RetrogeneDB ID: retro_rnor_1184

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:26020227..26020734(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrps25
• Ensembl ID: ENSRNOG00000010912
• Aliases: Mrps25, Shd10
• Description: 28S ribosomal protein S25, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q4QR80]

Sequence

>retro_rnor_1184
ATGCTGATGAAGGGCGGGTTGCCTCACCTTTCGCTGCAGTACCTGGGTCATGGGATGTGGTATTCAAGGACTCAGTGAAG
GTCATGACCGTGAACTACAACACGAATGGGGAAATGGGCAAAATTGCCAGGAAATTCGTGGTTTTCAACATCCCTCAGAT
CCAGTATAAGAATCTTCAGGTGCAGATCATGCTGGTTAAGAACATGACGCCATCGCCCTTCCTGCAGTTCTATCTAGATT
TTGGGAGCAGGTCCCGGTAGACACGGAGACGAAGAGTAATAAGAAGATCGTGGAGTACATAAAGAAAATCATGGGCAAGA
AAGAGGAGCCCCTCAGGGAGGAGGAGCTGGAGAAGCAGCAGGGCTTTCATCGAGGCAACTTCGGCTCCGGAAGTACTGCC
TGCAGGAGTGCCTGTGGGAAGTGGAAGGTCGGTGTCCTGCCCTGGCATGGTGCGTGCCCTCACCTAAGGAGATGACAGGG
AAGTACAAAGCTGCTCTGAAAGCCAAT

Alignment

ORF - retro_rnor_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 99.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPMKGRFPIRRTLQYLGSG-DVVFKESVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNPWVQIMLFKN
          M.MKG..P....LQYLG.G.DVVFK.SVKVMTVNYNT.GE.G..ARKFV.FNIPQIQYKN..VQIML.KN
Retrocopy MLMKGGLP-HLSLQYLGHG<DVVFKDSVKVMTVNYNTNGEMGKIARKFVVFNIPQIQYKNLQVQIMLVKN

Parental  MTPSPFLRFYLESG-EQVLVDVETKSNTEIVEHIKKILGKKEETLREEELEKQQRFHPGNFGP-RKYCLR
          MTPSPFL.FYL..G.EQV.VD.ETKSN..IVE.IKKI.GKKEE.LREEELEKQQ.FH.GNFG..RKYCL.
Retrocopy MTPSPFLQFYLDFG<EQVPVDTETKSNKKIVEYIKKIMGKKEEPLREEELEKQQGFHRGNFGS<RKYCLQ

Parental  ECMCEVEGQVPCPG-LVPLPKEMTGKYKAALKAN
          EC..EVEG..P.....VP.PKEMTGKYKAALKAN
Retrocopy ECLWEVEGRCPALAWCVPSPKEMTGKYKAALKAN

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	22.79 RPM
SRP017611_kidney	0.00 RPM	49.06 RPM
SRP017611_liver	0.00 RPM	14.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1184 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1184 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184 ,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,