RetrogeneDB ID:

retro_ocun_1505

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:9:43316017..43318747(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DENND4B
Ensembl ID:ENSOCUG00000011771
Aliases:None
Description:DENN/MADD domain containing 4B [Source:HGNC Symbol;Acc:29044]


Retrocopy-Parental alignment summary:






>retro_ocun_1505
GCCTTCCTTACCTTCCTCTACCGCGACTCTGTCTCAGGCCCCCACCGCCTGCCCTTGGAAGCGCACATCTTCCACTTCAT
TCACAACATCGCCTTCCCCTCCCCATAGAGACCCCGCATCCTAGTGCAGATGTCTCCCTACGACAACCTGCTCCTCTGTC
AACCTGTGTCTTCACCCCTGCCCCTCAGCGGTGCCAGCTTCTTGCAGCTGCTGCAGAGCCTGGGCCCTGAGCTGGCTGTC
ATGCTGCTGCTGGCCGTGCTCACGGAGCACAAACTGCTGGTGCACTCGCTGCGGCCAGACCTGCTCACCAGTGTCTGTGA
GGCCCTTGTCTCGATGATCTTTCCGCTGCACTGGCAGTGCCCCTACATTCCGCTGTGCCCGCTGGTGCTGGCAGATGTGC
TGAGCACCCCTGTGCCCTTCATCGTGGGCATCCACTCCAGCTACTTTGATCTGCATGATCCCCCGGCCTACGTCGTCTGT
GCCGACCTTGACACCAACACATTCTGCCAGACCGAGGAAAAGAAGCCCCTCTCCCCTCGGACCCTGCCTCGCAGACCCTA
CAAGCTTCTGCTGGCCACTCTGACTAACCTGTACCAGCAGCTGGACCAGACGTACACTGGACCTGAGCAGGAGGCCTCCC
TGGAATTCCTGCTGACCGACTATGAGGCAGTGTGTGGTCGCTGGGCCGACTGGAGCTAGAGGTCCAAGGCGCCTTCCTCC
GCTTCATGGCCTGCCTGCTCAAGGGCTACCGGGAATTCCTGCGCCCACTCAGCCAGGCCCCCTTGAGGGCGCTCCCACGT
GGACAACTTTTTCTATCTTCATGGCTTCCTGAAGTCCCACGAGCACTCCAGCCACAAGCTGTACTTCCAGCTGCTGCACA
CACAGATGTTCTCCCAGTTCATTGAGGAGTGCTCTTTTGGCTCTGCTCGGCACGCTGCCCTGGAATTCTTTGACTCCGGC
GTCGACGAGGTCCATGCCGAGTAGGAAAGGCCTGAGCCCACTCCGTTAGTGGAGCTGGAAGAGTTGTCGGGAAGTGAGCT
CACAGTCTTCATCACGCCTCCCGAGGAGCCCCCGGTCCCAGACAGCAGCGAACCAACTCCCCAGTTCTGTTACATGGGTT
CCCAGAACTACGGGCTGAGCTGTTTGAATCTCCCCAAGAGCAACCTGGGGCACTGCCTGTGCCGGGCACCTCCAGTAGTG
CCCCCAGCAGTCCTGCCCCTCGCAGTACCAAACAGGAGATGAAGGTTGCACAGCGCATGGCACAGAAGTCAGCGACCGTG
CCTGAGCTGTGGGCCCAGTGCCTGCTGGGGCACTGCTACGGGCTGTGGTTCCTGTGCCTGCCTGCCTACATACAGTCGGC
ACCATCCCAGGTACCAGCACTGAACACAGCCTACCATGTGCTGCGCGAGATGGAGAGCTGTAAAGTGGTGCTCCCTGACG
AGGTGTGTTACCGGGTGCTGATGCAGCTCTGCTCACACTATGGGCAGCCTGTGCTGTCTGTGCGGGTCATGCTGGAGATG
CGGTGGGCGGGCATTTTGCCCAATACCATCACCTGTGGCTACTACAACAAGGCTGTGCTGGAAAGCAAGTGGCTGTGGGC
ACACTGGGTGGGCGCCTGCGCTGGGCCAAGCTCTGGAATGTTGTCCTGGGAGCTACTTAGTTCCACCAACCCCTGAGAGA
GCCATGGCGGCAGCAACAGCAGCCACAGCCAGCGGCAGCACAGCAAGAGGTAGGCAGCTCCCAGACAGAGCCCTGTCTGG
AGCGCCCCTCCCCTACCCGCCCACTCCAGCACCAGACTACCTGGGCTGGGTGAAGTCTGAGGAACCCAGCCTCCCCTGTG
GGGCACCTGATGAAGAGCGGGAGCCTGGGCAGTGCCCGAGGTGCACAGCCCACTGTGGAGGCCGGTGTGGCCCACATGAT
AGAGGCCTTGGGGGTTCTGGAACCCCTCAGCTCACTTGTGCCCTGGCATGGTGGAAGTCTCTCAGACCTGAGCCTTACCG
AGGAGGAGCTGGCACCTGGGGGCAGCCCAGGGGGCTCAGGCCTTGCCCTGAGTGCCCAGTCCACTGAGGCCCTGGAAGGG
CTAAATGGCCGTGGGTCCAAGGCTGGTGGGCATCAGGAGGAGGCGGGCACCCCCCGACGAGGGCTGGGTGCCTGCCTTCA
GCAGCTGCTCACCCCCTCCCATCGCTCCCCTGCCTCCCGCATTCCCCCATCTGAGCTGCCCGCTGACCTGCCACCCCCAG
TTCGCCGCAGCCCCATGGACAGCCTCCTGCACCCCCGGGAGCGCCCTGGATCTACTGCGTCCAAGAGTTCAGCCTCTCTG
GGCAGTGAGTGGGACCTCTCAGACTCTTCTCTCAGCAGCCTGCGCCTCCGCCGTTCCTCAGCGACACCCCTGGGTCCTCC
CAGACACTTTCCCTGGAAATTCTGCTGTCCATCTGCTCCCTGTGCCGTGCCTGTGATTTGCAGGTGTAGGATGAGGAAAT
CATGGCTGGCTGGGCACCGGATGACTCTAACCTCAACACAACCTGTCCCTTCTGCGCCTGTCCCTTCGTGCCCCTGCTCA
GCGTCCAGACCCTTGATTCCCGACCCAGTGCCCCCAGCCCCAAGCCGACCCCTGCTGGTGCCAGTGGCAGCAAAGATGCT
CCCATCCCTGGGGGTCCTGGCCCTGTACTCAGTGACCGGAGGCTCTGCCTCGCCCTGGATGAGCCCCAGCTCTGCAATGG
GCACATGGGG

ORF - retro_ocun_1505 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.53 %
Parental protein coverage: 61.18 %
Number of stop codons detected: 5
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalAFLTFLYRYSVSGPHRLPLEAHISHFIHNVPFPSPQRPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL
AFLTFLYR.SVSGPHRLPLEAHI.HFIHN..FPSP.RPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL
RetrocopyAFLTFLYRDSVSGPHRLPLEAHIFHFIHNIAFPSP*RPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL
ParentalLQSLGPELAVTLLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLSAPVPF
LQSLGPELAV.LLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLS.PVPF
RetrocopyLQSLGPELAVMLLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLSTPVPF
ParentalIVGIHSSYFDLHDPPADVICVDLDTNTLFQTEEKKPLSPRTLPRRPYKVLLATLTNLYQQLDQTYTGPEQ
IVGIHSSYFDLHDPPA.V.C.DLDTNT..QTEEKKPLSPRTLPRRPYK.LLATLTNLYQQLDQTYTGPEQ
RetrocopyIVGIHSSYFDLHDPPAYVVCADLDTNTFCQTEEKKPLSPRTLPRRPYKLLLATLTNLYQQLDQTYTGPEQ
ParentalEASLEFLLTDYEAVCGRRA-RLEREVQGAFLRFMACLLKGYREFLRPLTQA-PSEGA-RDVDNLFHLQGF
EASLEFLLTDYEAVCGR.A.RLE.EVQGAFLRFMACLLKGYREFLRPL.QA.P.EGA...VDN.F.L.GF
RetrocopyEASLEFLLTDYEAVCGRWA<RLELEVQGAFLRFMACLLKGYREFLRPLSQA<PLEGA<SHVDNFFYLHGF
ParentalLKSRERSSHKLYSQLLHTQMFSQFIEECSFGSARHAALEFFDSCVDKVHAEQERPEPTPLVELEELSGSE
LKS.E.SSHKLY.QLLHTQMFSQFIEECSFGSARHAALEFFDS.VD.VHAE.ERPEPTPLVELEELSGSE
RetrocopyLKSHEHSSHKLYFQLLHTQMFSQFIEECSFGSARHAALEFFDSGVDEVHAE*ERPEPTPLVELEELSGSE
ParentalLTVFITPPEEPPVPDSSEPIPQFCY-DGFPELRAELFESPQEQPGALPVPGTSRSAPSSPAPRRTKQEMK
LTVFITPPEEPPVPDSSEP.PQFCY..GFPELRAELFESPQEQPGALPVPGTS.SAPSSPAPR.TKQEMK
RetrocopyLTVFITPPEEPPVPDSSEPTPQFCY<HGFPELRAELFESPQEQPGALPVPGTSSSAPSSPAPRSTKQEMK
ParentalVAQRMAQKSATVPELWARCLLGHCYGLWFLCLPAYVRSAPSRVRALHTAYQVLRQMESRKVVLPDEVCYR
VAQRMAQKSATVPELWA.CLLGHCYGLWFLCLPAY..SAPS.V.AL.TAY.VLR.MES.KVVLPDEVCYR
RetrocopyVAQRMAQKSATVPELWAQCLLGHCYGLWFLCLPAYIQSAPSQVPALNTAYHVLREMESCKVVLPDEVCYR
ParentalVLMQLCSHYGQPVLSVRVMLEMRRAGIVPNTITYGYYNKAVLESKW-PSGTPGGRLRWAKLRNVVLGAAQ
VLMQLCSHYGQPVLSVRVMLEMR.AGI.PNTIT.GYYNKAVLESKW...GT.GGRLRWAKL.NVVLGA..
RetrocopyVLMQLCSHYGQPVLSVRVMLEMRWAGILPNTITCGYYNKAVLESKW<AVGTLGGRLRWAKLWNVVLGAT*
ParentalFRQPLKERRRQQQQQQQQPAAQQEAGSSQTGGWGQTEPCLERPSPTRPLQRQTTWAGRSLRDPASPAGRL
F.QPL.E..R....QQQQP...Q.A...Q..G..QTEPCLERPSPTRPLQ.QTTWAG.SLR.PASP.G.L
RetrocopyFHQPLREPWR----QQQQP---QPAAAQQEVGSSQTEPCLERPSPTRPLQHQTTWAG*SLRNPASPVGHL
ParentalVKSGSLGSARGAQPTVEAGVAHMIEALGVLEPRGSPVPWHDGSLSDLSLTGEELAPGGSPGGSGPALSAQ
.KSGSLGSARGAQPTVEAGVAHMIEALGVLEP..S.VPWH.GSLSDLSLT.EELAPGGSPGGSG.ALSAQ
RetrocopyMKSGSLGSARGAQPTVEAGVAHMIEALGVLEPLSSLVPWHGGSLSDLSLTEEELAPGGSPGGSGLALSAQ
ParentalSTEALEGLSGRGPKAAGHQEEAGTPRRGLGARLQQLLTPSRRSPASRIPPPELPADLPPPARRSPMDSLL
STEALEGL.GRG.KA.GHQEEAGTPRRGLGA.LQQLLTPS.RSPASRIPP.ELPADLPPP.RRSPMDSLL
RetrocopySTEALEGLNGRGSKAGGHQEEAGTPRRGLGACLQQLLTPSHRSPASRIPPSELPADLPPPVRRSPMDSLL
ParentalHPRERPGSTASESSASLGSEWDLSESSLSSLSLRRSSER-LSDTPGSSQPPSLEILLSSCSLCRACDSLV
HPRERPGSTAS.SSASLGSEWDLS....SSLS..R.....LSDTPGSSQ..SLEILLS.CSLCRACD..V
RetrocopyHPRERPGSTASKSSASLGSEWDLSD---SSLSSLRLRRS<LSDTPGSSQTLSLEILLSICSLCRACDLQV
ParentalYDEEIMAGWAPDDSNLNTTCPFCACPFVPLLSVQTLDSRPSAPSPKPTPAGASGSRDAPVPGGPGPVLSD
.DEEIMAGWAPDDSNLNT............LSVQTLDSRPSAPSPKPTPAGASGS.DAP.PGGPGPVLSD
Retrocopy*DEEIMAGWAPDDSNLNTXXXXXXXXXXXXLSVQTLDSRPSAPSPKPTPAGASGSKDAPIPGGPGPVLSD
ParentalRRLCLALDEPQLCNGHMG
RRLCLALDEPQLCNGHMG
RetrocopyRRLCLALDEPQLCNGHMG

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .33 RPM 60 .38 RPM
SRP017611_kidney 0 .10 RPM 18 .04 RPM
SRP017611_liver 0 .00 RPM 13 .49 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1505 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1505 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1505 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Oryctolagus cuniculus ENSOCUG00000011771 1 retrocopy
retro_ocun_1505 ,




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