RetrogeneDB ID: retro_ogar_3114

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873720.1:2514039..2515058(-)
• 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_3114
ATGGAGGAACTTATGATGGAGAAGGACTCCCTGGACCCCTCCTTCATGCATGCTCTGTGACTGGTGAACCAAGAAATAGA
AAAGTTTCAAAAAGGAGAAGTCAAGGATGAATAAAGTACATTGACGTGATTAATAAGAACATGAAGCTGGGACTGAAAGT
GTTAATTCCTGTAAAACAGTTTTCTAAGTTCAACTTTGTGGGGAAACTTTTGGGTCCACATGGCAATTCTCTGAAGTGTT
TACAAGAAGAAACTTGGACAAAAATGTCCATCTTTGGAAAAGGTTCCATGAGAGACAAAGCAAAGGAAGAAGAGTTGAAG
AAAAGTGGAGAAGCCAAGTACTTCCATCTCAATGATGATCTCCATGTTCTCATTGAAGTCTTTGCTCCACCTACAGAAGC
ATATGCCCACATGGGACATCCTTTGGAAGAAATCAAAAAATTCTTCATCCTTGACTATAATCATGAAATTAGGCAAGCAC
AGCTTCAAGAATTAACATATTTAAATGGTGGTTCAGAAAATGCAAATGTTCCAGTGATTCAGGGAAAACCTACCTTGCTT
ACAAGAGGTGTACCAACCCCAACAATAACCAGGGGAAGGGAAGGAGTCATAGCCCATCCAGTTGGAGTTGGTGTCCCTAG
TGGGACAGTAGCTCCCAGGGGAGTTCTATCCAGCAGAGGTCCCATGAGTCGGGGAAGAGGACTTCTCACCCCCAAAGCAA
GAGGAGTTCCCCCAACTGGGTACAGACCTCCATCACCACCCCCAACACAAGAAACCTATGGAAAATATGACTATGATGAT
GGATATGGCACTGCTTATGATGAACAGAGTTATGATTCCTATGATAATAGCTATAGCACCCCAGACCAAAGTGGTGCTGA
TTACTATGATTATGGACACGGACTCAGTGAGGAGACCTATGATTCCTACAGGCAATAGGAGTGGGCTAACTCCGGATACA
AGGCACCTTCAGCGAGATCAGCAAAGGGTGTTTATAGAGACCAACCATATGGCAGATAC

Alignment

ORF - retro_ogar_3114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPELMAEKDSLDPSFTHALRLVNQEIEKFQKGEGKDE-EKYIDVVINKNMKLGQKVLIPVKQFPKFNFVG
          ..ELM.EKDSLDPSF.HAL.LVNQEIEKFQKGE.KDE..KYIDV.INKNMKLG.KVLIPVKQF.KFNFVG
Retrocopy MEELMMEKDSLDPSFMHAL*LVNQEIEKFQKGEVKDE<IKYIDV-INKNMKLGLKVLIPVKQFSKFNFVG

Parental  KLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLIEVFAPPAEAYARM
          KLLGP.GNSLK.LQEET.TKMSI.GKGSMRDKAKEEEL.KSGEAKYFHLNDDLHVLIEVFAPP.EAYA.M
Retrocopy KLLGPHGNSLKCLQEETWTKMSIFGKGSMRDKAKEEELKKSGEAKYFHLNDDLHVLIEVFAPPTEAYAHM

Parental  GHALEEIKKFLIPDYNDEIRQAQLQELTYLNGGSENADVPVVRGKPTLRTRGVPTPTITRGRGGVTARPV
          GH.LEEIKKF.I.DYN.EIRQAQLQELTYLNGGSENA.VPV..GKPTL.TRGVPTPTITRGR.GV.A.PV
Retrocopy GHPLEEIKKFFILDYNHEIRQAQLQELTYLNGGSENANVPVIQGKPTLLTRGVPTPTITRGREGVIAHPV

Parental  GVGVPRGTPAPRGVLSTRGPVSRGRGLLTPRARGAPPTGYRPPPPPPTQETYGDYDYDDGYGTAYDEQSY
          GVGVP.GT.APRGVLS.RGP.SRGRGLLTP.ARG.PPTGYRPP.PPPTQETYG.YDYDDGYGTAYDEQSY
Retrocopy GVGVPSGTVAPRGVLSSRGPMSRGRGLLTPKARGVPPTGYRPPSPPPTQETYGKYDYDDGYGTAYDEQSY

Parental  DSYDNSYSTPAQSGADYYDYGHGLSEETYDSYGQEEWTNSRHKAPSARSAKGVYRDQPYGRY
          DSYDNSYSTP.QSGADYYDYGHGLSEETYDSY.Q.EW.NS..KAPSARSAKGVYRDQPYGRY
Retrocopy DSYDNSYSTPDQSGADYYDYGHGLSEETYDSYRQ*EWANSGYKAPSARSAKGVYRDQPYGRY

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_3114 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.

---

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,