RetrogeneDB ID: retro_rnor_1636

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:132654883..132655278(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl54
• Ensembl ID: ENSRNOG00000020464
• Aliases: None
• Description: 39S ribosomal protein L54, mitochondrial [Source:RefSeq peptide;Acc:NP_001100240]

Sequence

>retro_rnor_1636
GCCAGTCTCCTCGGGGCAACCCGGGTGTGGGCCCGCTGGCATCCCCGGGCGCTCCGGGTCCCCGGGAGACCTGGAGAATC
TTTATCCGGGAATATGCCAAGAAGTCAGTCAGCAAGGGTGGCAAGGGTGGCATGGCCGCTGAGGCCCTGAAGGACCCCGA
AGTGTGCACAGACCCCTCTCAGTTCACCACACATGCCATGGAGGTCAACATCTACAAGGAAGGCCAGTAGGTGGCCCTGA
AGTCAGACTCCGAGTACCCGACATGGCTGTTCCAGGTGGACCTGGGTCCCCCCAAAAAGCTAGAGGAACTAGTACTGGAG
TCCCGAGAGTACTGGCGACTGCTTCGCAAACAGAACATCTGGCGTCACAAGAGGCTGAGCAAAAACAAGAAGCTG

Alignment

ORF - retro_rnor_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 97.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASLLGATRVWARWHPRALPVPGRPGE-LFIREYAKKAVSKGGKGGVAAEALKDPEVCTDPSQLTTHAMGV
          ASLLGATRVWARWHPRAL.VPGRPGE..FIREYAKK.V........AAEALKDPEVCTDPSQ.TTHAM.V
Retrocopy ASLLGATRVWARWHPRALRVPGRPGE<IFIREYAKKSVXXXXXXXXAAEALKDPEVCTDPSQFTTHAMEV

Parental  NIYKEGQEVALKPDSEYPTWLFQVDLGPPKKLEDLEPESREYWRLLRKQNIWRHNRLSKNKKL
          NIYKEGQ.VALK.DSEYPTWLFQVDLGPPKKLE.L..ESREYWRLLRKQNIWRH.RLSKNKKL
Retrocopy NIYKEGQ*VALKSDSEYPTWLFQVDLGPPKKLEELVLESREYWRLLRKQNIWRHKRLSKNKKL

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	15.24 RPM
SRP017611_kidney	0.07 RPM	24.84 RPM
SRP017611_liver	0.00 RPM	13.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1636 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000033519	1 retrocopy	retro_ogar_223,
Pteropus vampyrus	ENSPVAG00000007137	1 retrocopy	retro_pvam_139,
Rattus norvegicus	ENSRNOG00000020464	1 retrocopy	retro_rnor_1636 ,
Tupaia belangeri	ENSTBEG00000004745	1 retrocopy	retro_tbel_965,