RetrogeneDB ID: retro_rnor_1548

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:165347129..165348050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif3i
• Ensembl ID: ENSRNOG00000047185
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit I [Source:MGI Symbol;Acc:MGI:1860763]

Sequence

>retro_rnor_1548
AAGATTTCTTTTGAAGGAGACCTCCTCTTCACTGTGACCAAAGCCCCTATGGTCAATGTGTGGTACTATGTCAATGGCGA
GAGGCTAGGCACCTACATGGGCCACACTGGAGCTGTGTGGTGTGTGGACGCTGACTGGGACACCAAGCATGCCCTTACTG
GCTCAGCTGACAACAGCTGTCGTCTCTGGGACTGTGAAACAGGGAAGCAGTTGGCCCTACTCAAGACCAACTCAGCCGTG
CGGACCTGTGGCTTTGACCTTGGGGGCAACATCATCATGTTCTCCACAGACAAGCAGATGGGGTATCAGTGTTTTGTGAG
CTTCTTTGATCTGCGGGATCCAAGCCAGATTGATAGCAACGAGCCCTACATGAAGATCCCCTGTAATGATTCCAAGATCA
CCAGTGCTGTTTGGGGTCCCCTGGGGGAGTGCATCGTCGCAGGCCACGAGAGCAGAGAGCTCAACCAGTACAGCGCCAAG
TCTGGAGAGGTGTTGGTGAACGTTAAGGAGTACTCCCGGCAGATCAATGACATCCAGTTGTCTAGAGGCATGACCATGTT
TGTCACCGCATCCAAGGACAACACAGCTAAGCTCTTCGACTCCACAAGTCTTGAACATCATTAGACTTTCCGAACAGAAC
GTCCCGTCAACTCGGCTGCTCTCTCTCCCAACTATGACCATGTGGTGCTGGGAGGTGGTCAGGAAGCCATGGATGTGACC
ACAACCTCCACCAGGATTGGCCAGTTTGAGGACAGGTTCTTCCATTTGGCTTTTGAGGAAGAGTTTGGAAGAGTCAAGGG
CCACTTTGGACCTATCAACAGCGTTGTCTTCCGTCCTGATGGCAACAGCAGCGGTGGCGAAGACGGCTATGTCCGCATCC
ACTACTTCGACCCTCAGTACTTCGAGTTCGAGTTTGAGGCC

Alignment

ORF - retro_rnor_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 95.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDADWDTKHVLTGSADNSCRLWDCETGKK
          K...EGDLLFTV.K.P.VNVWY.VNGERLGTYMGHTGAVWCVDADWDTKH.LTGSADNSCRLWDCETGK.
Retrocopy KISFEGDLLFTVTKAPMVNVWYYVNGERLGTYMGHTGAVWCVDADWDTKHALTGSADNSCRLWDCETGKQ

Parental  WPTTVYLSKQRQCTCLSKYNMFRKTRDKFIGGECFIKFMDVLSVCTLAYQEMALHPIGSYRQLRAAMWVL
          .......S..R.C......N......DK..G..CF..F.D..........E..............A.W..
Retrocopy LALLKTNSAVRTCGFDLGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDSNEPYMKIPCNDSKITSAVWGP

Parental  GIECRTSGRAASTLNCYTVFSGEVLVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTSLEHQKTF
          ..EC...G.....LN.Y...SGEVLVNVKE.SRQINDIQLSR.MTMFVTASKDNTAKLFDSTSLEH..TF
Retrocopy LGECIVAGHESRELNQYSAKSGEVLVNVKEYSRQINDIQLSRGMTMFVTASKDNTAKLFDSTSLEHH*TF

Parental  RTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRVKGHFGPINSVAFHPD
          RTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIG.FE.RFFHLAFEEEFGRVKGHFGPINSV.F.PD
Retrocopy RTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGQFEDRFFHLAFEEEFGRVKGHFGPINSVVFRPD

Parental  GKSYSSGGEDGYVRIHYFDPQYFEFEFEA
          G...SSGGEDGYVRIHYFDPQYFEFEFEA
Retrocopy GN--SSGGEDGYVRIHYFDPQYFEFEFEA

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	19.63 RPM	23.58 RPM
SRP017611_kidney	24.56 RPM	33.64 RPM
SRP017611_liver	10.96 RPM	15.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_1548 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DW297778	165347344	165347518	98.9	165	2	163

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1548 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Mus musculus	ENSMUSG00000028798	2 retrocopies	retro_mmus_1375, retro_mmus_607,
Rattus norvegicus	ENSRNOG00000047185	1 retrocopy	retro_rnor_1548 ,