RetrogeneDB ID: retro_ogar_2456

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873624.1:1171198..1172194(-)
• Located in intron of: None

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_2456
ATGGAGGAGAAGTACCTGCTGGAGCTGATGGTGGAGAAGGACTCTCTGGACTCCTCTTTCACCCACGCTTTGCGGCTGGT
GAACCAAGAAATAGAAAAGTTTCAAAAAGGAGAAGGCAAGGATAAAGAAAAGTACATTAATGTGGTGATTAATAAGAACA
TGAAACTGGGACAGAAAGTGTTAATTCCTATAAAACAGTTTCTTAAATTCAACTTTGTGGGGAAATTTTTGGGTCCACAT
GGCAATTCCCTGAAGAATTTACAAGAAGAAACTTTGACAAAAATGTCCATCCTTGGAAAAGGTTCCATGAGAGATAAAGC
AAAGGAAGAGAGTTGAGGAAAAGTGGAGAAGCCAAGTACTTCCACCTCAATGACATCTCCATGTTCTCATTGAAGGGTTT
TCTCTACCTGCAGAAGCATATGCCCACATGGGACATGCTTTGGAAGAAATCAAAAAGTTCCTCATCCCTGACTATAATGA
TGAGATTAGGCAAGCACAGCTTCAAGAATTAACATATTTAAATGGTGGTTCAGAAAATCCAGATGTTCCAGTGGTTTGAG
GAGAACTTACCTTGGGAATGAGAGGTGTACCAACTCCAACAATAACCAGGGAAAGGGGAGGAGTCACAGCCCAGCCAATT
GGAGTTGGTGTCCCTCGGGGGACATCTGTTCTCAGGGGAGTTCTATCCACCAGAAGTTCAGTGAGTTGGGGAAGAGGACT
TCTCAACTCCAGAGCAAGGGAGTTCCCTAACAGTACAGACCTCCACTGCCACCCCCAACACAAGAGACCTATAGAGAATA
TGACTATGATGATGGATATGGCATTGCTTATGATGAACAGAGTTATGATTCCTATGATAACAGCCATAGCACCCCATCCC
AAAGTGGTGTTGATTACTATGATTATGGACACGGACTCAGTGAGGAGACCTACAGTTCCTATGGGCAAGAGGAGTGAACT
AACTCCAGACACAAGGCACCTTCAGCGAGATCGTCT

Alignment

ORF - retro_ogar_2456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 96.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEEKYLPELMAEKDSLDPSFTHALRLVNQEIEKFQKGEGKDEEKYIDVVINKNMKLGQKVLIPVKQFPKF
          MEEKYL.ELM.EKDSLD.SFTHALRLVNQEIEKFQKGEGKD.EKYI.VVINKNMKLGQKVLIP.KQF.KF
Retrocopy MEEKYLLELMVEKDSLDSSFTHALRLVNQEIEKFQKGEGKDKEKYINVVINKNMKLGQKVLIPIKQFLKF

Parental  NFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEE-ELRKSGEAKYFHLND-DLHVLIEVFAPPA
          NFVGK.LGP.GNSLK.LQEETLTKMSILGKGSMRDKAKEE.ELRKSGEAKYFHLND..LHVLIE.F..PA
Retrocopy NFVGKFLGPHGNSLKNLQEETLTKMSILGKGSMRDKAKEE<ELRKSGEAKYFHLND<HLHVLIEGFSLPA

Parental  EAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPTPTITRGRGG
          EAYA.MGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSEN.DVPVV.G..TL..RGVPTPTITR.RGG
Retrocopy EAYAHMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENPDVPVV*GELTLGMRGVPTPTITRERGG

Parental  VTARPVGVGVPRGTPAPRGVLSTRGPVSRGRGLLTPRAR-GAPPTGYRPPPPPPTQETYGDYDYDDGYGT
          VTA.P.GVGVPRGT...RGVLSTR..VS.GRGLL..RAR.G.P.....P.P.PPTQETY..YDYDDGYG.
Retrocopy VTAQPIGVGVPRGTSVLRGVLSTRSSVSWGRGLLNSRAR<GVP*QYRPPLP-PPTQETYREYDYDDGYGI

Parental  AYDEQSYDSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARSA
          AYDEQSYDSYDNS.STP.QSG.DYYDYGHGLSEETY.SYGQEE.TNSRHKAPSARS.
Retrocopy AYDEQSYDSYDNSHSTPSQSGVDYYDYGHGLSEETYSSYGQEE*TNSRHKAPSARSS

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_2456 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,