RetrogeneDB ID: retro_rnor_1731

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:28439255..28439830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3g
• Ensembl ID: ENSRNOG00000020619
• Aliases: Eif3g, Eif3s4
• Description: Eukaryotic translation initiation factor 3 subunit G [Source:UniProtKB/Swiss-Prot;Acc:Q5RK09]

Sequence

>retro_rnor_1731
ATGCCGACTGGAGACCTTTACAAAAGCCCAGCAGGGCTGACCGAGTGGAAGAGGAAGGAGAGGATGACAAGGGTGTCACC
AGCGAGCTCCTGAAAGGAATCCCTCTGCCCACCAGTGACACCAGTCCAGAGCCTGAGTTACAGCCTGGAGACCCACTGCT
ACCTCCCAAGGAAGCCATCAGTGGGAAAATGAAGATGGTGACAGAGTACAAGATAGAGGAAGATGGGAAATTCTAGATTG
TCAGAACCCTCAGGTTTGAGACCCAGAAAGCATCAAAGGCTGTGGCAAAGACGAAGAAATGGAAGAATTGGCAACTCGGA
GTTTGACCCACCGGGGCCCAGTGTGGCCACTACCACAGTCAGTGATGACGTCTCCATGACATCCATCACTGGCAAAGAGG
ACCTAAACTGGAGGAGGAGGACCCAAAGAACAAGCTCAAGGGCCAGAAGATCATGTCCTGCCGCATTTCCCAGGGTGACC
ACTGGACCATCTACTGCCCCTACAAGGACACACTAGAACCCATGCAGAAGGAGCTGGCTGAGCAGCTGGACCTGTCTACA
GGGGAGAAAGAGAAA

Alignment

ORF - retro_rnor_1731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 60.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPTGDFDS-KPSWADQVEEEGEDDKCVTSELLKGIPLPTGDTSPEPELLPGDPLPPPKEVINGNIKTVTE
          MPTGD....KPS.AD.VEEEGEDDK.VTSELLKGIPLPT.DTSPEPEL.PGDPL.PPKE.I.G..K.VTE
Retrocopy MPTGDLYK<KPSRADRVEEEGEDDKGVTSELLKGIPLPTSDTSPEPELQPGDPLLPPKEAISGKMKMVTE

Parental  YKVEEDGKKFKIVRTFRIETRKASKAVA-RRKNWKKFGNSEFDPPGPNVATTTVSDDVSMTFITSKEDLN
          YK.EEDGK.F.IVRT.R.ET.KASKAVA.RR.N....GNSEFDPPGP.VATTTVSDDVSMT.IT.KEDLN
Retrocopy YKIEEDGK-F*IVRTLRFETQKASKAVA>RRRNGR-IGNSEFDPPGPSVATTTVSDDVSMTSITGKEDLN

Parental  -CQEEEDPMNKLKGQKIVSCRICKGDHWTTRCPYKDTLGPMQKELAEQLGLSTGEKEK
          ...EE.DP.NKLKGQKI.SCRI..GDHWT..CPYKDTL.PMQKELAEQL.LSTGEKEK
Retrocopy <LEEE-DPKNKLKGQKIMSCRISQGDHWTIYCPYKDTLEPMQKELAEQLDLSTGEKEK

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	50.04 RPM
SRP017611_kidney	0.00 RPM	55.34 RPM
SRP017611_liver	0.00 RPM	25.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1731 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1731 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021436	1 retrocopy	retro_ecab_713,
Myotis lucifugus	ENSMLUG00000014196	1 retrocopy	retro_mluc_2407,
Otolemur garnettii	ENSOGAG00000014463	3 retrocopies	retro_ogar_101, retro_ogar_1577, retro_ogar_1661,
Rattus norvegicus	ENSRNOG00000020619	1 retrocopy	retro_rnor_1731 ,