RetrogeneDB ID: retro_rnor_555

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:281165537..281166235(+)
• Located in intron of: ENSRNOG00000012084

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl2
• Ensembl ID: ENSRNOG00000018057
• Aliases: None
• Description: 39S ribosomal protein L2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q498T4]

Sequence

>retro_rnor_555
ATGGCCCTGTGCACGCTGGCCAGCGCTCTGCGCTCCTTGAACCTGGCCTCCCCGGCCATTACCGTCCTGGGTTCCGCCTC
TGCTCCCTGTTGGCCAGAGCAATGTCCTCCTTCAGCTGCCCTCTGCCCCGGCGTTGCCCTCCCACTGCCCAGTGCGTATG
TCTGCGGACCACAGCACCAAGCTTGTGTCCTGGAAGAGTCCTACCAAGTGCACAGTTAAACCAGTGAAGATGAGGAAGTC
TGGGGGTCGAAACCATACGGGCCACACCCGAGTGCCCGGTAATGGTGGAGGCCACAGGCAGAATTATTGAATGATTGACT
TTCTCCGGTTCCGGCCAGAAAAGGGGACTGAGCCAGGACCCTTGGAGGAGAAGAAGGCTGTGGTAGTCCGCTATGATCCT
TGTAGGTCTGCAGACTATCTCTGGTTGCAGGGGGCAGCCGGAAATGCTGGATCATTGCCACAGAAAGCATGAAGGCAGGA
GACACAATCCTGAACTCTAACCACGTCGGCGGAATGACAGTGGCTGCTCAGGAAGGGGATGCACATCCACTTGGGGCACT
GCTGAGGGGACCCTCAACAACAACACAGAGGGCGAGCTTGGCCGAGGAGCCCAGAATATCCGAGCAGCAGGGACATGGGG
TGTGCTGCTCTGGAAGGTGAATGGAACAGCCATTATCCAGCTGCCCTCTGCATTGCAA

Alignment

ORF - retro_rnor_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALCALASALRSLSLASPAITAR-VPTLLPVGQSNVLLQLPSALALPAHRPVHMSADRSAKFVSWKSRIK
          MALC.LASALRSL.LASPAIT...VP.LLPVGQSNVLLQLPSA.ALP.H.PV.MSAD.S.K.VSWKS..K
Retrocopy MALCTLASALRSLNLASPAITVL>VPPLLPVGQSNVLLQLPSAPALPSHCPVRMSADHSTKLVSWKSPTK

Parental  YTVKPVKMRKSGGRDHTGRIRVHGIGGGHKQNYRMIDFLRFRPEKGTEPEPFEE-KVVVVRYDPCRSAD-
          .TVKPVKMRKSGGR.HTG..RV.G.GGGH.QNY.MIDFLRFRPEKGTEP.P.EE.K.VVVRYDPCRSAD.
Retrocopy CTVKPVKMRKSGGRNHTGHTRVPGNGGGHRQNY*MIDFLRFRPEKGTEPGPLEEKKAVVVRYDPCRSAD<

Parental  IALVAGGSRKRWIIATENMKAGDTILNSNHIGRMAVAAQEGDAHPLGAL-PVGTLINNVESEPGRGAQYI
          ..LVAGGSRK.WIIATE.MKAGDTILNSNH.G.M.VAAQEGDAHPLGAL...GTL.NN.E.E.GRGAQ.I
Retrocopy LSLVAGGSRKCWIIATESMKAGDTILNSNHVGGMTVAAQEGDAHPLGAL<AEGTLNNNTEGELGRGAQNI

Parental  RAAGTCGVLLRKVNGTAIIQLPSKRQ
          RAAGT.GVLL.KVNGTAIIQLPS..Q
Retrocopy RAAGTWGVLLWKVNGTAIIQLPSALQ

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	12.94 RPM
SRP017611_kidney	0.21 RPM	21.07 RPM
SRP017611_liver	0.07 RPM	18.42 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_555 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_555 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_555 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555 ,