RetrogeneDB ID: retro_rnor_2284

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:46891155..46891532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps10
• Ensembl ID: ENSRNOG00000022609
• Aliases: None
• Description: 28S ribosomal protein S10, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q7TQ82]

Sequence

>retro_rnor_2284
ATGTCCGTTTTAGTGAAAGTCCATGACAAGGCTGTATTAGACAGTTCTGAGTATTTTGCCGTGCTTGCTGCTAAAGAACT
TGGCATTTCTATTAAAGTAGACGAGCCACCAAGGAAAATGAGTGCTTCACTCTCCTCAAGTCAGTACACATCTTCAAGAA
GCACAGAGTCCAATATGAGATGAGGATGCTCTACAGATGTCTGGAGTTAAAACATTTGACTGGATGCACAGCCAATATCT
ACCTGGAATATATCCAGCGAAACTTACCTGAAGGGGTGGCCACGGAAGTAATAAAGTCATAGATACAGCAGTTGCCAGAA
GACAGCAAGGAGCCAATGTGGGAAACAGTTTCCGAGGAGAAAGAAGAAAGCAAGGCT

Alignment

ORF - retro_rnor_2284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 81.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSILVKAHDKAVLDSYEYFAVLAAKELGLSIKVHEPPRKI-ERFTLLKSVHIFKKHRVQYEMRTLYRCLE
          .S.LVK.HDKAVLDS.EYFAVLAAKELG.SIKV.EPPRK..E.FTLLKSVHIFKKHRVQYEMR.LYRCLE
Retrocopy MSVLVKVHDKAVLDSSEYFAVLAAKELGISIKVDEPPRKM<ECFTLLKSVHIFKKHRVQYEMRMLYRCLE

Parental  LKHLTGCTANVYLEYIQRNLPEGVAMEVTKTQIQQLPEHIKEPMWETVSGEKEETKS
          LKHLTGCTAN.YLEYIQRNLPEGVA.EV.K..IQQLPE..KEPMWETVS.EKEE.K.
Retrocopy LKHLTGCTANIYLEYIQRNLPEGVATEVIKS*IQQLPEDSKEPMWETVSEEKEESKA

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	5.10 RPM
SRP017611_kidney	0.00 RPM	6.42 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2284 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2284 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007,
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284 ,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,