTTTGGCACACTGCAGGGAAATACA
AGAGAAGTCCTGCACAAATTCACTGTGGATCTCCCAAAGAAACACGGTAGAGGAGGTCAGTCAGCCTTGCGTTTTGCCCG
TTTAGGAATGGAAAAGCGACACAACTATGTTCGGAAAGTAGCAGAGACCGCTGTACAGCTGTTTATTTCTGGGGACAAAG
TGAATGTGGCTGGTCTCGTTTTAGCTGGATCAGCTGACTTTAAAACTGAACTAAGTCAATCTGATATGTTTGATCAGAGG
TTGCAATCAAAAGTTTTAAAATTAGTTGATATATCCTATGGCAGTGAAAATGGATTCAACCAAGCTATTGAGTTATCTAC
TGAGGTCCTCTCCAACATGAAATTCATTCAAGAGAAGAAATTAATAGGACGATACTTTGATGAAATCAGTCAAGACACGG
GCAAGTACTGTTTTGGAGTTGAAGATACGCTAAAAGTTTTGGAAATGGGAGCCGTAGAAATTCTAATAGTCTATGAAAAT
TTGGATATAATGAGATACGTTCTTCATTGCCAAGGCACAGAAGAGGAGAAAATTCTTTACCTAACTCCAGAACAAGAGAA
GGATAAATCTCATTTCACAGACAAAGAGACAGGACAGGAACATGAGCTGATCGAGAGCATGCCCCTGTTGGAATGGTTTG
CTAACAACTATAAAAAAATTTGGAGCTACATTGGAAATTGTCACAGATAAGTCACAAGAAGGATCCCAGTTTGTGAAAGG
ATTTGGTGGAATTGGAGGTATCTTGCGGTACCGAGTAGATTTCCAGGGAATGGAATATCAAGGAGGAGACCATGAATTTT
TTGATCTTGATGACTAC

Alignment

ORF - retro_ocun_1614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADDPSAADRNVEIWKIKKLIK-SLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRL
          M.D.PSAADRNVEIWKIKKLI..SL...R.NGTSMISLIIPPKDQISRVAK.....FGTASNIKSRVNRL
Retrocopy MVDYPSAADRNVEIWKIKKLIR<SLSGPR-NGTSMISLIIPPKDQISRVAK----KFGTASNIKSRVNRL

Parental  SVLG-AITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTA
          SVL..AITSVQQRLKLYNK.PPNGLVVYCGTIVTE.GKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTA
Retrocopy SVLR>AITSVQQRLKLYNKAPPNGLVVYCGTIVTEKGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTA

Parental  LLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAET
          LLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARL.MEKRHNYVRKVAET
Retrocopy LLSDDSKFGFIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLGMEKRHNYVRKVAET

Parental  AVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNV
          AVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYG.ENGFNQAIELSTEVLSN.
Retrocopy AVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGSENGFNQAIELSTEVLSNM

Parental  KFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTP
          KFIQEKKLIGRYFDEISQDTGKYCFGVEDTLK.LEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTP
Retrocopy KFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKVLEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTP

Parental  EQEKDKSHFTDKETGQEHELIESMPLLEWFANNY-KKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRV
          EQEKDKSHFTDKETGQEHELIESMPLLEWFANNY.KKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRV
Retrocopy EQEKDKSHFTDKETGQEHELIESMPLLEWFANNY>KKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRV

Parental  DFQGMEYQGGDDEFFDLDDY
          DFQGMEYQGGD.EFFDLDDY
Retrocopy DFQGMEYQGGDHEFFDLDDY

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	0.11 RPM	53.04 RPM
SRP017611_kidney	0.10 RPM	79.97 RPM
SRP017611_liver	0.00 RPM	51.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1614 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1614 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,