RetrogeneDB ID: retro_ogar_550

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873523.1:31588074..31588732(+)
• Located in intron of: ENSOGAG00000000917

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS3
• Ensembl ID: ENSOGAG00000005150
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:HGNC Symbol;Acc:18117]

Sequence

>retro_ogar_550
AATAATAATCTTCATGTTCTCATTGAAGCATTTTCTCCACCTGTAGAAGCTTAAGCCCACGTCGGACACGCTTCTGGTAG
AAATCAAAAATTTCCTTATCCTTGACTGCAATAATGATGAGATTAGGCAAGTACTTCAATAATTAACATATTTAAATGCT
AGTTCAGAAAATGCAGATGTTTCAGCAGTTCCAGGAAAACCTCTCTTGCATACAAGAGGTATACCAACCCCAACAATAAC
CAGGGTAAGTGGAGAAGTCACAGCCCAGCCAGCTGGAATTGGTATGCAGAGAGGGATAGGATACCAAGTTCCAGGAGAGT
CCTATTCACCAGAAGGTCAGTAAGGTGGGGGAGAGAACTTATTTCCAGAGCAAGAGTAGTCCTTCTGACTGGGTACAGAT
CTCCACAGCCACCCCCAACACAAGAGACCCATGGAGAATAAGATTATGATGATAAATATGATATTGCTTATGAACTGAGT
TATGAATCCCATGATTAACACCCCAGCCCAAAGTGGTGCTGATTATCATAATTATGACACAGACTCAGTGAGGAGAGTTA
CGATTCCTACGTGCGAGAGTAGACTAACTCCAGACAACAAGGCACCTTCAGCAAGATCAGCAAAGGGCATCTACAGAGAC
CAGTCATATGGCAGATAC

Alignment

ORF - retro_ogar_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.71 %
• Parental protein coverage: 64.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NDDLHVLIEVFAPPAEAYARMGHA-LEEIKKFLIPDYN-DEIRQAQLQELTYLNGGSENADVPVVRGKPT
          N..LHVLIE.F.PP.EA.A..GHA.L.EIK.FLI.D.N.DEIRQ..LQ.LTYLN..SENADV..V.GKP.
Retrocopy NNNLHVLIEAFSPPVEA*AHVGHA>LVEIKNFLILDCNNDEIRQV-LQ*LTYLNASSENADVSAVPGKPL

Parental  LRTRGV--PTPTITRGRGGVTARPVGVGVPRG-TPAPRGVLSTRGPVSRGRGLLTPRARGAPPTGYRPPP
          L.TRG...PT.T...G.........G.....G..P..R.VL.TR..V..GR.L...RAR....TGYR.P.
Retrocopy LHTRGIPTPTITRVSGEVTAQPAGIGMQRGIG<IPSSRRVLFTRRSVRWGRELIS-RARVVLLTGYRSPQ

Parental  PPPTQETYGDYDYDDGYGTAYDEQSYDSYDNS-YSTPAQSGADYYDYG-HGLSEETYDSYGQEEWTNSR-
          PPPTQET.G..D....Y...YD.....SY......TPAQSGADY..Y..H.LSEE.YDSY..E..TNSR.
Retrocopy PPPTQETHGE*D----YDDKYDIAYELSYESH>INTPAQSGADYHNYD<HRLSEESYDSYVRE*-TNSR>

Parental  HKAPSARSAKGVYRDQPYGRY
          .KAPSARSAKG.YRDQ.YGRY
Retrocopy NKAPSARSAKGIYRDQSYGRY

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_550 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550 ,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929,