RetrogeneDB ID: retro_rnor_714

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:93823705..93824319(+)
• Located in intron of: ENSRNOG00000026364

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snupn
• Ensembl ID: ENSRNOG00000005426
• Aliases: Snupn, Rnut1
• Description: Snurportin-1 [Source:UniProtKB/Swiss-Prot;Acc:Q68FP5]

Sequence

>retro_rnor_714
CTTTCTGAGTGCTTAATTGATGTCCCTTCAGATTTGGGGCAAGAGTGGACTGTGATTGTGTGTCCTGTTAGGAAGAGAGC
CCTTATCGTGACCTCCAGGGGTTCAACTAGTACCTACACCAAGAGTAGCTACTGTGTCAATAGGTTTTCTCCCACTTCTG
CCAGGAGGCAACAGGAGAAACTCCACGACAACCAAAGACTGCATCATTTTGTACTGCATTTACAGTGAGATGAACCAGAC
CGACTATGTTTTGAATGTGATGTGTTGGTAGGGACACCCTTTCTATGCATGTCAGACTGATTTCCAGTTCTACTGGGTAC
ATTCAAAGTTGACAGAAGAAGAACTCAGAGAGAAAACCAAGATTAATCCTTTTAACTCTATGGGACTAAGAATTCCCTGT
GTACCCCCGAGAGCCTGTGTAAGGTGGTGTCTGTGGATTTTTCTTATGAAGTAAATGGCTTCTCTTCTGCCATAAAAAGA
CCCACTATAGCCCTGGGAGTACTCCCGTGGTGGGCTGGCTATGCCTCTACATGGTATCAGATATTCTATGAGTAGTTGTG
CCAGCTGATCCACTGGCCACCAAGCCAGATGGTGCTGGGTAACAGCTAGCACAA

Alignment

ORF - retro_rnor_714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.56 %
• Parental protein coverage: 57.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSS-LLPGGNRRNSTTAKDYTI
          LSE.LIDVPSDLGQEW.V.VCPV.KRALIV.SRGSTS.YTKS.YCVNRFS..LLPGGNRRNSTT.KD..I
Retrocopy LSECLIDVPSDLGQEWTVIVCPVRKRALIVTSRGSTSTYTKSSYCVNRFSP>LLPGGNRRNSTTTKDCII

Parental  LDCIYSEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWMNSKLPEEEGLGEKTKINPFKFVGL-KNFPCTPE
          L.CIYSE.NQT.YVL.VMCW.GHPFY.CQTDF.FYW..SKL.EEE.L.EKTKINPF...GL.KN..CTPE
Retrocopy LYCIYSEMNQTDYVLNVMCW*GHPFYACQTDFQFYWVHSKLTEEE-LREKTKINPFNSMGL<KNSLCTPE

Parental  SLCKVLSMDFPFEVDG-LLFYHKQTHYSPGSTPLVGWLRPYMVSDILGVAVPAGPLTTKPEYAGHQLQQ
          SLCKV.S.DF..EV.G.LLF.HK.THYSPGSTP.VGWL..YMVSDIL.V.VPA.PL.TKP..AG.QL.Q
Retrocopy SLCKVVSVDFSYEVNG<LLFCHKKTHYSPGSTPVVGWLCLYMVSDIL*VVVPADPLATKPDGAG*QLAQ

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	8.20 RPM
SRP017611_kidney	0.00 RPM	6.28 RPM
SRP017611_liver	0.00 RPM	3.83 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_714 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_714 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014501	1 retrocopy	retro_meug_1444,
Mus musculus	ENSMUSG00000055334	1 retrocopy	retro_mmus_752,
Otolemur garnettii	ENSOGAG00000004915	1 retrocopy	retro_ogar_1420,
Rattus norvegicus	ENSRNOG00000005426	2 retrocopies	retro_rnor_2283, retro_rnor_714 ,