RetrogeneDB ID: retro_rnor_1328

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:6057026..6057446(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps18b
• Ensembl ID: ENSRNOG00000000804
• Aliases: Mrps18b, Ptd017
• Description: mitochondrial ribosomal protein S18B [Source:RefSeq peptide;Acc:NP_997699]

Sequence

>retro_rnor_1328
AGCAGACCCGAATGTATGAATCACAATAAAGTTGCTGGGAATCCTTGCCCCATCTGCCAGGATCAAAAGTTGCATGTTGA
CATTCGGAATGTAAAGCTATTGGAACAGTTCGTTTGTGCCCACACGGGTATCATCTTCAATGCCTCATACACAGGGGTCT
GTATGAAGCAGCACAAGAAGCTGACCCAGGCCATCCAGAAAGCCAGGAAGTGTGGTCTTCTCATTTACTACGTTCCCCAG
GTTCAGCCCTGAGATGTTGACTTTCGTATTGTACATGGAGCTGTCAGTGTTACTCCACCAGTCCCCACATTGTTGTTGGG
TGAACCTTGGTATCTGTGGTACAGCTGGCAACAGCAACCAGAGAGAGAGCTGTCTCGCCTTCGCCGACTCTATCAAGGAA
ATTTCCTGAAAGAAAGTGGC

Alignment

ORF - retro_rnor_1328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.71 %
• Parental protein coverage: 54.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TRKTCIRKDKVAGNPCPICRDHKLHVDFRNVKLLEQFVCAHTGIIFHAPYTGVCMKQHKKLTQAIQKARE
          .R..C....KVAGNPCPIC.D.KLHVD.RNVKLLEQFVCAHTGIIF.A.YTGVCMKQHKKLTQAIQKAR.
Retrocopy SRPECMNHNKVAGNPCPICQDQKLHVDIRNVKLLEQFVCAHTGIIFNASYTGVCMKQHKKLTQAIQKARK

Parental  YGLLSYYVPQVEPRDADLRTVHGAVSVTPPAPTLLSGEPWYPWYSWQQPPERELSRLRRLYQGNLLEASG
          .GLL.YYVPQV.P.D.D.R.VHGAVSVTPP.PTLL.GEPWY.WYSWQQ.PERELSRLRRLYQGN.L..SG
Retrocopy CGLLIYYVPQVQP*DVDFRIVHGAVSVTPPVPTLLLGEPWYLWYSWQQQPERELSRLRRLYQGNFLKESG

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	19.41 RPM
SRP017611_kidney	0.00 RPM	34.89 RPM
SRP017611_liver	0.00 RPM	24.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1328 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1328 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328 ,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,