RetrogeneDB ID: retro_rnor_55

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:118812132..118812570(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004843
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pole3
• Ensembl ID: ENSRNOG00000015392
• Aliases: None
• Description: DNA polymerase epsilon subunit 3 [Source:UniProtKB/Swiss-Prot;Acc:Q642A5]

Sequence

>retro_rnor_55
ATGGCGGAGAGGCCTGAGGACCTAAATCTGCCCAACGCCGTCATTACCAGGATCATCAAGGAGGCGCTACCGGACGGTGT
CAACATCTCCAAGGAGGCCCGAAGCGCCATCTCCCGCGCGGCCAGTGTTTTCGTTTTGTATGCCACATCCTGTGCCAATA
ACTTTGCAATGAAAGGAAAGCGCAAGACTCTCAATGCCAGTGATGTACTGTCAGCCATGGAAGAGATGGAGTTCCAACGG
TTCGTAACGCCATTGAAAGAAGCGCTAGAAGCATACAGGCGGGAGCAGAAAGGCAAGAAGGAAGCCTCAGAGCAAAAGAA
GAAGGACAAAGACAAAAAAGATTGCGAAGAGCAGGACAAAAGCAGAGAGGAGGAGGATGAAGATGAAGAAAGACTGGATG
AGGAAGAACAGAACGAAGAGGAGGAGGTAGACAACTGA

Alignment

ORF - retro_rnor_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL
          MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL
Retrocopy MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL

Parental  SAMEEMEFQRFVTPLKEALEAYRREQKGKKEASEQKKKDKDKKDCEEQDKSREEEDEDEERLDEEEQNEE
          SAMEEMEFQRFVTPLKEALEAYRREQKGKKEASEQKKKDKDKKDCEEQDKSREEEDEDEERLDEEEQNEE
Retrocopy SAMEEMEFQRFVTPLKEALEAYRREQKGKKEASEQKKKDKDKKDCEEQDKSREEEDEDEERLDEEEQNEE

Parental  EEVDN
          EEVDN
Retrocopy EEVDN

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	0.50 RPM	20.56 RPM
SRP017611_kidney	0.77 RPM	46.13 RPM
SRP017611_liver	0.20 RPM	11.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_55 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_55 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55 ,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,