RetrogeneDB ID: retro_ogar_759

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873527.1:12833630..12834396(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF8
• Ensembl ID: ENSOGAG00000016885
• Aliases: None
• Description: TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa [Source:HGNC Symbol;Acc:17300]

Sequence

>retro_ogar_759
ATGGCTGATGTGGTGGCCACAACTGGGGTCAGCAGCTCCGGAACAAGATCAGGAAGTAAATAGTTTTCTAACCCTGCTGA
TAACTACCATTTGGCCTGGAGGAGAACCCTACAAGTGGCTGTGAGCTCCTTGCTGACAGAGGCAGGGTTTGAGAGCGCTG
AAAAAGCATCCGTGGAAACACTGACAGAGATCCTGCAGAGCTTCATTTCAGACATTGGGAGGAAGGCCAAGTTTTACCGT
GAGCACACAGCCAGGACTCAGCTCTCACTGTTGGATAAGGTGGTCACACTTGTTGAGATGGGTTTTAATGTGAACACTCT
CTCAACTTATACAAAATGGTCTCAGAGGATGGTCATCACCGCTCCTCCAGTGACCATTCAACCAGTGATTCCCAAGGTCC
TCACTGCAGGGCAGAACCAACCTCATACCACACATCCCCAGCCATTTCCCTAAGTTCCCTGATCCCCACACTTACGTCAA
AACTCCAATGTACTGTGAGCCTATGTTAGACTACCAGGTCCTGGAAGAGAAGGCTGCACTCCAGAGATGCGATGTGGAGC
AGGCACTCACCCGGTTCATGGCCAAGACAGGAGAGGCTGAGAGTTTTTTCAAAGGTGATGTTAGCACATTTCCATTAACT
GCTGCCAGACCATTCACCGTTCCCTCCCTGACAGCTCTTCTTCCATCTGAGCTGGAGATGCAATAAATGGAAGAGATGGA
TTCCTTGGAGCAGGATGAGCAGACAGAGAGAACCTATCTGTTCTTA

Alignment

ORF - retro_ogar_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.65 %
• Parental protein coverage: 82.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADAAATTGAGGSGTRSGSKQSTNPADNYHLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSYIS
          MAD..ATTG...SGTRSGSK...NPADNYHLA.RRTLQV.VSSLLTEAGFESAEKASVETLTE.LQS.IS
Retrocopy MADVVATTGVSSSGTRSGSK*FSNPADNYHLAWRRTLQVAVSSLLTEAGFESAEKASVETLTEILQSFIS

Parental  EIGRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNR
          .IGR.AK.Y.EHTARTQ..L.D.VVTLVEMGFNV.TL..Y.K.SQRMVITAPPVT.QPV.PK.LTAGQN.
Retrocopy DIGRKAKFYREHTARTQLSLLDKVVTLVEMGFNVNTLSTYTKWSQRMVITAPPVTIQPVIPKVLTAGQNQ

Parental  PHPPHIPSHF-PEFPDPHTYIKTPTYREPVSDYQVLREKAASQRRDVERALTRFMAKTGETQSLFKDDVS
          PH..H.P..F.P.FPDPHTY.KTP.Y.EP..DYQVL.EKAA.QR.DVE.ALTRFMAKTGE..S.FK.DVS
Retrocopy PHTTH-PQPF>PKFPDPHTYVKTPMYCEPMLDYQVLEEKAALQRCDVEQALTRFMAKTGEAESFFKGDVS

Parental  TFPLIAARPFTIPYLTALLPSELEMQQMEETDSSEQDEQTDTENLSL
          TFPL.AARPFT.P.LTALLPSELEMQ.MEE.DS.EQDEQT....L.L
Retrocopy TFPLTAARPFTVPSLTALLPSELEMQ*MEEMDSLEQDEQTERTYLFL

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_759 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Macropus eugenii	ENSMEUG00000006952	1 retrocopy	retro_meug_150,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759 ,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,