RetrogeneDB ID: retro_ogar_1145

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873537.1:97440..98472(+)
• Located in intron of: ENSOGAG00000027058

Retrocopy information

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

Parental gene information

• Parental gene symbol: UGDH
• Ensembl ID: ENSOGAG00000004941
• Aliases: None
• Description: UDP-glucose 6-dehydrogenase [Source:HGNC Symbol;Acc:12525]

Sequence

>retro_ogar_1145
ATGTTTAAAATTAAGAAGATCTGTTGCATGGGTGTGGTCTATGTTGGAGGACCCACATGTAGTGTCATTGCTTACATGTG
CCCTAAAATCAGGGTAATGGTTGTTGATGTCAGTGAGTCAAGAATCAATGCATGGAATTCTACACTTCCTATTTATGAGC
CAGGACTAACAGGAGTGGTAGAATCTTGCTGAGGAAAAAATCTATTTTTTTTTTCTACCAATATTGATGATGCCATCAAG
AAACCTGATGATGTATTTATTTCTGTGAATACACCAACAAAAACCTATGGAATGGGGAAAGGTCGTGCAGCAGGATCTAA
AGTATACTAAAGCTTGTGCTAGACGTGTTGTACAAAATTGAAACTGGTACAAACTTGTGACAGAAAAGCATAGTTCCACA
GTGCAGGCAGCAGAAAGTATCGTCGCATATTTGATGCTAACACAAAACCCAACTTGAATTTACAGGTGCTGTCCAACCCA
GAATTCTTGGCAGAGAAGATAGCCATCAAAAACCTAAAGAACCCGTACAGAATACTGATTGGAGGGGATGAAACCCAGAA
GGCCAGAGAGCCATGAGGGCCCTGTGTGTTGTATATGAGTACTGGGTTCTCAGAGAAAAGATTCTCACCACTGACACTTG
GTCTTCAGAGCTTTCCAAACTGGCAGCAAATGCTTTTCTTGCCCAAAGAATCAGCAGCATTAACTCTGTAAGTGCCCTGT
GTGAAGCAACAGGAGCCGATGTAGAAGAGGTAGCAACAGCCATTGGAATGGACCAGAGAATTGGAAGTAAGTTTCTGAAA
GTCAGTGTTGGTTTTGGTGGGAGCTATTTCCAAAAAAGATGTTCTAAATGTGGTTTATTTCTGTGAGGTTCTGAATTTGC
CTGAAGTAGCTCATTATTGGCAGCAGGTAATAGACAAGAATGACTACCAGAGTGGGAGGTTTGCTTCCTGAATCATAGAC
AGTCTGTTTAATGCAGTGACTGAGAAGAAGATAGCTATTTTGAGGTTTATATTCAAAAAGGACACTAGTGAT

Alignment

ORF - retro_ogar_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 69.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MFEIKKICCIGAGYVGGPTCSVIAHMCPKIRVTVVDVNESRINAWNSSTLPIYEPGLKEVVESCRGKNLF
          MF.IKKICC.G..YVGGPTCSVIA.MCPKIRV.VVDV.ESRINAWNS.TLPIYEPGL..VVESC.GKNL.
Retrocopy MFKIKKICCMGVVYVGGPTCSVIAYMCPKIRVMVVDVSESRINAWNS-TLPIYEPGLTGVVESC*GKNLX

Parental  FS-TNIDDAIKEADLVFISVNTPTKTYGMGKGRAA-DLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAE
          ...TNIDDAIK..D.VFISVNTPTKTYGMGKGRAA.DLKY..ACARR.VQN.N.YK.VTEK....V.AAE
Retrocopy XXXTNIDDAIKKPDDVFISVNTPTKTYGMGKGRAA>DLKYTKACARRVVQN*NWYKLVTEKHSSTVQAAE

Parental  SI-RRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDET-PEGQRAVQALCAVYEHWVPRE
          SI.RRIFDANTKPNLNLQVLSNPEFLAE..AIK.LKNP.R.LIGGDET.PEGQRA..ALC.VYE.WV.RE
Retrocopy SI<RRIFDANTKPNLNLQVLSNPEFLAEKIAIKNLKNPYRILIGGDET<PEGQRAMRALCVVYEYWVLRE

Parental  KILTTNTWSSELSKLAANAFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGKG-GA
          KILTT.TWSSELSKLAANAFLAQRISSINS.SALCEATGADVEEVATAIGMDQRIG.KFLK.SVG.G.GA
Retrocopy KILTTDTWSSELSKLAANAFLAQRISSINSVSALCEATGADVEEVATAIGMDQRIGSKFLKVSVGFG>GA

Parental  CGSKEVLNFIQFINSLIFPHLNFRWFQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGD
          ...K.VLN...F...L..P.....W.QVID.NDYQ..RFAS.IIDSLFN.VT.KKIAIL.F.FKKDT.D
Retrocopy ISKKDVLNVVYFCEVLNLPEVAHYWQQVIDKNDYQSGRFAS*IIDSLFNAVTEKKIAILRFIFKKDTSD

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_1145 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
Choloepus hoffmanni	ENSCHOG00000008890	1 retrocopy	retro_chof_2472,
Monodelphis domestica	ENSMODG00000020549	1 retrocopy	retro_mdom_118,
Otolemur garnettii	ENSOGAG00000004941	1 retrocopy	retro_ogar_1145 ,