RetrogeneDB ID: retro_ogar_2754

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873661.1:818111..818635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIH1D1
• Ensembl ID: ENSOGAG00000004612
• Aliases: None
• Description: PIH1 domain containing 1 [Source:HGNC Symbol;Acc:26075]

Sequence

>retro_ogar_2754
ATGGTGAACTCGAAGCTGCTGGCACCGGAGTTAAGCAAGACAGAGATGATGGGTGCTGAGACGGTGCGATCCGAGGAGCT
CCGTCTTGGAGGTGCCTCCAAGGAGTTCCAGCAAGCCCAGACAACCAGAACAGATTCTACACAAATTCAACCTCAGCCTG
GTTTCTGCATAAAGACTAACTCACCAGAAGAGAAGCTTTTCATCAACATCTGTCACTCTGCCATCCATCCCTCCTCCAAC
TTGACATGACTGACGATGAGATTCTTCAAATGCTAGAGGAGGACCAAGCTGGGTTTTGCATCCCCATGAATCTGGGAGAG
CCTCATGCTGAACTGGATGCAAAAGGCCAGGGCTGTACCACCTATGATGTAGCTATCAACAGCAACTTCTACAGGTGGAT
GCAGAACAGTGATTTCTTGCAAGAGCTCGTGGTCACCATTGCCAGGGAGGTCCCTGAGGATAAATACAGCTTGCAGCTGA
ATCCAGAATGGTGCACGTTGAAGAATGGGACTTTCCTGGGTTCC

Alignment

ORF - retro_ogar_2754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 59.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MANSKLLAPELCETETMGAETARFEELLLLQASKEFQQAQITRPDSTQIQPQPGFCIKTNSSEGKVFINI
          M.NSKLLAPEL..TE.MGAET.R.EEL.L..ASKEFQQAQ.TR.DSTQIQPQPGFCIKTNS.E.K.FINI
Retrocopy MVNSKLLAPELSKTEMMGAETVRSEELRLGGASKEFQQAQTTRTDSTQIQPQPGFCIKTNSPEEKLFINI

Parental  CHSA-SIPPPA-DVTEDELLQMLEEDQAGFRIPMSLGEPHAELDAKGQGCTAYDVAVNSDFYRRMQNSDF
          CHSA.SIPPP..D.T.DE.LQMLEEDQAGF.IPM.LGEPHAELDAKGQGCT.YDVA.NS.FYR.MQNSDF
Retrocopy CHSA>SIPPPT>DMTDDEILQMLEEDQAGFCIPMNLGEPHAELDAKGQGCTTYDVAINSNFYRWMQNSDF

Parental  LRELVVTIAREGLEDKYSLQLNPEWRMLKNRTFLGS
          L.ELVVTIARE..EDKYSLQLNPEW..LKN.TFLGS
Retrocopy LQELVVTIAREVPEDKYSLQLNPEWCTLKNGTFLGS

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_2754 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004612	2 retrocopies	retro_ogar_1564, retro_ogar_2754 ,