RetrogeneDB ID: retro_ogar_3408

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873820.1:660536..661421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26B
• Ensembl ID: ENSOGAG00000015370
• Aliases: None
• Description: vacuolar protein sorting 26 homolog B (S. pombe) [Source:HGNC Symbol;Acc:28119]

Sequence

>retro_ogar_3408
AGTTTTCTTGGAGGCTTTTTCGGTCCAATTTGCGAGATTGATATTGTCCTTCATGATGGAGAAACCAGGAAAATGGCAGA
AATGAAAACTGAAGATGGCAAAGTGGAAAAACACTGTGTCTTCTAGGATGGAGAATCTGTTCAGGGAAGGTAAACGTAGC
CTTTTAGCAACCTGGAAAGAAGCTAGAGCACCAGGGAATTAGAATTGAATTTGTAGGTCAAATTGAACTTTTCAATGACA
AGAGTAATACTCATGAATTTGTAAACCTAGTGAAAGAACCAGCCCTACCTGGAGAACTGACTCAGAGCACAAGTTAGGAT
TTTGCATTTATGCAAGTTGAAAAGCCATCAGAATCTTACATGGGTGCCAATGTCTGCTTGAGGTATTTTCTTAAAGTGAC
AATAGTAAGAAGACTGACAGATTTGGTAAAAGAATATGATCTTATTATTCACCAGCTTGCCACCTATTCAGATGTTAAAT
TCTATCAAGATGGAAGTGGGCATTGAAGATTGTCCACATAGAGAATTTGAATATAATAAATCAAAGTATCATTTAAAGGA
TGTGATTGTTAGAAAAATTTACTTTTTATTAGTAAGAATAAAAATATAACATATGGAGTTACAACTGATCAAAATAGAGA
TAACAGGAATTGGACCCAGTACCACAATGGAAACAGAAACAATTGCCAAATGTGAAATAAAGGATGGTGCACCAGTGAAA
GGGGAATCAATTCCAGTAAGACTATTTTTAGCAGGGTATGACCCAATTCCAACAAGGAGAGATGTGAACAAAAAGTTTTC
AGTAAGATACTTTTTGAATTTAGTGCTTGTTGATGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAGATCGTTTTATGGA
GAAAA

Alignment

ORF - retro_ogar_3408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.46 %
• Parental protein coverage: 87.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFFG--FGQSVEVEILLNDAESRKRAEHKTEDGKKEKYFLFYDGETV-SGKVSLALKNPNKRLEHQGIKI
          SF.G..FG...E..I.L.D.E.RK.AE.KTEDGK.EK...F.DGE.V.SGKV..A...P.K.LEHQGI.I
Retrocopy SFLGGFFGPICEIDIVLHDGETRKMAEMKTEDGKVEKHCVF*DGESV<SGKVNVAF*QPGKKLEHQGIRI

Parental  EFIGQIELYYDRGNHHEFVSLVKDLARPGEITQSQAFDFEFTHVEKPYESYTGQNVKLRYFLRATISRRL
          EF.GQIEL..D..N.HEFV.LVK..A.PGE.TQS...DF.F..VEKP.ESY.G.NV.LRYFL..TI.RRL
Retrocopy EFVGQIELFNDKSNTHEFVNLVKEPALPGELTQSTS*DFAFMQVEKPSESYMGANVCLRYFLKVTIVRRL

Parental  NDVVKEMDIVVHTLSTYPE-LNSSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIKHMEI
          .D.VKE.D...H.L.TY...LNS.IKMEVGIEDC.H.EFEYNKSKYHLKDVIV.KIYFLLVRIKI.HME.
Retrocopy TDLVKEYDLIIHQLATYSD>LNS-IKMEVGIEDCPHREFEYNKSKYHLKDVIVRKIYFLLVRIKI*HMEL

Parental  DIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGESIPIRLFLAGYELTPTMRDINKKFSVRYYLNLVLI
          ..IK.E.TG.GP....E..TIAK.EI.DGAPV.GESIP.RLFLAGY...PT.RD.NKKFSVRY.LNLVL.
Retrocopy QLIKIEITGIGPSTTMETETIAKCEIKDGAPVKGESIPVRLFLAGYDPIPTRRDVNKKFSVRYFLNLVLV

Parental  DEEERRYFKQQEVVLWRK
          DEE.RRYFKQQE.VLWRK
Retrocopy DEEDRRYFKQQEIVLWRK

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_3408 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015370	2 retrocopies	retro_ogar_3407, retro_ogar_3408 ,