RetrogeneDB ID: retro_rnor_2283

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:42142859..42143624(+)
• Located in intron of: None

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_2283
ATGGAAGAATTGAGCCAAGCCCTAGCTAGTAGCTTTTCTGTGTCTCAAGAACTGAACAGCACAGCTGCCCCACACCCTCG
CCTGTCCCAATACAAGTCCAAGTATAGCTCCTTGGAGCAGAGTGAGCGGCGGCGCCGGTTGCTAGAGCTGCAGAAATCCA
AGCGGTTGGACTATGTGAACCATGCCAGAAGACTGGCTGAAGATGACTGGACAGGGATGGAGAGTGGGGAAGAGGAGAAG
AAGAAAGATGAGGAGGAAATGGATTTGGACCCTGTCAAGGAGTTACCAAAACGCTATGCTAATCAACTGATGCTTTCTGA
GTGGTTAACTGACGTCCCTTCAGATTTGGGGCAGGAATGGATTGTGGTTGTGTGCCCTGTTGAGAAAAGAGCCCTTATCG
TGGCCTGCAGGGGCTCAACCAGTGCCTACACTAAGAGTGGCTACTGCATCAATAGGTTTTCTTCCCTTCTTCCAGGAGGC
AATAGGAGAAACTCAACAACAGCCAAAGACTACACCATTCTGGATTGCATTTACAGTGAAGTGAACCAGACGTACTATGT
TTTGGATGTGATGTGCTGGTGGGGACATCCTTTTTATGATTGTCAGACTGATTTCCGATTCTACTAGATGCATTCAAAGT
TACCAGAAGAAGAAGGACTTGGAGAGAAAACCAAGATTAATCCCTTTAAGTTTGTGTGGCTTCAGAATTTCCCATGTACC
CAGGAGAGCCTGTGCAAGGTGCTGTCTATGGATTTTCCTTTTGAG

Alignment

ORF - retro_rnor_2283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.29 %
• Parental protein coverage: 71.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEELSQALASSFSVSQELNSTAAPHPRLSQYKSKYSSLEQSERRRQLLELQKSKRLDYVNHARRLAEDDW
          MEELSQALASSFSVSQELNSTAAPHPRLSQYKSKYSSLEQSERRR.LLELQKSKRLDYVNHARRLAEDDW
Retrocopy MEELSQALASSFSVSQELNSTAAPHPRLSQYKSKYSSLEQSERRRRLLELQKSKRLDYVNHARRLAEDDW

Parental  TGMESGEEEKKKDEEEMDLDPVKKLPKRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGKRALIVASRGST
          TGMESGEEEKKKDEEEMDLDPVK.LPKRYANQLMLSEWL.DVPSDLGQEWIVVVCPV.KRALIVA.RGST
Retrocopy TGMESGEEEKKKDEEEMDLDPVKELPKRYANQLMLSEWLTDVPSDLGQEWIVVVCPVEKRALIVACRGST

Parental  SAYTKSGYCVNRFSSLLPGGNRRNSTTAKDYTILDCIYSEVNQTYYVLDVMCWRGHPFYDCQTDFRFYWM
          SAYTKSGYC.NRFSSLLPGGNRRNSTTAKDYTILDCIYSEVNQTYYVLDVMCW.GHPFYDCQTDFRFY.M
Retrocopy SAYTKSGYCINRFSSLLPGGNRRNSTTAKDYTILDCIYSEVNQTYYVLDVMCWWGHPFYDCQTDFRFY*M

Parental  NSKLPEEEGLGEKTKINPFKFVGLKNFPCTPESLCKVLSMDFPFE
          .SKLPEEEGLGEKTKINPFKFV.L.NFPCT.ESLCKVLSMDFPFE
Retrocopy HSKLPEEEGLGEKTKINPFKFVWLQNFPCTQESLCKVLSMDFPFE

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	0.07 RPM	3.83 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2283 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2283 has 0 orthologous retrocopies within eutheria group .

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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,