RetrogeneDB ID: retro_rnor_460

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:95591096..95591514(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl32
• Ensembl ID: ENSRNOG00000015989
• Aliases: None
• Description: 39S ribosomal protein L32, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001099586]

Sequence

>retro_rnor_460
CGGACTGGGGAGCTATTGCAATGGCAACTGCAGCAGAGTTGGAGCGGCTTTGCCAGTCCTCAGTGGGCACCAGCATGAGC
AGTCCCCAGTCCATCCATCCTCACAGAACTAGCATATGATACCAGTACAAATAAAGAGAATTCCAGCTTCTTAGATAGTT
ATCTTTCGGATGGCAGCTCCCAAAAACAGATGCACCATCGAAGTTAACCGATGTAGGAGAAGAAACCCTCACAAGCTTGT
TAAAATTAAGAATAATGTAGACATTTGCCCTGAATGCGGTCACCTGAAGCAGAAACAGGTCCCTCGTGGCTATTGCTATG
AGAAAGCACACCAGGGGACAACAAAAACCAGACAACAAATATGGGCTCAAGAAGGCGGCCCTTTCGGAGCTCCTTCCATC
GAGACTGTGGTACTGTAC

Alignment

ORF - retro_rnor_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 74.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RCWELLQRQLKQTWSGFASPQWAPALAVQSPSTLTELAYDTSKNKENSSFLDS-IFWMAAPKNRRTIEVN
          R..ELLQ.QL.Q.WSGFASPQWAPA.AV.SPS.LTELAYDTS.NKENSSFLDS.IF.MAAPKNR.TIEVN
Retrocopy RTGELLQWQLQQSWSGFASPQWAPA*AVPSPSILTELAYDTSTNKENSSFLDS>IFRMAAPKNRCTIEVN

Parental  RCRRRNPHKLIKIKNNIDICPECGHLKQKHVLCGYCYEKVSQETTKIRQQIWAQEGGPFKAPSIETVVLY
          RCRRRNPHKL.KIKNN.DICPECGHLKQK.V..GYCYEK..Q.TTK.RQQIWAQEGGPF.APSIETVVLY
Retrocopy RCRRRNPHKLVKIKNNVDICPECGHLKQKQVPRGYCYEKAHQGTTKTRQQIWAQEGGPFGAPSIETVVLY

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	7.84 RPM
SRP017611_kidney	0.00 RPM	12.56 RPM
SRP017611_liver	0.00 RPM	9.75 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_460 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_460 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_460 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000018146	1 retrocopy	retro_mputfur_60,
Mus musculus	ENSMUSG00000015672	1 retrocopy	retro_mmus_61,
Oryctolagus cuniculus	ENSOCUG00000012098	1 retrocopy	retro_ocun_474,
Otolemur garnettii	ENSOGAG00000016806	2 retrocopies	retro_ogar_1965, retro_ogar_2797,
Rattus norvegicus	ENSRNOG00000015989	1 retrocopy	retro_rnor_460 ,
Ictidomys tridecemlineatus	ENSSTOG00000013340	1 retrocopy	retro_itri_1122,
Tarsius syrichta	ENSTSYG00000014296	1 retrocopy	retro_tsyr_1710,