RetrogeneDB ID: retro_ogar_440

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873521.1:8963499..8963961(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRUB2
• Ensembl ID: ENSOGAG00000003511
• Aliases: None
• Description: TruB pseudouridine (psi) synthase homolog 2 (E. coli) [Source:HGNC Symbol;Acc:17170]

Sequence

>retro_ogar_440
ATGATGTCCGCTGGCCTGGCATGGCTGAGTGGGCTCTTCATGGTCTATAAGCCCCTGGGGTTAATATGGAAGCACCTGAG
GGATACCATAGAGCTGCAACTTCTGAAGGGTCTCAATGCTAAGAAACCTCTGGCCCTTGAACAGAGGGGCCCCACATTCT
TACTGGGCCCCACATAAGGCAGTGGTAAGAAGGAGTTGACACTCACAGCCTCCAGTGTGCCCACCCTCACCAGCCATCCA
CTGGTACATGGACCAGCATTCACTAGTCTGAAGGTTGTTGTGAGACACCATCTGGATGCCCAGGCTTCCGGGGTGCTTGT
GTTCAGTATGGGACAGGGATGCAGTCTCCTCACCAGCATCTATGAAGCTCATCTCACCAAGGATTATACAGCCCACGGCC
TCCTGGGCAAAGCCACAGATGACTTCTGTGAGGATGGGCGGCTGGTAGAGAAGACCACATAT

Alignment

ORF - retro_ogar_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 93.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRSAALARLNGLFAVYKPPGLKWKHLRDTIELQLLKGLNAKKPPAPEQR-VRFLLGPIEGSEEKELTLTA
          M.SA.LA.L.GLF.VYKP.GL.WKHLRDTIELQLLKGLNAKKP.A.EQR...FLLGP..GS..KELTLTA
Retrocopy MMSAGLAWLSGLFMVYKPLGLIWKHLRDTIELQLLKGLNAKKPLALEQRGPTFLLGPT*GSGKKELTLTA

Parental  TSVPTLTSHPLVRGPAFTSLKVGVGHRLDAQASGVLVFGVGRGCGLLTSMYEAHLTKDYTVRGLLGKATD
          .SVPTLTSHPLV.GPAFTSLKV.V.H.LDAQASGVLVF..G.GC.LLTS.YEAHLTKDYT..GLLGKATD
Retrocopy SSVPTLTSHPLVHGPAFTSLKVVVRHHLDAQASGVLVFSMGQGCSLLTSIYEAHLTKDYTAHGLLGKATD

Parental  DFCEDGRLVEKTTY
          DFCEDGRLVEKTTY
Retrocopy DFCEDGRLVEKTTY

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_440 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009114	1 retrocopy	retro_etel_1975,
Otolemur garnettii	ENSOGAG00000003511	2 retrocopies	retro_ogar_440 , retro_ogar_441,
Tupaia belangeri	ENSTBEG00000000586	1 retrocopy	retro_tbel_4734,