RetrogeneDB ID: retro_ogar_1420

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873546.1:16899272..16900138(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNUPN
• Ensembl ID: ENSOGAG00000004915
• Aliases: None
• Description: snurportin 1 [Source:HGNC Symbol;Acc:14245]

Sequence

>retro_ogar_1420
GTGGAAGAGTTGAGCCAAGCCCTGGCTAGTAGGTTTTCTGTGTCTCAAGATCTGAACAGCACGGCTGCCCCACATCCCCG
CCTGTCCCAGTACAAATCCAAGTACAGTTCCTTGGAGCAGAGTGAGCAGTGCCGCCAGTTACTGAAACTGCAGAAATGTA
AGCAGCTAGATTATGTGAACCACGCCAGAAGACTGGCTGAAGATGACTGGACAGGGATAGAGAGTGAAGACAAAGAGAAG
AAAGATGATGAGGAAATGGACATTGACAGAGGCGAGAAGTTACCAAAACGCTGTGCTAACCAACTGATGCTCTCCGAGTG
GTTAACTGATGTCCCTTCAGATCTGGGGCAGGAATGGCTTGTGGTCGTGTGCCCTGTTGAGAAAGAGCCCTTACTGTAGC
ATCCAGGGGCTCTATCAGTGCCTGCACCAAGAGTGGCTACTCTGTCAACAGGTTTTCCTCTCTTCTGCCAGGAGGCAACA
GGCAAAACTCAACAACAGCAAAAGACTACACCGTTCTAGATTCCATTTACAGTGTGGTGAACCAGACCTACTAGGCTCTA
GGTGTGATGTGCTGGCGGGGACACCCGTTTTATGACTGCCAGACTGATTTCCGATTCTACTAGATGCATTCAAAGTTACC
AGAAGGACTAAGAGAGAAAACCAAACCCAACCCCTTTAAATTTGTGGGTCTAAAGAATTTCCCTTGTACCCCTGAAAGCC
TGTGTAAGGTGCTTTGAATGGATTTCCCTTCTGAGGTAGATGAACTTCTCTTCTACTACAAGCAGACCCACTATCGCCCT
GGAAGCACTCCCTCGGTGAGCTGGCTGCAACCCTCCATGGTGTCTGATGTCCTTGGTGTAGCTGTC

Alignment

ORF - retro_ogar_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.23 %
• Parental protein coverage: 80.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEELSQALASSFSVSQDLNSTAAPHPRLSQYKSKYSSLEQSERRRRLLELQKCKRLDYVNHARRLAEDDW
          .EELSQALAS.FSVSQDLNSTAAPHPRLSQYKSKYSSLEQSE..R.LL.LQKCK.LDYVNHARRLAEDDW
Retrocopy VEELSQALASRFSVSQDLNSTAAPHPRLSQYKSKYSSLEQSEQCRQLLKLQKCKQLDYVNHARRLAEDDW

Parental  TGIESEEEDKKDDEEMDIDSGKKLPKRYANQLMLSEWLIDVPSDLGQEWIVVVCPVGK-RALIVASRGST
          TGIESE...KKDDEEMDID.G.KLPKR.ANQLMLSEWL.DVPSDLGQEW.VVVCPV.K.RAL.VASRGS.
Retrocopy TGIESEDKEKKDDEEMDIDRGEKLPKRCANQLMLSEWLTDVPSDLGQEWLVVVCPVEK<RALTVASRGSI

Parental  SAYTKSGYCVNRFSSLLPGGNRQNSTTAKDYTILDCIYSEVNQTYYVLDVMCWRGHPFYDCQTCFFFFFF
          SA.TKSGY.VNRFSSLLPGGNRQNSTTAKDYT.LD.IYS.VNQTY..L.VMCWRGHPFYDCQT.F.F...
Retrocopy SACTKSGYSVNRFSSLLPGGNRQNSTTAKDYTVLDSIYSVVNQTY*ALGVMCWRGHPFYDCQTDFRFY*M

Parental  FSLVAESPGIAQKKKKSGPFKFVGLKNFPCTPESLCKVLSMDFPFEVDGLLFYHKQTHYSPGSTPLVGWL
          .S...E.......K.K..PFKFVGLKNFPCTPESLCKVL.MDFP.EVD.LLFY.KQTHY.PGSTP.V.WL
Retrocopy HSKLPEG---LREKTKPNPFKFVGLKNFPCTPESLCKVL*MDFPSEVDELLFYYKQTHYRPGSTPSVSWL

Parental  RPYMVSDVLGVAV
          .P.MVSDVLGVAV
Retrocopy QPSMVSDVLGVAV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1420 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,