RetrogeneDB ID: retro_rnor_619

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:174301846..174302413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nras
• Ensembl ID: ENSRNOG00000023079
• Aliases: None
• Description: GTPase NRas [Source:UniProtKB/Swiss-Prot;Acc:Q04970]

Sequence

>retro_rnor_619
ATGACTAAGTACAAACTGGTGGTGGTTGGAGCAGGTGGCATTGGGAAAAGTGCTTTGACAATCCAGCTAATCCAGAACCA
CTTTGTGGATGAATATGATCCCACCATAGAGGATTCTTACTGAAAAGAAGTGGTGATTGACGGTGAGACCTGTCTACTGG
ACATACTGGACACAGCTGGACAAGAGGAGTACAGTGCCATGAGAGAACAATACATGAGGACAGGCGAAGGGTTCCTCTGT
GTGTTTGCCATCAATAATAGCAAATCCTTTGTAGATATTAACCTCTACAGGGAGCAAATTAAGCATGTGAAAGACTCTGA
TGATGTACCCATGGTGCTGGTAGGGAACAAGTGTGACTTGCCAACAAGGACAGTTGACACAAAGCAAGCCCACGAGCTGG
CCAAGAGCTATGGAATTCCATTCATTGAAACCTCAGCCAAAACCTGACAGGGTGTGAAGGATGCCTTTTACATGCTCATA
AGGGAGATACACCAGTACTGCATGAAGAAGCTCAACAGCAGTGAGGATGGCACTCAAGGCTGTATGGGGCTGCCCTGTGT
GGTGATG

Alignment

ORF - retro_rnor_619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MT.YKLVVVGAGG.GKSALTIQLIQNHFVDEYDPTIEDSY.K.VVIDGETC..........EEYSAMR.Q
Retrocopy MTKYKLVVVGAGGIGKSALTIQLIQNHFVDEYDPTIEDSY*KEVVIDGETCXXXXXXXXXXEEYSAMREQ

Parental  YMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP
          YMRTGEGFLCVFAINNSKSF.DINLYREQIK.VKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP
Retrocopy YMRTGEGFLCVFAINNSKSFVDINLYREQIKHVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP

Parental  FIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSEDGTQGCMGLPCVVM
          FIETSAKT.QGV.DAFY.L.REI.QY.MKKLNSSEDGTQGCMGLPCVVM
Retrocopy FIETSAKT*QGVKDAFYMLIREIHQYCMKKLNSSEDGTQGCMGLPCVVM

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	20.78 RPM
SRP017611_kidney	0.07 RPM	17.24 RPM
SRP017611_liver	0.07 RPM	10.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_619 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_619 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Rattus norvegicus	ENSRNOG00000016611	1 retrocopy	retro_rnor_2941,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619 ,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,