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. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMNLFNLDRFRFEKRNKSEETPEATPQPSQPGPSSPISLSAEEENAEGEVSRANTPDSDITEKTEDSSVPE
.NLFNLD.F.FEKRNKSEETPEATPQPS.P.PSS.I.LSAEEEN.EGEVSRA.TPDS.IT.K.ED.SV.E
RetrocopyINLFNLDHFHFEKRNKSEETPEATPQPSRPSPSSLIYLSAEEENTEGEVSRATTPDSEITGKAEDASVLE
ParentalT-PDNERKASISYFKNQR-GIQYIDLSSDSEDVVSPDCSNTVQEKKFNKDTVIIVSEPSEDEESQGLPAM
.......K.....F.....G.QYIDLSSD.EDV.SPD.SN.VQEKKFNKDTVIIVSEPS..EE.QGLPAM
RetrocopyS>SRQRKKSKFIIFQESK>GLQYIDLSSDREDVISPDSSNIVQEKKFNKDTVIIVSEPS--EEPQGLPAM
ParentalARRNNDDISELEDLSELEDLKDAKLQTLKELFPQRSDSDLIKLIESTSTMDGAIAAALLMFGDAGGGPRK
ARRNNDDISELEDLSEL..LK.A.LQ.LKE.FP...DSDL.KLI.STSTMD.AIA.AL.MFGDA.GGPRK
RetrocopyARRNNDDISELEDLSELANLKEANLQILKERFPHKTDSDLRKLIDSTSTMDDAIATALRMFGDARGGPRK
ParentalRKLSSSSEPYEEDDF-DDQSLKKTRLDHGEESNESAESSSNWEKQESIVLKLQKEFPHFDKQELREVLKE
RKLSSSSEPYEEDDF.DDQSLKKTR.DHG.ESNESAES.SNW.K.E.IVLKLQKEFPHFDKQELREVLKE
RetrocopyRKLSSSSEPYEEDDFNDDQSLKKTRPDHGKESNESAESRSNWKKRERIVLKLQKEFPHFDKQELREVLKE
ParentalHEWMYTEALESLKVFAEDQDMQYASQSEVPNGKDVSSRSQNYPKNAAKTKLKQKFSMKPQNGFNKKRKKN
HEWMY.EAL.SL..F.EDQDMQ.ASQSEVPNGKDVSSRSQNYPKNAAKT..KQKFS.KPQNGFNKK.K..
RetrocopyHEWMYAEALGSLRLFSEDQDMQSASQSEVPNGKDVSSRSQNYPKNAAKT--KQKFSTKPQNGFNKKCKTK
ParentalVFNPKRVVEDSEYDSGSDAGSSLDEDYSSGEEV-MEDGYKGKILHFLQDASIGELTLIPQCSQKKAQKIT
.FNPK.V.EDSE.DSG.DA.SS.DEDY.S.EEV.MEDGYK.KIL.FLQDASI.ELTLIP.C.QKKAQKI.
RetrocopyIFNPKQVMEDSENDSGPDADSSWDEDYTSDEEVKMEDGYKRKILRFLQDASISELTLIPHCHQKKAQKII
ParentalELRPFNCWETLFTKMSKTNGLSEDLIWNCKTLIQERDVVIRLMNKCEDISNKLTKQVTMLTGNGSGWNVE
E.RPFNCWE.LFTK.SKT.GLSEDLIWNCKTLIQ.RDVVIRLMNKCEDISNKLT.QVTMLTGNGSGWNVE
RetrocopyESRPFNCWEALFTKLSKTKGLSEDLIWNCKTLIQQRDVVIRLMNKCEDISNKLTRQVTMLTGNGSGWNVE
ParentalQPSILNQSLSLKPYQKVGLNWLALVHKHGLNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST
QPSILN.SLSLKPYQKVGLNWLALVHKH.LNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST
RetrocopyQPSILNPSLSLKPYQKVGLNWLALVHKHELNGILADEMGLGKTIQAIAFLAYLYQQGNNGPHLIVVPAST
ParentalIDNWLREVNLWCPTLKVLCYYGSQEERKQIRFNIHSRYEDYNVIVTTYNCAISSSDDRSLFRRLKLNYAI
IDNWLREVNLWCPTLKVLCYYGSQEER.QIR.NIHSR.EDYNVIVTTYNCAISSS.DRSLFRRLKL.YAI
RetrocopyIDNWLREVNLWCPTLKVLCYYGSQEERLQIRCNIHSRSEDYNVIVTTYNCAISSSEDRSLFRRLKLKYAI
ParentalFDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSSTSEIRRMFSSKTKS
FDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSST.EIRRMFSSKTK.
RetrocopyFDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQNNLLELMSLLNFVMPHMFSSSTNEIRRMFSSKTKA
ParentalADEQSIYEKERIAHAKQIIKPFILRRVKEEVLKQLPPKKDQIELCAMSEKQEQLYLGLFNRLKKSINNLV
A.EQS.YEKERIAHAKQIIKPFILRR.KEEVLKQLPPKKDQ.ELCAMSEKQEQLYLGL..RLKKSINN..
RetrocopyAEEQSTYEKERIAHAKQIIKPFILRRAKEEVLKQLPPKKDQVELCAMSEKQEQLYLGLLSRLKKSINN--
ParentalIEKNTEMCNVMMQLRKMANHPLLHRQYYTAEKLKEMAQLMLKEPTHCEANPDLIFEDMEVMTDFELHVLC
.EKNTEM.N.MMQLRKMANHPLLHRQYYTAEKLKEMA.L.LKEPTH..ANPDLIFEDM.VMTDFELHVLC
RetrocopySEKNTEMGNIMMQLRKMANHPLLHRQYYTAEKLKEMARLLLKEPTHRTANPDLIFEDMAVMTDFELHVLC
ParentalKQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVVLFSQFTMMLDILEVLLKHHQHRYLRLDGKT
KQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVV.FSQFT.MLDILE.LLKHHQHRYLRLDGKT
RetrocopyKQYRHINDFQLDMDLILDSGKFRALGCILSELKQKGDRVVVFSQFTTMLDILEILLKHHQHRYLRLDGKT
ParentalQISERIHLIDEFNTDMDIFVFLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV
QISERIHLIDEFNTDM.IF.FLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV
RetrocopyQISERIHLIDEFNTDMNIFIFLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAEDRCHRVGQTKEVLV
ParentalIKLISQGTIEESMLKINQQKLKLEQDMTTXXXXDEGNMPADIATLLKTSMGL
IKLISQGTIEESMLKINQQKLKLEQDMTT....DEGNMPADIATLLK.SMGL
RetrocopyIKLISQGTIEESMLKINQQKLKLEQDMTTADEGDEGNMPADIATLLKASMGL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

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 ,


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