RetrogeneDB ID: retro_ogar_3080

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873711.1:2677786..2678357(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSOGAG00000013601
• Aliases: None
• Description: E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]

Sequence

>retro_ogar_3080
GGGGGTATTTTTGACTTAAACAAGGTTGCCACAAAACTGGGAGTACAAAAACAAAATGATATCACCAATATCTTAGGTGA
AATCGACATACTTGAAAAATATAAGAGCCATATTAAGTAGATGGGATCTGATTTCAACAATTTGGAGAAGTACCCCAACA
AAAGAAGCTACAGGAGGAACTTTCTAACTTAACAGCAATGGAGGATACTTTGAATGAGTTAATTAAGGATTGTGCTCAGC
AGTTATTTGACTTAACAAATGACATAGAAAATGAAAGGCTGCCATATGTAACATACCAGGATATTCACAGCATTCCAATC
TTCCATAAACAGATTGTTATTGTTGTTAAAGCTCCAGCAGAAACTAGATTGGATGTTCCAGTTCCCAAAGAAGATTCTAT
TACAGTACACATAAGGAGTACCAATGGGCCTATTGATGTCTGCTTGTGTGAAGTTGAACAAAGTAATCACGAAAAGTCTG
AAGGTATCACCTCTTCACTTGAGAGCAGATAACCCAAATGCCCTAAGAAGAAAATTCTCAGTAAAGTGAAGAATTGCTTG
AAGTGAGCAAC

Alignment

ORF - retro_ogar_3080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 70.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGILDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLSN-FGAVPQQKKLQEELSDLSA
          GGI.DLNKVATKLGV.K....DITN.L..ID..EK..K.HI...GSD..N.FG.VPQQKKLQEELS.L.A
Retrocopy GGIFDLNKVATKLGVQKQN--DITNILGEIDILEKY-KSHIK*MGSDFNN<FGEVPQQKKLQEELSNLTA

Parental  MEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHSIQAFHEQIVIAVKAPAETRLDVPAPREDSITV
          MED.L.ELIKDCAQQLF.LT.D.ENERL.YVTYQDIHSI..FH.QIVI.VKAPAETRLDVP.P.EDSITV
Retrocopy MEDTLNELIKDCAQQLFDLTNDIENERLPYVTYQDIHSIPIFHKQIVIVVKAPAETRLDVPVPKEDSITV

Parental  HIRSTNGPIDVYLCEVEQGHSAHKKSEGGVTPSPEDRHPERSE-EEENPQQTEELLEVSN
          HIRSTNGPIDV.LCEVEQ..S.H.KSE.G.T.S.E.R.P.....EE...Q..EELLEVSN
Retrocopy HIRSTNGPIDVCLCEVEQ--SNHEKSE-GITSSLESR*PKCPK<EENS-Q*SEELLEVSN

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_3080 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 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005114	5 retrocopies	retro_chof_1613, retro_chof_2316, retro_chof_2487, retro_chof_2627, retro_chof_537,
Dipodomys ordii	ENSDORG00000013213	1 retrocopy	retro_dord_369,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Otolemur garnettii	ENSOGAG00000013601	2 retrocopies	retro_ogar_2337, retro_ogar_3080 ,