RetrogeneDB ID: retro_rnor_2122

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:248179028..248179660(-)
• Located in intron of: ENSRNOG00000036911

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3s6ip
• Ensembl ID: ENSRNOG00000011020
• Aliases: Eif3l, Eif3s6ip
• Description: eukaryotic translation initiation factor 3, subunit 6 interacting protein [Source:RefSeq peptide;Acc:NP_001029306]

Sequence

>retro_rnor_2122
CTGGAATGTGCACATTCTCTTGTAGACAAATCCAACATCAGCTGGCAACTGGAAGTCTACACCAGTGGAGGTGACCCCAA
AAGTGTGGCTGGAGAATATGGATGACACTCCCTCTGCAAGATGCTTGGCTACTTCAGCCTGGTGGGGCTTCTGCACCTGC
ATTCTCTACTGAGGCATTACTACCAGGCTATCAAGGTGCTGGAGAATATTGAGCTGAACAAGAAAAGCATGTATTCACGT
GTGCCTGAGTGCCATGTTACCACCTACTATTATGTTGGTTTTGCATATTTAATGATGTGTCGATACCAAGATGCTATCCA
GGTCTTTGCCAACATCCTCTTATACACCCAGAGGACCAAGAGTATGTTCCAGAGAACCACATACAAGTATGAAATGATTA
ACAAGCAGAATGAGCAGATGCATGCTCTGTTGGCCATTGCTCTCACCATGTACCCCATGAGGACTGACGAGAGTATACAC
CTCCAGCTGCGGGAGAAATACGGCGACAAGAAGCTGTGCATGCAGAAGGGCGACCCCCGGGTCTATGAGGAACTTTTCAG
CTATGCCTGCCCAAGTTCCTGTCGCCTGTGGTGCCTAACTACGACAGTGTGCATCCTAACTACCTCAAAGAG

Alignment

ORF - retro_rnor_2122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENI
          L...HSLVDKSNI..QLEVYTSGGDP.SVAGEYG.HSL.KMLGYFSLVGLL.LHSLL..YYQAIKVLENI
Retrocopy LECAHSLVDKSNISWQLEVYTSGGDPKSVAGEYG*HSLCKMLGYFSLVGLLHLHSLLRHYYQAIKVLENI

Parental  ELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMINKQNEQM
          ELNKKSMYSRVPEC.VTTYYYVGFAYLMM.RYQDAI.VFANILLY.QRTKSMFQRTTYKYEMINKQNEQM
Retrocopy ELNKKSMYSRVPECHVTTYYYVGFAYLMMCRYQDAIQVFANILLYTQRTKSMFQRTTYKYEMINKQNEQM

Parental  HALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYAC-PKFLSPVVPNYDNVHPNYH
          HALLAIALTMYPMR.DESIHLQLREKYGDK.L.MQKGDP.VYEELFSYAC.PKFLSPVVPNYD.VHPNY.
Retrocopy HALLAIALTMYPMRTDESIHLQLREKYGDKKLCMQKGDPRVYEELFSYAC<PKFLSPVVPNYDSVHPNYL

Parental  KE
          KE
Retrocopy KE

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	41.70 RPM
SRP017611_kidney	0.00 RPM	98.18 RPM
SRP017611_liver	0.00 RPM	52.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2122 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Rattus norvegicus	ENSRNOG00000011020	1 retrocopy	retro_rnor_2122 ,