RetrogeneDB ID: retro_ogar_2677

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873646.1:2377221..2377932(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YIPF6
• Ensembl ID: ENSOGAG00000002223
• Aliases: None
• Description: Yip1 domain family, member 6 [Source:HGNC Symbol;Acc:28304]

Sequence

>retro_ogar_2677
ATGGCGGAAGCAGTGGAGTCTCTAGAAGACCCAGGGACAGCATCACACAGGCTCCTGTTTTCAGGCCTTTCAGATACATC
TATCTCACAATACGTCCCTGTAGAAGGAGAAATCACCGTTTCTGTGAGATCTCAAGTTCAGGAATTTGACAACTCCACAC
TGAATGAATCTGTTCAGAATACCATCATGCGTGATCTAAAAGCTGTTGGGAAAAAAATTCATGCATGTTTTGTACTCAAG
GAAAAGTAATACAATTTTAAGGGATTGGGATTTGTGGGGTCCTTTGATCCTTTGTGTGACACTTGCATTAATACTGCAAA
AAGGTTCTGCAGATAGTGAAAAAGATGGAGGGCTCCAGTTTGCAGAAGTGTTTGTCGTTGTCTGGTTTGGTGCAATTACC
ATCACCCTAAACTCAAAATTTCTTGGAGGAAACATCATTTTTTCAGAACCCCTGTGTCCTGGGTTACCATATACTTACTT
CCCTTGATGGTGGCCATGCTAATTTGCTGGCTAGTACTTCTGGCTGAACCAGGACCAGTGAACCTCATGCTTTGGCTTTT
TGTGGTGATCATGATGTTTGCCTGGTCTGTAGTTGCCTCTATAGCTTCTCTTGCTGATAGCCAGCCTCCAAACCATAAAG
CCCTTGATGTTGATCCTGATTTCCTGTTCTACTTTGTCATCAGTTGGATGATTCTCCTTTACTCCTCAGAA

Alignment

ORF - retro_ogar_2677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEAAESPGNAGTASPRPLFAGLSDISISQDIPVEGEITIPVRSQIREFDSSTLNESVQNTIMRDLKAVG
          MAEA.ES....GTAS.R.LF.GLSD.SISQ..PVEGEIT..VRSQ..EFD.STLNESVQNTIMRDLKAVG
Retrocopy MAEAVESLEDPGTASHRLLFSGLSDTSISQYVPVEGEITVSVRSQVQEFDNSTLNESVQNTIMRDLKAVG

Parental  KK-FMHVLYPRKSNTLLRDWDLWGPLILCVTLALMLQRGSADSEKDGGPQFAEVFVIVWFGAVTITLNSK
          KK.FMHVLY.RKSNT.LRDWDLWGPLILCVTLAL.LQ.GSADSEKDGG.QFAEVFV.VWFGA.TITLNSK
Retrocopy KK>FMHVLYSRKSNTILRDWDLWGPLILCVTLALILQKGSADSEKDGGLQFAEVFVVVWFGAITITLNSK

Parental  LLGGNISFFQSLCV-LGYCILP-LTVAMLICRLVLLAEPGPVNFMVRLFVVIVMFAWSIVASTAFLADSQ
          .LGGNI.F...LC..L.Y...P.L.VAMLIC.LVLLAEPGPVN.M..LFVVI.MFAWS.VAS.A.LADSQ
Retrocopy FLGGNIIFSEPLCPGLPYTYFP<LMVAMLICWLVLLAEPGPVNLMLWLFVVIMMFAWSVVASIASLADSQ

Parental  PPNRKALAVYPVFLFYFVISWMILTFTPQ
          PPN.KAL.V.P.FLFYFVISWMIL.....
Retrocopy PPNHKALDVDPDFLFYFVISWMILLYSSE

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_2677 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023551	1 retrocopy	retro_fcat_103,
Otolemur garnettii	ENSOGAG00000002223	1 retrocopy	retro_ogar_2677 ,
Pteropus vampyrus	ENSPVAG00000014526	1 retrocopy	retro_pvam_215,