RetrogeneDB ID: retro_ogar_2243

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873605.1:3058048..3058486(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLGRKT
• Ensembl ID: ENSOGAG00000003280
• Aliases: None
• Description: plasminogen receptor, C-terminal lysine transmembrane protein [Source:HGNC Symbol;Acc:23633]

Sequence

>retro_ogar_2243
ATGGGGTTTATAGTTTCAAAATCTATGAGTGAAAACATGAAAAATCAAGAAGAGTTCATGCTTATGAATGCTCGACTTCA
GCTGGAAAGACAACTAATGATGGAGAATGAAATGAGGACAGACGGACGGACATGCAGATTGCTTGGTCTCCAGAATTCCT
CAAATATTTTGGAACTTTTTTGGCATTACAGCCAACTTTTTAACAGCTAGAGCAATAAAAAGTAAAAAGCCAGCCTTCCT
CTTCCCTATTGTTCCATAAACCTTTATTTTCACCTACCAGTATGACTTGGGCCATGGAACCTTCTAGAAAGAATGAAAAG
TGAAGCTGAGGACTTACTAGAAACAGAAAAGAATAAGTTGCAGCTGCCAAGAGGAATGATCACTTTTGAAAGCCTTGAAA
AAACCAGAAGGGACCCCAGTAAATTCTTCACAGACAAA

Alignment

ORF - retro_ogar_2243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGFIFSKSMNENMKNQQEFMQMNARLQLERQLMMQNEMR-ERQMAMQIAWSREFLKYFGTF-FGVTAISL
          MGFI.SKSM.ENMKNQ.EFM.MNARLQLERQLMM.NEMR..R...MQIAWS.EFLKYFGTF.FG.TA..L
Retrocopy MGFIVSKSMSENMKNQEEFMLMNARLQLERQLMMENEMR<DRRTDMQIAWSPEFLKYFGTF<FGITANFL

Parental  TAGAIKSKKPALLIPIVPLSFIFTYQYDLGYGT-LLQRMKSEAEDVLETEKNKLELPRGMITFESLEKAR
          TA.AIKSKKPA.L.PIVP..FIFTYQYDLG.GT.LL.RMKSEAED.LETEKNKL.LPRGMITFESLEK.R
Retrocopy TARAIKSKKPAFLFPIVP*TFIFTYQYDLGHGT<LLERMKSEAEDLLETEKNKLQLPRGMITFESLEKTR

Parental  REQSKFFIEK
          R..SKFF..K
Retrocopy RDPSKFFTDK

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_2243 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004320	1 retrocopy	retro_dnov_1300,
Dipodomys ordii	ENSDORG00000000109	1 retrocopy	retro_dord_553,
Otolemur garnettii	ENSOGAG00000003280	1 retrocopy	retro_ogar_2243 ,
Sarcophilus harrisii	ENSSHAG00000001757	1 retrocopy	retro_shar_822,