RetrogeneDB ID: retro_rnor_433

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:46487199..46487860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl46
• Ensembl ID: ENSRNOG00000018547
• Aliases: None
• Description: 39S ribosomal protein L46, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RK00]

Sequence

>retro_rnor_433
ATGGCAGCGCCCATAGGGCGTACTCTTTTAGGGGTGGCTAGAGGCTGGCAGCAGCTTGACAGGCTCTGGGCAGGTAGTTC
TCCTGGTCTGTCCCTTGAGGCTGTGCCTTCAAGCAGCTGGTCTCCTTGGCACTTGTTGGGCACCTTGTATCTGCAGAGGC
CATCGCTGATCACCAAGCCACTCACTCCATTGCTGGAAGAGATGGTGGGTCTATTACAGCAGGTAAAGACAGAGAGAAGC
CTGTATTCAGACCATGTGCTTCATGCTGTAGATGAAGCTCGGCAACTGGCAAAGAAGAAAGCTGACCTTCATGATGAGGA
ACAATGTCAGGGCATTATGCTCGCACAAGATTTAGAAGATATGCAGAACAGCCATTCCTATAGAGTTCAGACCTGGAGCT
CGAGAAGCGGAAGTCAATGAAAATAATGACGGAATCTCATTGCATTGTAAGCTAGACAGAAACCTTGTCCTCTTAGTCAG
AGAGAAACTTGGAGACAAATATTTTTGGATGTGTCCTCAGGTTGAGTGGTAGCCTGGGGAGACCCTCTGAGGGACAGCTG
AGTGAATGTTGGCCACACTCTCAGAAAACAACATGAAAGTCAAGGTCCTAGGGAATGCCCCCTGAGGCCACTACAAGTGC
AAGCTCCCCATGCAATTCAGA

Alignment

ORF - retro_rnor_433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.76 %
• Parental protein coverage: 79.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAPIGRTLLGVAKGWRQLDRLWAGSSRGLSLEAAPSSSRSPWRLSGALCLQRPPLITKPLTPLQEEMAG
          MAAPIGRTLLGVA.GW.QLDRLWAGSS.GLSLEA.PSSS.SPW.L.G.L.LQRP.LITKPLTPL.EEM.G
Retrocopy MAAPIGRTLLGVARGWQQLDRLWAGSSPGLSLEAVPSSSWSPWHLLGTLYLQRPSLITKPLTPLLEEMVG

Parental  LLQQVEVERSLYSDHELRALDEAQRLAKKKADLYDEEQDQDVTLAQDLEDMWEQEF-LQFRPGARETEAD
          LLQQV..ERSLYSDH.L.A.DEA..LAKKKADL.DEEQ.Q...LAQDLEDM........FRPGARE.E..
Retrocopy LLQQVKTERSLYSDHVLHAVDEARQLAKKKADLHDEEQCQGIMLAQDLEDMQNSHS>IEFRPGAREAEVN

Parental  KKNDRTSLHRKLDRNLILLVREKLGDQDLWMLPQVEWQPGETLRGTAERILATLSENNMEAKFLGNAPCG
          ..ND..SLH.KLDRNL.LLVREKLGD...WM.PQVEW.PGETL.GTAE..LATLSENNM..K.LGNAP.G
Retrocopy ENNDGISLHCKLDRNLVLLVREKLGDKYFWMCPQVEW*PGETL*GTAE*MLATLSENNMKVKVLGNAP*G

Parental  HYKFKFPKAIR
          HYK.K.P...R
Retrocopy HYKCKLPMQFR

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	14.31 RPM
SRP017611_kidney	0.00 RPM	14.65 RPM
SRP017611_liver	0.00 RPM	9.68 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_433 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013019	1 retrocopy	retro_cjac_3018,
Felis catus	ENSFCAG00000014966	1 retrocopy	retro_fcat_480,
Microcebus murinus	ENSMICG00000015826	1 retrocopy	retro_mmur_741,
Otolemur garnettii	ENSOGAG00000004736	1 retrocopy	retro_ogar_1280,
Rattus norvegicus	ENSRNOG00000018547	1 retrocopy	retro_rnor_433 ,