RetrogeneDB ID: retro_rnor_2785

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:36683778..36684160(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl15
• Ensembl ID: ENSRNOG00000008566
• Aliases: None
• Description: 39S ribosomal protein L15, mitochondrial [Source:RefSeq peptide;Acc:NP_001100103]

Sequence

>retro_rnor_2785
AGGAGAAAGAACTCTGTCCAACTATGCTTTGTGGGAGGGCAGACTCCATTTTACATCCTAATCCCAAAATATGGACTTGA
AGAAGGACATAGTTTGAGGCACCAATACCAGCCTTCGAGTCTTGGAAACTACAGTATCTCATTCATTTATGTTGAGTTGA
TCCAACTGTATTTATTGACTTAACCTAGCTTGTGAATGGGAGAGGTGTGTCCATCAAACCACTTAAAAAGGATTACAGGA
TCCAGCTGTTTGAAGACAGTGCTGATACTTTTCAAGCAAAAGTTAATTAAAGGTGTAGTTGGCTTCAGAATTAGCCATTA
CTCCAATTGAAAAAAAAAGTCAGTAGGTTGTTATTACTGCCTTCTATGATCCAAGAAGACTA

Alignment

ORF - retro_rnor_2785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 61.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRGTRPRLGFEGGQTPFYIRIPKYGFNEGHSFRHQYQPLSLR-RLQYLIDLGRVDPTQPIDLTQLVNGRG
          .R.....L.F.GGQTPFYI.IPKYG..EGHS.RHQYQP.SL...LQYLI.L..VDPT..IDLT.LVNGRG
Retrocopy RRKNSVQLCFVGGQTPFYILIPKYGLEEGHSLRHQYQPSSLG<KLQYLIHLC*VDPTVFIDLT*LVNGRG

Parental  VTIQPLKRDYGVQLVEEGADTFQAKVN-IEVQMASELAIAAIEKNGG-VVTTAFYDPRSL
          V.I.PLK.DY..QL.E..ADTFQAKVN...V..ASELAI..I......VV.TAFYDPR.L
Retrocopy VSIKPLKKDYRIQLFEDSADTFQAKVN<LKV*LASELAITPIXXXXQ*VVITAFYDPRRL

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	0.00 RPM	44.17 RPM
SRP017611_liver	0.00 RPM	22.39 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2785 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2785 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3534

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001174	1 retrocopy	retro_btau_324,
Canis familiaris	ENSCAFG00000006988	2 retrocopies	retro_cfam_1573, retro_cfam_511,
Choloepus hoffmanni	ENSCHOG00000005299	3 retrocopies	retro_chof_1379, retro_chof_1719, retro_chof_746,
Callithrix jacchus	ENSCJAG00000016719	1 retrocopy	retro_cjac_2230,
Dasypus novemcinctus	ENSDNOG00000017664	1 retrocopy	retro_dnov_364,
Erinaceus europaeus	ENSEEUG00000001454	2 retrocopies	retro_eeur_128, retro_eeur_707,
Echinops telfairi	ENSETEG00000001724	1 retrocopy	retro_etel_1304,
Mustela putorius furo	ENSMPUG00000010533	1 retrocopy	retro_mputfur_149,
Mus musculus	ENSMUSG00000033845	2 retrocopies	retro_mmus_1709, retro_mmus_3534,
Ornithorhynchus anatinus	ENSOANG00000007286	1 retrocopy	retro_oana_114,
Otolemur garnettii	ENSOGAG00000003768	1 retrocopy	retro_ogar_534,
Ochotona princeps	ENSOPRG00000000921	2 retrocopies	retro_opri_241, retro_opri_364,
Rattus norvegicus	ENSRNOG00000008566	2 retrocopies	retro_rnor_1344, retro_rnor_2785 ,
Sus scrofa	ENSSSCG00000030578	1 retrocopy	retro_sscr_617,
Tarsius syrichta	ENSTSYG00000014106	1 retrocopy	retro_tsyr_37,
Tursiops truncatus	ENSTTRG00000011844	2 retrocopies	retro_ttru_1139, retro_ttru_733,