RetrogeneDB ID: retro_ogar_2861

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:3140503..3141326(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSOGAG00000007978
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 6 [Source:HGNC Symbol;Acc:2747]

Sequence

>retro_ogar_2861
ATGAGGCTTCATGACACAGTTCACGTGGTGATCGCTACCCCTGGGAGAATCCTAGATCTTATTAAGAAAGGAGTAACAAA
GGTTGATCACGTCCAAATGATAGTATTGGATGAGGCAGGTAAGTTGCTATCACAGGATTTTGTGCAGATAATGGAGAATC
TCATTCTCACACTACCTAAAAACAGGCAGATTTTACTGTATTTGAGCTACTTTCCCTCTTCGTATGCAGAAATTCATGAA
TTCCCATTTGCCGAAACCCTATGAGATTAACATGATGGAGGAACTAACTTTGAAGGGAGTAACCCAGTACTACACATATG
TAACTGGGTGCCAGAAAGTACACTGCCTCAACACAATTTTCTCCAGGCTTCAGATAAACCAGTTGATCATTTTCTGTAAC
TCCTCTTAGCGAGTGGAATTGCTAGCCAAGACGATTTCTCAACTGGGTTATTCTTGCTTCTATATTCATGCTAAAATGAG
GCAGAAACATCAAAAATGTGTATTTCATGATTTCCAAAATGGCTTATGCCAAAATCTTGTTTGCACTCATCTGTTTACCT
GAGATGTTGATATACAAGCTGTGAATGTGGTAATAAACTTTGACTTCTCAAAGATGGCAGAGACCTATCTCCATCGTATT
GGAAGATCAGGTCGCCTTGGTCATCTTGGCTTAGCCATCAACTTGATCACATACAATGATTGCTTTGATCTGAAAAGTAT
TGAGGAGCAGCTGGGAACAGAAATTAAACCTATCCCAAGCAACCTTGACAAGAGCCTGTATGTGGCAGGATACCACAGCG
AGCCTGTAGAAGATGAAAAACCT

Alignment

ORF - retro_ogar_2861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.91 %
• Parental protein coverage: 56.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYS-A
          MRL.DTVHVVIATPGRILDLIKKGV.KVDHVQMIVLDEA.KLLSQDFVQIME..ILTLPKNRQILLY..A
Retrocopy MRLHDTVHVVIATPGRILDLIKKGVTKVDHVQMIVLDEAGKLLSQDFVQIMENLILTLPKNRQILLYL>A

Parental  TFPLSVQKFMNSHLQKPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVE
          TFPL..QKFMNSHL.KPYEIN.MEELTLKGVTQYY.YVT..QKVHCLNT.FSRLQINQ.IIFCNSS.RVE
Retrocopy TFPLRMQKFMNSHLPKPYEINMMEELTLKGVTQYYTYVTGCQKVHCLNTIFSRLQINQLIIFCNSS*RVE

Parental  LLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETY
          LLAK.ISQLGYSCFYIHAKMRQ.H...VFHDF.NGLC.NLVCT.LFT...DIQAVNVVINFDF.K.AETY
Retrocopy LLAKTISQLGYSCFYIHAKMRQKHQKCVFHDFQNGLCQNLVCTHLFT*DVDIQAVNVVINFDFSKMAETY

Parental  LHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          LHRIGRSGR.GHLGLAINLITY.D.F.LKSIEEQLGTEIKPIPSN.DKSLYVA.YHSEPVEDEKP
Retrocopy LHRIGRSGRLGHLGLAINLITYNDCFDLKSIEEQLGTEIKPIPSNLDKSLYVAGYHSEPVEDEKP

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_2861 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861 ,
Otolemur garnettii	ENSOGAG00000008730	1 retrocopy	retro_ogar_2862,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,