RetrogeneDB ID: retro_rnor_2836

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:93422260..93423367(+)
• Located in intron of: None

Retrocopy information

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

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_2836
ATGTCTACCATACTCCTGAATTTGGACTTTGGGGAACCTTCGAAAAAGGCATTTGGAGGAAATGCCAAACATCAACGTTT
TGTCAAGAAGCGAAGGTTCTTGGAACAGAAAGGATTTCTGAGTAAAAAGAACCAACCCCCTAGCAAGGTGTCTAAATTAA
ACTCAGAACCTCCAAAGAAAGGGGAAACTTCAAGAGTAGATAGCATTTCGAAGATCCTTTCATGCCTAAAGAAGAAGAAA
GAGGCAGCTGCATCCAAGAGGGACTCCGAACAGTCCAAAGACAAGAAAGCATCATTGTCATGGCTGACCCCTGCTCCTTC
AAAGAAGACTGATTCTGTTGTGGCTAAAATAGATTTGCTTGGGGAGTTGCAGAGTGCCCTTCCAAAGCCTAAGAGACGCA
CCCAGAAGAAGGGCTCTAAGAAGCCCTTGAAAAAGAAAATTGCTACAGAAAACTCCACCCAAACTCAGTCAAAGGATAAA
GGCTCCAACAGGAAGCCCTTGAAGAAAAATGCTGTACAGAACTCCACCCAAGCTCAACCAGAGGATAAGTGCCCTAAAGT
CCCTCAAAGCTTGCCAAGGAAGATGGTGGCAATAGACTGTGAAATGGTGGGCACGGGACCCAAGGGGCGTGTGAGTTCCT
TGGCTCACTGCAGCATCGTGAATTACAATGGAGATGTGCTTTATGATGAGTACATCTGCCCCCCATGCTATATCGTGGAC
TACCGGACCAGGTGGAGTGGCATCCGGAAGTGCCACATGGTTAATGCTACCCCCTTTAAGACTGCTCGGAGTCAGATCTT
GAAGATACTCTCAGGGAAGGTAGTGGTAGGACATGCCATTCATAATGACTACAAAGCCCTACAGTACTTTCATCCCAAGT
CCCTCACTCGAGACACTTCCCAAATACCGCTCCTCAACCGGAAGGCTGACTGCCCAGAAAATGTCACTTTGTCACTGAAG
CATCTCACCAAGAAGCTGCTGAGTCGGGACATCCAGACTGGACTAAGTGGACATTCCTCGGTGGAAGATGCCCAGGCCAC
ATTGGAGCTGTACAAGTTGGTTGAAGTTGAATAGGAACAGCATCTGGCCCAGAATCCTCCAGAAAAT

Alignment

ORF - retro_rnor_2836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS
          MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS
Retrocopy MSTILLNLDFGEPSKKAFGGNAKHQRFVKKRRFLEQKGFLSKKNQPPSKVSKLNSEPPKKGETSRVDSIS

Parental  KILSCLKKKKEAAASKRDSEQSKDKKASLSWLTPAPSKKTDSVVAKIDLLGEFQSALPKPKRRTQKKGSK
          KILSCLKKKKEAAASKRDSEQSKDKKASLSWLTPAPSKKTDSVVAKIDLLGE.QSALPKPKRRTQKKGSK
Retrocopy KILSCLKKKKEAAASKRDSEQSKDKKASLSWLTPAPSKKTDSVVAKIDLLGELQSALPKPKRRTQKKGSK

Parental  KPLKKKIATENSTQTQSKDKGSNKKPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR
          KPLKKKIATENSTQTQSKDKGSN.KPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR
Retrocopy KPLKKKIATENSTQTQSKDKGSNRKPLKKNAVQNSTQAQPEDKCPKVPQSLPRKMVAIDCEMVGTGPKGR

Parental  VSSLARCSIVNYNGDVLYDEYIRPPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI
          VSSLA.CSIVNYNGDVLYDEYI.PPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI
Retrocopy VSSLAHCSIVNYNGDVLYDEYICPPCYIVDYRTRWSGIRKCHMVNATPFKTARSQILKILSGKVVVGHAI

Parental  HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLKHLTKKLLSRDIQTGLSGHSSVEDAQATLEL
          HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLKHLTKKLLSRDIQTGLSGHSSVEDAQATLEL
Retrocopy HNDYKALQYFHPKSLTRDTSQIPLLNRKADCPENVTLSLKHLTKKLLSRDIQTGLSGHSSVEDAQATLEL

Parental  YKLVEVEWEQHLAQNPPEN
          YKLVEVE.EQHLAQNPPEN
Retrocopy YKLVEVE*EQHLAQNPPEN

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	3.81 RPM
SRP017611_kidney	0.00 RPM	4.81 RPM
SRP017611_liver	0.00 RPM	3.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2836 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2836 has 0 orthologous retrocopies within eutheria group .

---

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,