RetrogeneDB ID: retro_rnor_2879

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:147253793..147254485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3e
• Ensembl ID: ENSRNOG00000027690
• Aliases: Eif3e, Eif3s6
• Description: Eukaryotic translation initiation factor 3 subunit E [Source:UniProtKB/Swiss-Prot;Acc:Q641X8]

Sequence

>retro_rnor_2879
CTGGTCTCTGTTTGTTTGTTTTTTTTTTTCAGCCATCCAAAAGGACATGATAATATTATTGATCTCTTCCTTTACCAACT
ACAGTACCTTAATGCAATTCAGAAAATGTGTCCACATAGTCTCCGCTATTTGACCACTGCCATAATAACCAACAAAGATA
TGCAGAAACGCTGGCAGGTGCTGAAAGATCTAGTGAAAGTTATTCAACAGGAGTCTTACACATATAAAGAACCAATTACA
GAATTTGTTGAATGCCTATATGTTAACTTTGATTTTGATGGAGCTCAGAAAAAGGTAAGAGAATGTGAATTAGTGCCTGT
GAATGACTTCTTCCTGGTAGCATGTCTTGAGGACTTCATTGAGAATGTCCGTCTCTTCATATTTGAGAGTTTCTATCGTA
TCCACCAGTGTATCAGCATTAATATGTTAGCAGAGAAACTTAATATGACTCCAAGAGAAGCTGAAAGATGGATTGTGAAT
TTGATTAGAAATGTGAGGCTGGATGCCAGGACTGATTCTAAACTAGGTTATGTGGTAATGGGCAACAATGCAGTCTCACC
CTACCAGCAAGGGATTGAAAAGACTAAAAGTCTTTGTTGTAGAAGCCAAATATTGGCCATGAATATAGAAAAGAAACTTA
ACAGAACAGTAGACCAGAGGCTCCCAACTGGGCAACCCAAGATTCCGGCTTC

Alignment

ORF - retro_rnor_2879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 51.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIHWSLFVFFNHPKGRDNIIDLFLYQPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQ
          L....L.....HPKG.DNIIDLFLYQ.QYLNAIQ.MCPH.LRYLTTA.ITNKD..KR.QVLKDLVKVIQQ
Retrocopy LVSVCLXXXXSHPKGHDNIIDLFLYQLQYLNAIQKMCPHSLRYLTTAIITNKDMQKRWQVLKDLVKVIQQ

Parental  ESYTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISI
          ESYTYK.PITEFVECLYVNFDFDGAQKK.RECE.V.VNDFFLVACLEDFIEN.RLFIFE.F.RIHQCISI
Retrocopy ESYTYKEPITEFVECLYVNFDFDGAQKKVRECELVPVNDFFLVACLEDFIENVRLFIFESFYRIHQCISI

Parental  NMLADKLNMTPEEAERWIVNLIRNARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFRSQMLAMNIE
          NMLA.KLNMTP.EAERWIVNLIRN.RLDA..DSKLG.VVMGNNAVSPYQQ.IEKTKSL..RSQ.LAMNIE
Retrocopy NMLAEKLNMTPREAERWIVNLIRNVRLDARTDSKLGYVVMGNNAVSPYQQGIEKTKSLCCRSQILAMNIE

Parental  KKLN-QNSRSEAPNWATQDSGF
          KKLN.QNSR.EAPNWATQDSGF
Retrocopy KKLN<QNSRPEAPNWATQDSGF

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	25.52 RPM
SRP017611_kidney	0.00 RPM	39.15 RPM
SRP017611_liver	0.00 RPM	21.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2879 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2879 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879 , retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,