RetrogeneDB ID: retro_rnor_1067

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:80612094..80612829(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000008241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif6
• Ensembl ID: ENSRNOG00000049497
• Aliases: Eif6, Itgb4bp, eIF-6
• Description: Eukaryotic translation initiation factor 6 [Source:UniProtKB/Swiss-Prot;Acc:Q3KRD8]

Sequence

>retro_rnor_1067
ATGGTGGTCAGAGCGTCGTTCGAGAACAACTGTGAGGTCAGTTGTTTTGCCAGACTCACTAACACCTACTCCCTGGTGGC
CATTGGAGGATCAGAGAACTTCTATAGTGTGTTCGAGGGCGAGCTCTCTGATACCATTCCTGTAGTGCACGCGTCCATCG
CCAGCTGCCGAATCATCGGGCGGGGCACATCTGTGTGGGGAACAGGCATGGGCTACTGGTACCCAACAACCACCACTGAC
CAGGAGCTACAGCATATCCACGACAGCCTTCTGGATTCAGTGCAGATACGGCGAGTAGAGGAGGGGCTCTCAGCCCTTGA
CAATGTCACCACCTGCAATGACTATGTGGCCTTGGTCCACCCAGACTTGGACAGGGAGACAGAAGAAATCCTGGCTGGTG
TGCTCAAGGTGGAAGTCTTGACAGTTGCTGACCAGGTGTTAGTTGGAAGCTATTGTGTCTTCAGTAATCAAGGAGGTCTG
GTGTACCCTAAAACTTCAATCGAGGACCAGGATGAGTTGTCCTCCCCTCTTCAGGTCCCCCTTGTGGCAGGTACTGTGAA
CCGAGGGAGCGAAGTGATTGCTGCTGGGATGGTAGTGAATGATTGGTGTGCTTTCTGTGGTCTGGACACAACCAGCACAG
AGCTGTCAGTGGTGGAGAGCGTCTTCAAGCTAAATGAAGCCAAGCCTAGCACCATTGCCACCAGCATGCGGGACTCCCTC
ATTGACAGACTCACA

Alignment

ORF - retro_rnor_1067 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVRASFENNCEVGCFAKLTNTYCLVAIGGSENFYSVFEGELSDTIPVVHASIAGCRIIGR--MCVGNRH
          M.VRASFENNCEV.CFA.LTNTY.LVAIGGSENFYSVFEGELSDTIPVVHASIA.CRIIGR.....G...
Retrocopy MVVRASFENNCEVSCFARLTNTYSLVAIGGSENFYSVFEGELSDTIPVVHASIASCRIIGRGTSVWGTGM

Parental  GLLVPNNTTDQELQHIRNSLPDSVQIRRVEERLSALGNVTTCNDYVALVHPDLDRETEEILADVLKVEVF
          G...P..TTDQELQHI..SL.DSVQIRRVEE.LSAL.NVTTCNDYVALVHPDLDRETEEILA.VLKVEV.
Retrocopy GYWYPTTTTDQELQHIHDSLLDSVQIRRVEEGLSALDNVTTCNDYVALVHPDLDRETEEILAGVLKVEVL

Parental  RQTVADQVLVGSYCVFSNQGGLVHPKTSIEDQDELSSLLQVPLVAGTVNRGSEVIAAGMVVNDWCAFCGL
          ..TVADQVLVGSYCVFSNQGGLV.PKTSIEDQDELSS.LQVPLVAGTVNRGSEVIAAGMVVNDWCAFCGL
Retrocopy --TVADQVLVGSYCVFSNQGGLVYPKTSIEDQDELSSPLQVPLVAGTVNRGSEVIAAGMVVNDWCAFCGL

Parental  DTTSTELSVVESVFKLNEAKPSTIATSMRDSLIDSLT
          DTTSTELSVVESVFKLNEAKPSTIATSMRDSLID.LT
Retrocopy DTTSTELSVVESVFKLNEAKPSTIATSMRDSLIDRLT

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	35.66 RPM
SRP017611_kidney	0.00 RPM	65.80 RPM
SRP017611_liver	0.07 RPM	27.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1067 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1067 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007169	1 retrocopy	retro_meug_26,
Monodelphis domestica	ENSMODG00000019689	1 retrocopy	retro_mdom_1926,
Mus musculus	ENSMUSG00000027613	1 retrocopy	retro_mmus_2569,
Oryctolagus cuniculus	ENSOCUG00000010588	1 retrocopy	retro_ocun_1935,
Rattus norvegicus	ENSRNOG00000049497	1 retrocopy	retro_rnor_1067 ,