RetrogeneDB ID: | retro_ogar_3220 | ||
Retrocopy location | Organism: | Bushbaby (Otolemur garnettii) | |
| Coordinates: | GL873743.1:597243..600317(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOGAG00000027156 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SMARCAD1 | ||
| Ensembl ID: | ENSOGAG00000011444 | ||
| Aliases: | None | ||
| Description: | SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 [Source:HGNC Symbol;Acc:18398] |
Retrocopy-Parental alignment summary:
>retro_ogar_3220
ATAAATCTTTTCAACTTGGACCATTTTCACTTTGAGAAAAGGAATAAGAGTGAGGAAACACCTGAAGCAACCCCGCAACC
TTCTCGACCTAGCCCTTCGTCTCTAATTTATCTTAGTGCTGAAGAGGAGAATACTGAAGGGGAAGTTAGCAGGGCAACCA
CTCCAGATTCAGAGATAACGGGAAAAGCAGAAGATGCTAGTGTTCTAGAAAGTATCTAGACAACGAAAGAAAAGTAAGTT
TATCATATTTCAAGAATCAAAGAGGATTACAGTATATTGATTTGTCTTCGGATAGGGAAGATGTTATTTCCCCAGATTCC
TCTAATATAGTTCAAGAGAAAAAGTTTAACAAGGACACAGTGATTATAGTTTCTGAGCCATCTGAAGAGCCCCAGGGCCT
TCCAGCCATGGCACGTAGAAATAATGATGATATTTCAGAATTGGAAGACCTCTCGGAGTTGGCGAATCTTAAAGAAGCCA
ACCTTCAGATTTTGAAGGAACGTTTTCCACACAAAACTGACAGTGATCTACGTAAGTTGATTGACTCAACGAGCACTATG
GATGACGCAATTGCCACCGCCCTGCGGATGTTTGGTGATGCACGTGGTGGGCCAAGGAAAAGAAAATTATCTTCTTCTTC
AGAGCCATACGAGGAAGATGACTTTAATGATGATCAATCTCTAAAAAAGACAAGACCGGATCATGGAAAAGAATCCAATG
AGTCTGCAGAATCTCGCAGTAATTGGAAAAAGCGGGAAAGGATTGTTTTGAAATTACAAAAGGAATTTCCCCATTTTGAT
AAACAGGAACTAAGAGAAGTACTCAAGGAACATGAATGGATGTACGCAGAAGCTTTAGGATCTCTAAGATTGTTTTCAGA
AGACCAAGATATGCAATCCGCGTCACAAAGTGAGGTTCCAAATGGAAAAGACGTTTCTTCAAGAAGTCAGAATTACCCTA
AAAATGCAGCTAAAACGAAACAGAAATTTTCCACGAAACCACAAAATGGTTTTAACAAGAAATGTAAAACAAAAATCTTT
AATCCAAAGCAAGTCATGGAAGACTCTGAGAATGATTCAGGTCCCGATGCTGATAGTTCATGGGATGAGGACTATACTAG
TGATGAAGAAGTGAAGATGGAGGATGGCTATAAACGTAAAATTCTTCGCTTCCTTCAGGATGCTTCAATTAGTGAACTGA
CTCTGATACCTCACTGTCATCAGAAGAAGGCTCAGAAGATTATAGAATCCCGACCCTTTAATTGTTGGGAAGCTCTGTTC
ACAAAGTTGTCCAAAACAAAAGGCTTATCAGAAGATTTGATATGGAACTGTAAAACACTGATCCAACAAAGGGATGTAGT
TATCAGGCTTATGAACAAATGTGAAGACATTTCAAATAAACTGACCAGACAAGTCACCATGCTCACGGGAAATGGCAGTG
GATGGAATGTAGAACAGCCATCCATTCTAAATCCAAGTTTGTCGCTTAAGCCGTATCAGAAGGTTGGTTTGAATTGGCTC
GCATTGGTACATAAACACGAACTTAACGGCATTTTAGCAGACGAAATGGGCCTCGGAAAAACTATTCAAGCCATTGCATT
TCTGGCATACCTCTATCAACAGGGTAATAATGGCCCTCATTTGATCGTTGTTCCAGCCTCCACCATAGATAACTGGTTAA
GGGAAGTTAATTTATGGTGCCCTACTCTAAAGGTGCTCTGTTACTATGGTTCTCAAGAAGAACGACTGCAAATTCGATGC
AACATTCATAGTAGATCCGAAGATTACAACGTAATTGTGACCACGTATAACTGTGCAATTAGCAGTTCAGAGGACCGTAG
TCTGTTTCGACGGCTAAAACTTAAATATGCAATTTTTGATGAGGGCCATATGCTGAAGAACATGGGCTCCATCCGATACC
AGCACCTTATGACAATTAATGCAAACAACCGTTTGCTGCTCACAGGCACACCAGTACAGAATAATCTGTTAGAACTCATG
TCGCTGTTGAATTTTGTTATGCCACACATGTTCAGTAGCAGCACCAACGAAATACGCAGAATGTTTTCTTCCAAAACGAA
AGCAGCAGAGGAGCAAAGCACATATGAAAAGGAGAGAATAGCACATGCAAAACAAATTATAAAGCCATTTATTCTCAGAA
GAGCGAAAGAAGAGGTTCTCAAACAGCTGCCCCCCAAGAAGGATCAAGTTGAGTTGTGTGCAATGTCAGAGAAGCAGGAG
CAGCTTTATTTGGGTCTTCTCAGCAGACTAAAGAAATCCATCAACAACTCGGAAAAAAACACAGAGATGGGTAACATCAT
GATGCAGCTGAGAAAAATGGCCAATCATCCTTTATTACATCGCCAATATTACACAGCTGAAAAACTCAAGGAAATGGCTC
GGCTTTTGCTGAAGGAACCTACACATCGCACAGCTAACCCTGACCTGATCTTTGAAGATATGGCAGTTATGACAGACTTT
GAACTACACGTACTTTGTAAACAGTATCGACACATTAATGACTTCCAGTTAGACATGGACTTGATTCTCGATTCCGGAAA
ATTTCGAGCTTTAGGATGCATCTTATCCGAATTAAAACAGAAAGGTGACAGAGTTGTAGTATTTAGCCAGTTTACCACGA
TGCTGGATATTTTAGAGATACTCTTAAAACATCATCAGCATAGGTACCTCAGATTAGATGGAAAGACTCAAATTTCTGAA
CGGATTCATCTCATTGATGAGTTTAATACCGATATGAATATCTTTATATTTCTGCTATCAACAAAAGCCGGTGGCCTGGG
GATCAATCTGACCTCAGCAAATGTTGTCATACTTCATGATATCGACTGTAATCCTTACAACGACAAACAAGCAGAAGATA
GGTGCCACAGAGTAGGGCAGACGAAAGAAGTGCTAGTTATAAAATTAATAAGCCAAGGGACTATTGAAGAATCTATGCTA
AAAATTAACCAACAGAAACTGAAACTAGAACAAGATATGACCACAGCAGACGAAGGTGATGAGGGGAATATGCCAGCGGA
TATAGCCACGTTACTAAAGGCGTCAATGGGCCTG
ORF - retro_ogar_3220 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.4 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MNLFNLDRFRFEKRNKSEETPEATPQPSQPGPSSPISLSAEEENAEGEVSRANTPDSDITEKTEDSSVPE |
| .NLFNLD.F.FEKRNKSEETPEATPQPS.P.PSS.I.LSAEEEN.EGEVSRA.TPDS.IT.K.ED.SV.E | |
| Retrocopy | INLFNLDHFHFEKRNKSEETPEATPQPSRPSPSSLIYLSAEEENTEGEVSRATTPDSEITGKAEDASVLE |
| Parental | T-PDNERKASISYFKNQR-GIQYIDLSSDSEDVVSPDCSNTVQEKKFNKDTVIIVSEPSEDEESQGLPAM |
| .......K.....F.....G.QYIDLSSD.EDV.SPD.SN.VQEKKFNKDTVIIVSEPS..EE.QGLPAM | |
| Retrocopy | S>SRQRKKSKFIIFQESK>GLQYIDLSSDREDVISPDSSNIVQEKKFNKDTVIIVSEPS--EEPQGLPAM |
| Parental | ARRNNDDISELEDLSELEDLKDAKLQTLKELFPQRSDSDLIKLIESTSTMDGAIAAALLMFGDAGGGPRK |
| ARRNNDDISELEDLSEL..LK.A.LQ.LKE.FP...DSDL.KLI.STSTMD.AIA.AL.MFGDA.GGPRK | |
| Retrocopy | ARRNNDDISELEDLSELANLKEANLQILKERFPHKTDSDLRKLIDSTSTMDDAIATALRMFGDARGGPRK |
| Parental | RKLSSSSEPYEEDDF-DDQSLKKTRLDHGEESNESAESSSNWEKQESIVLKLQKEFPHFDKQELREVLKE |
| RKLSSSSEPYEEDDF.DDQSLKKTR.DHG.ESNESAES.SNW.K.E.IVLKLQKEFPHFDKQELREVLKE | |
| Retrocopy | RKLSSSSEPYEEDDFNDDQSLKKTRPDHGKESNESAESRSNWKKRERIVLKLQKEFPHFDKQELREVLKE |
| Parental | HEWMYTEALESLKVFAEDQDMQYASQSEVPNGKDVSSRSQNYPKNAAKTKLKQKFSMKPQNGFNKKRKKN |
| HEWMY.EAL.SL..F.EDQDMQ.ASQSEVPNGKDVSSRSQNYPKNAAKT..KQKFS.KPQNGFNKK.K.. | |
| Retrocopy | HEWMYAEALGSLRLFSEDQDMQSASQSEVPNGKDVSSRSQNYPKNAAKT--KQKFSTKPQNGFNKKCKTK |
| Parental | VFNPKRVVEDSEYDSGSDAGSSLDEDYSSGEEV-MEDGYKGKILHFLQDASIGELTLIPQCSQKKAQKIT |
| .FNPK.V.EDSE.DSG.DA.SS.DEDY.S.EEV.MEDGYK.KIL.FLQDASI.ELTLIP.C.QKKAQKI. | |
| Retrocopy | IFNPKQVMEDSENDSGPDADSSWDEDYTSDEEVKMEDGYKRKILRFLQDASISELTLIPHCHQKKAQKII |
| Parental | ELRPFNCWETLFTKMSKTNGLSEDLIWNCKTLIQERDVVIRLMNKCEDISNKLTKQVTMLTGNGSGWNVE |
| E.RPFNCWE.LFTK.SKT.GLSEDLIWNCKTLIQ.RDVVIRLMNKCEDISNKLT.QVTMLTGNGSGWNVE | |
| Retrocopy | ESRPFNCWEALFTKLSKTKGLSEDLIWNCKTLIQQRDVVIRLMNKCEDISNKLTRQVTMLTGNGSGWNVE |
| Parental | QPSILNQSLSLKPYQKVGLNWLALVHKHGLNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST |
| QPSILN.SLSLKPYQKVGLNWLALVHKH.LNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST | |
| Retrocopy | QPSILNPSLSLKPYQKVGLNWLALVHKHELNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST |
| Parental | IDNWLREVNLWCPTLKVLCYYGSQEERKQIRFNIHSRYEDYNVIVTTYNCAISSSDDRSLFRRLKLNYAI |
| IDNWLREVNLWCPTLKVLCYYGSQEER.QIR.NIHSR.EDYNVIVTTYNCAISSS.DRSLFRRLKL.YAI | |
| Retrocopy | IDNWLREVNLWCPTLKVLCYYGSQEERLQIRCNIHSRSEDYNVIVTTYNCAISSSEDRSLFRRLKLKYAI |
| Parental | FDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSSTSEIRRMFSSKTKS |
| FDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSST.EIRRMFSSKTK. | |
| Retrocopy | FDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSSTNEIRRMFSSKTKA |
| Parental | ADEQSIYEKERIAHAKQIIKPFILRRVKEEVLKQLPPKKDQIELCAMSEKQEQLYLGLFNRLKKSINNLV |
| A.EQS.YEKERIAHAKQIIKPFILRR.KEEVLKQLPPKKDQ.ELCAMSEKQEQLYLGL..RLKKSINN.. | |
| Retrocopy | AEEQSTYEKERIAHAKQIIKPFILRRAKEEVLKQLPPKKDQVELCAMSEKQEQLYLGLLSRLKKSINN-- |
| Parental | IEKNTEMCNVMMQLRKMANHPLLHRQYYTAEKLKEMAQLMLKEPTHCEANPDLIFEDMEVMTDFELHVLC |
| .EKNTEM.N.MMQLRKMANHPLLHRQYYTAEKLKEMA.L.LKEPTH..ANPDLIFEDM.VMTDFELHVLC | |
| Retrocopy | SEKNTEMGNIMMQLRKMANHPLLHRQYYTAEKLKEMARLLLKEPTHRTANPDLIFEDMAVMTDFELHVLC |
| Parental | KQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVVLFSQFTMMLDILEVLLKHHQHRYLRLDGKT |
| KQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVV.FSQFT.MLDILE.LLKHHQHRYLRLDGKT | |
| Retrocopy | KQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVVVFSQFTTMLDILEILLKHHQHRYLRLDGKT |
| Parental | QISERIHLIDEFNTDMDIFVFLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV |
| QISERIHLIDEFNTDM.IF.FLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV | |
| Retrocopy | QISERIHLIDEFNTDMNIFIFLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV |
| Parental | IKLISQGTIEESMLKINQQKLKLEQDMTTXXXXDEGNMPADIATLLKTSMGL |
| IKLISQGTIEESMLKINQQKLKLEQDMTT....DEGNMPADIATLLK.SMGL | |
| Retrocopy | IKLISQGTIEESMLKINQQKLKLEQDMTTADEGDEGNMPADIATLLKASMGL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Otolemur garnettii was not studied using RNA-Seq expression data.
Otolemur garnettii was not studied using ChIP-Seq data.
Otolemur garnettii was not studied using EST data.
Otolemur garnettii was not studied using FANTOM5 data.
retro_ogar_3220 was not experimentally validated.
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.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000011444 | 1 retrocopy |
retro_ogar_3220 ,
|