RetrogeneDB ID: retro_ogar_1351

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873543.1:9868987..9869720(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VRK3
• Ensembl ID: ENSOGAG00000008746
• Aliases: None
• Description: vaccinia related kinase 3 [Source:HGNC Symbol;Acc:18996]

Sequence

>retro_ogar_1351
GGACAAGAGTGGGCAGCAGTAGAAGCATCCAAGACCAGGAGAGACCAGGGAATTCTCTAGGAAGCTTAGCCCACCTCTGT
GCTCACCTGTGAGTCAGGTCCCCAGAAACAAAATTTCTCGCTCAAATTGGATGTGAGGATCCATCCAAGGATGGGCGCTT
GTTCAATGAGCAGAACTTCTTCCAGTGGGCTGCAAGCCAGCAAGTGGAAGATGCTTTACTTGACTGCCCTACTGCCATCC
CCAACTACATGGGCTTTGGTGTTCACCAGGACAACTACAAGTTCTTGTTGTTCCCCAGCCTGGGGTGGAGCCTTCAGTCA
TCCCAGGATGACAGCCTGAAGGATGTGATGTCAGAGAGGTCTGTGCTCCAGGTGGCCTGCTGGCTGCTGGATGCCCTGGA
GTTCCTCCATGAGAATGAATATGTCCAAGGCAATGTGACAGCTGAGAATATCTTTGTGATCCAGGGTATCTGAATTAGAT
GACCCTGATGGACTATGGCTTCACCTTCCACTATTGCCCAAGTGGCGGACATATAGCCTACATGGAGCTCAGTGGGAGCC
CACATGAGTGGGCTCTTGAGTTCATTATCATGGACCTGCACAAGGGATGTCGGCCCTCCCACCACAGTGATCTCCAGACC
CTAGGATACTCTATACTGACATGGCTCTCTGGGTTTCTGTCATGGACAAACTGCCTTCTGAACATTGAGGTTATCATGAA
TCAGAAGCAGAAG

Alignment

ORF - retro_ogar_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQQWK-LGCLQTRDDQGILYEAEPASVLTCGSGPQKQKFSLKLDAKDGRLFNEQNFFQRAAKPLQVSKWK
          GQ.W.......TR.DQGIL.EA.P.SVLTC.SGPQKQ.FSLKLD...................LQ.SKWK
Retrocopy GQEWAAVEASKTRRDQGIL*EA*PTSVLTCESGPQKQNFSLKLDVRIHPRMGACSMSRTSSSGLQASKWK

Parental  KLHSTPLL-AIPTCIGFGVHQDKYRFLVFPSLGRSLQSALDDNPKHVMSERSVLQVACRLLDALEFLHEN
          .L..T.LL.AIP...GFGVHQD.Y.FL.FPSLG.SLQS..DD..K.VMSERSVLQVAC.LLDALEFLHEN
Retrocopy MLYLTALL<AIPNYMGFGVHQDNYKFLLFPSLGWSLQSSQDDSLKDVMSERSVLQVACWLLDALEFLHEN

Parental  EYVHGNVTAENIFV-NPEDLSQVTLAGYGFTFRYCPSGRHVAYMEGSRSPHEGDLEFISMDLHKGCGPSR
          EYV.GNVTAENIFV..P..L...TL..YGFTF.YCPSG.H.AYME.S.SPHE..LEFI.MDLHKGC.PS.
Retrocopy EYVQGNVTAENIFV<DPGYLN*MTLMDYGFTFHYCPSGGHIAYMELSGSPHEWALEFIIMDLHKGCRPSH

Parental  RSDLQTLGYCMLKWLYGFLPWTNCLPNTEDIMKQKQK
          .SDLQTLGY..L.WL.GFL.WTNCL.N.E.IM.QKQK
Retrocopy HSDLQTLGYSILTWLSGFLSWTNCLLNIEVIMNQKQK

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_1351 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000002205	1 retrocopy	retro_mmus_915,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Otolemur garnettii	ENSOGAG00000008746	1 retrocopy	retro_ogar_1351 ,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Otolemur garnettii	ENSOGAG00000014866	1 retrocopy	retro_ogar_264,
Otolemur garnettii	ENSOGAG00000016063	1 retrocopy	retro_ogar_47,
Otolemur garnettii	ENSOGAG00000016785	1 retrocopy	retro_ogar_2000,