RetrogeneDB ID: retro_ogar_3395

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873817.1:127508..129060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX17
• Ensembl ID: ENSOGAG00000001539
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 17 [Source:HGNC Symbol;Acc:2740]

Sequence

>retro_ogar_3395
TTCCCACAATAAACAGATGTGTTGATGTGTCAGCACTTTACAAACACAATTCCAATTCCATGTCAGGGATTTCCATTGGC
TCTTAGTGGCCAGAAAATGTTAGGCATTGCTCAGAATGGCTCTGGGAAATCATTGGCATATTTGCTGCCTGCAGTTGTGC
ATATTAACCCCCAGCCATACTTGGAAAGGGGAGATAGCCTAATTTGTCTAGTTCTGGCTCCAACCAGAGATGTTGGCCAC
CAAGTACAGCAGGTGGTTGATAACTATAGAAAATCTTCTAGATTGACGAGTACTTGAATTTATGGAGGTGCCCCTAAAGG
TCCCCAGATTCGAAATTTAGAGAGAGGTGTTGAGATCTGCATATATACTCTTGGACGCCTGATAGATTTCCTGCAGTCAA
GAAAGACAATCTTCACCGATGTACTTACGTTGTACTGGATGAGGCTGATAGAATGCTTGATATGGGCTTTGAACCCCAGA
TCCCTAAAGTTGTTGACCAAATCAAGACAGATAGTCAGACATTGATGTGGAGTGCAACCTGGCCAAAATAAGTAAGACAG
CTTGTGGACGATTTCCTTCCTGATTACACCCAGATCAACGTAGGCAATCTGGAGTTGAGTGCCAAACACAACATCCTCCA
GATTGTGGATATCTGCGTGGAAAGTGAAAAAGACCTCAAATTGATCCAACTTATAGAGGAAATAATGGCTGAAAATGGCA
ATAAGACAGTATTTCTGGAGACAAAGAGACACTATGATGAATGACCTGACTCGAAGGATGGGCAGAGATGTTTGGCCAGC
CCTGTGTTCCCACAGAGACAAGAGTCAATCAGAAAGGAGTTGGTTACTTAATAAGTTCTGTTCTGGAAAGGCTCTGATCC
TTGTTGCCACAGATGTACCTCTGGTGGGCTACATGTAGAAGATGTCAAGTTTATGATCAATGGTGACTATCCAATCAGCT
CTAAGGATTATGTGCATCATATTGGCAGAACAGCCTCTAGCTCCAATACGGGCACTGCCTATACCTTCTGCATGGCAGAG
AATCTCAAACAGGCTGGAGAGCTAATCAAAGTACTGGAAGAAGCTAATCAGCCTATCGATCCAAAACTAATGCAGCTAGT
GGACTACAAAGGAAGCAGCAGAGGATGGGGAGGTCATTCACAACACCACACCACACTGGACCATTTCTTCAGCCAACAAT
TCTAATGGGATGTATGAAAATGAGTGTGACCAGAGGCTTCCAGGAGTTAAGGATGGTGGCTGGAGAAACTCCATAAGCTA
TTGGGATTGTGGTGAAATGGATAGAGCTAGATATGCTAATGGCAGTGGCTATGAAAGTCCAAATTCTAACTTTGGAGCAG
AAGCAGGTCAATACACTGATGGTCAAGACACCTATGGGACAGCTGCTTATGGCACCAGTGGCTGTACAGCCCAAGAATAT
GGTGCTGGCACTTATGGAGCTAATAGCACCACTCAATTGGGAGAAGTTCACAGAGCTCTAGGCAGCAGTTTAGTGGGTAA
GCAGGTCTGGGCAGCAGTAACAGCCACTGATG

Alignment

ORF - retro_ogar_3395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.52 %
• Parental protein coverage: 79.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  FPQYVMDVLMDQHFTEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPIC
          FPQ...DVLM.QHFT...PI.CQGFPLALSG..M.GIAQ.GSGK.LAYLLPA.VHIN.QPYLERGD..IC
Retrocopy FPQ*T-DVLMCQHFTNTIPIPCQGFPLALSGQKMLGIAQNGSGKSLAYLLPAVVHINPQPYLERGDSLIC

Parental  LVLAPTRELAQQVQQVADDYGKCSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKT-NL
          LVLAPTR....QVQQV.D.Y.K.SRL.ST.IYGGAPKGPQIR.LERGVEICI.T.GRLIDFL.S.KT.NL
Retrocopy LVLAPTRDVGHQVQQVVDNYRKSSRLTST*IYGGAPKGPQIRNLERGVEICIYTLGRLIDFLQSRKT<NL

Parental  RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYTQINVGNLELSA
          .RCTY.VLDEADRMLDMGFEPQI.K.VDQI..D.QTLMWSATWPK.VRQL..DFL.DYTQINVGNLELSA
Retrocopy HRCTYVVLDEADRMLDMGFEPQIPKVVDQIKTDSQTLMWSATWPK*VRQLVDDFLPDYTQINVGNLELSA

Parental  NHNILQIVDVCMESEKDHKLIQLMEEIMAEKENKTIIFVETKR-RCDDLTRRMRRDGWPAMCIHGDKSQP
          .HNILQIVD.C.ESEKD.KLIQL.EEIMAE..NKT............DLTRRM.RD.WPA.C.H.DKSQ.
Retrocopy KHNILQIVDICVESEKDLKLIQLIEEIMAENGNKTVFLETKRH>MMNDLTRRMGRDVWPALCSHRDKSQS

Parental  ERDWVLNEFRSGKAPILIATDV-ASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTP
          ER.W.LN.F.SGKA.IL.ATDV..S.GL.VEDVKF.IN.DYP.SS.DYVH.IGRTA.S.N.GTAYTF...
Retrocopy ERSWLLNKFCSGKALILVATDV<TSGGLHVEDVKFMINGDYPISSKDYVHHIGRTASSSNTGTAYTFCMA

Parental  GNLKQARELIKVLEEANQAINPKLMQLVDHRGGGGG-GGKG-GRSRYRTTSSANNPNLMYQDECDRRLRG
          .NLKQA.ELIKVLEEANQ.I.PKLMQLVD..G...G.GG.........T.SSANN.N.MY..ECD.RL.G
Retrocopy ENLKQAGELIKVLEEANQPIDPKLMQLVDYKGSSRGWGGHS>NTTPHWTISSANNSNGMYENECDQRLPG

Parental  VKDGGRRDSTSYRDRGETDRAGYANGSGYGSPNSAFGAQAGQYTYGQGTYGAAAYGTSGYTAQEYGAGTY
          VKDGG.R.S.SY.D.GE.DRA.YANGSGY.SPNS.FGA.AGQYT.GQ.TYG.AAYGTSG.TAQEYGAGTY
Retrocopy VKDGGWRNSISYWDCGEMDRARYANGSGYESPNSNFGAEAGQYTDGQDTYGTAAYGTSGCTAQEYGAGTY

Parental  GASSTT-STGRSSQSSSQQFSA-IGRSGQQPQPLM
          GA.STT.S.GRSSQSS.QQFS....RSGQQ.QPLM
Retrocopy GANSTT<SIGRSSQSSRQQFSG<VSRSGQQ*QPLM

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_3395 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006499	1 retrocopy	retro_dnov_1903,
Otolemur garnettii	ENSOGAG00000001539	1 retrocopy	retro_ogar_3395 ,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Rattus norvegicus	ENSRNOG00000013691	1 retrocopy	retro_rnor_1276,