RetrogeneDB ID: retro_rnor_463

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:99720947..99722051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000037348
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Isg20l2
• Ensembl ID: ENSRNOG00000011402
• Aliases: None
• Description: Interferon-stimulated 20 kDa exonuclease-like 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6AXU3]

Sequence

>retro_rnor_463
ATGTCTACCATACTCCTGAATTTGGACTTTGGGGAACCTTCGAAAAAGGCATTTGGAGGAAATGCCAAACATCAACGTTT
TGTCAAGAAGCGAAGGTTCTTGGAACAGAAAGGATTTCTGAGTAAAAAGAACCAACCCCCTAGCAAGGTGTCTAAATTAA
ACTCAGAACCTCCAAAGAAAGGGGAAACTTCAAGAGTAGATAGCATTTCGAAGATCCTTTCATGCCTAAAGAAGAAAAAA
GAGGCAGCTGCCTCCAAGAGGGACTCAGAGCAGTCCAAAGACAAGAAAGCATCGTCATGGCTGACCCCTGCTCCTTCAAA
GAAGACTGATTCTGTTGTGGCTAAAATAGATTTGCTTGGGGAGTTTCAGAGTGCCCTTCCAAAGCCTAAGAGACGCACCC
AGAAGAAGGGCTCCAAGAAGCCCTTGAAAAAGAAAATTGCTACAGAAAACTCCACCCAAGCTCAGTCAAAGGATAAAGGC
TCCAACAAGAAGCCCTTGAAGAAAAATGCTGTACAGAACTCCACCCAAGCTCAACCAGAGGATAAGTGCCCTAAAGTCCC
TCAAAGCTTGCCAAGGAAGATGGTGGCAATAGACTGTGAAATGGTGGGCACCGGACCCAAGGGGCGTGTGAGTTCCTTGG
CTCGCTGCAGCATCGTGAATTACAATGGAGATGTGCTTTATGATGAGTACATCCGCCCCCCCTGCTATATCGTGGACTAC
CGGACCAGGTGGAGTGGCATCCGGAAGTGCCACATGGTTAATGCTACCCCGTTTAAGACTGCTCGGAGTCAGATCTTGAA
GATACTCTCAGGGAAGGTAGTGGTAGGGCATGCCATTCACAATGACTACAAAGCCCTACAGTACTTTCATCCCAAGTCCC
TCACTCGAGACACTTCCCAAATACCACTCCTCAACCGGAAGGCTGACTGCCCAGAAAATGTCACTTTGTCACTGAAGCGT
CTCACCAAGAAGCTGCTGAGTCGGGACATCCAGACTGGACTAAGTGGACATTCCTCGGTAGAAGATGCCCAGGCCACATT
GGAGCTGTACAAGTTGGTTGAAGTTGAATGGGAGCAGCATCTGGCCCAGAATCCTCCAGAAAAT

Alignment

ORF - retro_rnor_463 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS
          MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS
Retrocopy MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS

Parental  KILSCLKKKKEAAASKRDSEQSKDKKASLSWLTPAPSKKTDSVVAKIDLLGEFQSALPKPKRRTQKKGSK
          KILSCLKKKKEAAASKRDSEQSKDKKAS.SWLTPAPSKKTDSVVAKIDLLGEFQSALPKPKRRTQKKGSK
Retrocopy KILSCLKKKKEAAASKRDSEQSKDKKAS-SWLTPAPSKKTDSVVAKIDLLGEFQSALPKPKRRTQKKGSK

Parental  KPLKKKIATENSTQTQSKDKGSNKKPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR
          KPLKKKIATENSTQ.QSKDKGSNKKPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR
Retrocopy KPLKKKIATENSTQAQSKDKGSNKKPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR

Parental  VSSLARCSIVNYNGDVLYDEYIRPPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI
          VSSLARCSIVNYNGDVLYDEYIRPPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI
Retrocopy VSSLARCSIVNYNGDVLYDEYIRPPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI

Parental  HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLKHLTKKLLSRDIQTGLSGHSSVEDAQATLEL
          HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLK.LTKKLLSRDIQTGLSGHSSVEDAQATLEL
Retrocopy HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLKRLTKKLLSRDIQTGLSGHSSVEDAQATLEL

Parental  YKLVEVEWEQHLAQNPPEN
          YKLVEVEWEQHLAQNPPEN
Retrocopy YKLVEVEWEQHLAQNPPEN

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	0.07 RPM	3.81 RPM
SRP017611_kidney	0.35 RPM	4.81 RPM
SRP017611_liver	0.27 RPM	3.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_463 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_463 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006559	1 retrocopy	retro_fcat_1999,
Macaca mulatta	ENSMMUG00000000037	1 retrocopy	retro_mmul_1519,
Nomascus leucogenys	ENSNLEG00000012742	1 retrocopy	retro_nleu_3048,
Rattus norvegicus	ENSRNOG00000011402	2 retrocopies	retro_rnor_2836, retro_rnor_463 ,