RetrogeneDB ID:

retro_ocun_700

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:14:62912002..62914276(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000023181
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CLCN5
Ensembl ID:ENSOCUG00000017336
Aliases:CLCN5, CLCN4
Description:chloride channel, voltage-sensitive 5 (CLCN5), mRNA [Source:RefSeq mRNA;Acc:NM_001082068]


Retrocopy-Parental alignment summary:






>retro_ocun_700
CACGCAGGAGCCATGAGCGGCCCGGGAAACCTGATGGACTTCTTGGACGAGCCGTTCCCCGACGTGGGGACCTACGAGGA
CTTCCACACCATCGACTGGCTGCGGGAGAAGTCGCGGGACACCGACCGGCACAGGAAGATCACCAGCAGGAGCAGGGAGT
CCGTGTGGGAGTTCGTCAAGAGCTTGCTGGACGCCTGGTCGGGGTGGGCGGTGATGCTGCTCATCGGGCTGCTGGCAGGC
ACCCTGGCCGGGGTCATCGACCTGGCCGTGGACTGGATGACCGACCTGAAGGAGGGCGTGTGCCTGTCCGCCTTCTGGTA
CAGCCACGAGCAGTGCTGCTGGACGTCCAACGAGACCACGTTCGAGGACCGCGACAGGTGCCCGCAGTGGCAGACGTGGT
CGGAGCTGCTGGTGAACCGGTCGGAGGGGGCCAGCGCCTACGTCCTCAACTACCTGATGTACATCCTGTGGGCGCTGCTC
TTTGCCTTCCTGGCCGTGTCCCTGGTGCGCGTCTTCGCGCCCTACGCCTGCGGCTCCGGGATCCCGGAGATCAAGACCAT
CCTGAGCGGCTTCATCATCCGGGGCTACCTGGGCAAGTGGACGCTGCTCATCAAGACGGTCACCCTGGTGCTGGTGGTGT
CGTCCGGGCTCAGCCTGGGCAAGGAGGGGCCGCTGGTGCACGTGGCCTGCTGCTGCGGGAACCTCTTCAGCGGCCTCTTC
TCCAAGTACAGCCGCAACGAGGGCAAGAGGCGGGAGGTGCTGTCGGCCGCCGCCGCCGCGGGCGTCTCCGTGGCCTTCGG
GGCCCCGATCGGGGGTGTGCTGTTCAGCCTGGAGGAGGTCAGCTACTACTTCCCCCTGAAGACGCTGTGGAGGTCCTTCT
TCGCGGCCCTGGTGGCGGCCTTCACGCTGCGGTCCATCAACCCCTTCGGCAACAGCCGGCTGGTGCTGTTCTACGTGGAG
TACCACACGCCCTGGTACATGGCCGAGCTGCTCCCCTTCATCCTGCTGGGCGTCTTCGGGGGCCTGTGGGGGGCGCTGTT
CATCCGCGGCAACATCGCCTGGTGCCGGAGGCGCAAGACCACCCGGCTGGGCCGGTACCCGGTGCTGGAGGTGCTGGCGG
TCACGGCCGTCACGGCCGTCGCCGCCTACCCGAACCCCTACACGCGGCGCAGCACCAGCGAGCTCATCTCCGAGCTGTTC
AATGACTGCGGCGCCCTGGCGTCCTCCCAGCTCTGCGACTACGTCAGCGACCCCAACATGACCCGGCCGCTGGACGACAT
CCCCGACCGGCCGGCCGGGCGCGGGGTCTACACCGCCATGTGGCAGCTGGCCCTGGCGCTGGTCTTCAAGGTCGTCATCA
CCGTCTTCACCTTCGGCATGAAGATCCCCTCGGGCCTCTTCATCCCCAGCATGGCCGTGGGCGCCATGGCGGGCAGGATG
GTGGGCGTGGGCGTGGAGCAGCTGGCCTACCATCACCACGACTGGATCGTCTTCAGGAACTGGTGCCGGCCCGGCGCCGA
CTGCGTCACGCCCGGACTCTACGCCATGGTGGGCGCCGCGGCGTGCCTAGGCGGCGTGACCAGGATGACCGTGTCCCTGG
TGGTCATCATGTTCGAGCTGACCGGCGGCCTGGAGTACATCGTGCCCCTGATGGCGGCGGCCGTGACCAGCAAGTGGGTG
GCCGACGCCTTCGGGAAGGAGGGCATCTACGAGGCGCACATCCACCTGAACGGGTACCCGTTCCTGGACGTCAAGGACGA
GTTCACGCACCGCACGCTGGCCACGGACGTCATGCGGCCCCGGCGCGGGGAGCCGCCGCTGTCGGTGCTCACCCAGGACG
GCATGACCGTGGAGGACGTGGAGGCGCTCATCAAGGACACCGACTACAACGGCTTCCCGGTGGTGGTGTCCCGGGACTCC
GAGCGCCTCATCGGCTTCGCCCAGAGGAGGGAGCTCATCCTGGCCATCAAGAATGCCCGGCAGCGGCAGGACGGCGTGGT
GAGCAGCTCCGTCACGTACTTCACGGAGGAGCCCCCGGAGCTGCCGGCCAACAGCCCGCAGCCCCTGAAGCTGCGGCGCA
TCGTGAACCTCAGCCCCTTCACCGTCACGGACCACACGCCCATGGAGACCGTGGTGGACATCTTCCGCAAGCTGGGGCTG
CGGCAGTGCCTGGTGACGCGCAGCGGGAGGCTCCTTGGCATCATCACCAAGAAGGACGTGCTGAGACACATGGCCCAGAT
GGCCAACCAGGACCCCGAATCCATCATGTTTAAC

ORF - retro_ocun_700 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.75 %
Parental protein coverage: 92.77 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNGGGIGSSNRIMDFLEEPIPGVGTYDDFNTIDWVREKSRDRDRHREITNKSKESTWALIHSVSDAFSGWL
..G........MDFL.EP.P.VGTY.DF.TIDW.REKSRD.DRHR.IT..S.ES.W....S..DA.SGW.
RetrocopyHAGAMSGPGNLMDFLDEPFPDVGTYEDFHTIDWLREKSRDTDRHRKITSRSRESVWEFVKSLLDAWSGWA
ParentalLMLLIGLFSGSLAGLIDISAHWMTDLKEGICTGGFWFNHEHCCWNSENVTFEDTDKCPEWNSWSQLIINT
.MLLIGL..G.LAG.ID....WMTDLKEG.C...FW..HE.CCW.S...TFED.D.CP.W..WS.L..N.
RetrocopyVMLLIGLLAGTLAGVIDLAVDWMTDLKEGVCLSAFWYSHEQCCWTSNETTFEDRDRCPQWQTWSELLVNR
ParentalDEGAFAYIVNYFMYVLWALLFAFLAVSLVKVFAPYACGSGIPEIKTILSGFIIRGYLGKWTLVIKTITLV
.EGA.AY..NY.MY.LWALLFAFLAVSLV.VFAPYACGSGIPEIKTILSGFIIRGYLGKWTL.IKT.TLV
RetrocopySEGASAYVLNYLMYILWALLFAFLAVSLVRVFAPYACGSGIPEIKTILSGFIIRGYLGKWTLLIKTVTLV
ParentalLAVSSGLSLGKEGPLVHVACCCGNILCHRFNKYRKNEAKRREVLSAAAAAGVSVAFGAPIGGVLFSLEEV
L.VSSGLSLGKEGPLVHVACCCGN.....F.KY..NE.KRREVL........SVAFGAPIGGVLFSLEEV
RetrocopyLVVSSGLSLGKEGPLVHVACCCGNLFSGLFSKYSRNEGKRREVLXXXXXXXXSVAFGAPIGGVLFSLEEV
ParentalSYYFPLKTLWRSFFAALVAAFTLRSINPFGNSRLVLFYVEFHTPWHLFELVPFILLGIFGGLWGALFIRT
SYYFPLKTLWRSFFAALVAAFTLRSINPFGNSRLVLFYVE.HTPW...EL.PFILLG.FGGLWGALFIR.
RetrocopySYYFPLKTLWRSFFAALVAAFTLRSINPFGNSRLVLFYVEYHTPWYMAELLPFILLGVFGGLWGALFIRG
ParentalNIAWCRKRKTTQLGKYPVIEVLIVTAITAILAFPNEYTRMSTSELISELFNDCGLLDSSKLCDYENRFNT
NIAWCR.RKTT.LG.YPV.EV..........A.PN.YTR.STSELISELFNDCG.L.SS.LCDY....N.
RetrocopyNIAWCRRRKTTRLGRYPVLEVXXXXXXXXXAAYPNPYTRRSTSELISELFNDCGALASSQLCDYVSDPNM
ParentalSKGA-DLPDRPAGVGVYNAMWQLALALILKIVITIFTFGMKIPSGLFIPSMAVGAIAGRLLGVGMEQLAY
.....D.PDRPAG.GVY.AMWQLALAL..K.VIT.FTFGMKIPSGLFIPSMAVGA.AGR..GVG.EQLAY
RetrocopyTRPLDDIPDRPAGRGVYTAMWQLALALVFKVVITVFTFGMKIPSGLFIPSMAVGAMAGRMVGVGVEQLAY
ParentalYHHDWTIFNSWCSQGADCITPGLYAMVGAAACLGGVTRMTVSLVVIMFELTGGLEYIVPLMAAAMTSKWV
.HHDW..F..WC..GADC.TPGLYAMVGAAACLGGVTRMTVSLVVIMFELTGGLEYIVPLMAAA.TSKWV
RetrocopyHHHDWIVFRNWCRPGADCVTPGLYAMVGAAACLGGVTRMTVSLVVIMFELTGGLEYIVPLMAAAVTSKWV
ParentalADALGREGIYDAHIRLNGYPFLEAKEEFAHKTLAMDVMKPRRNDPLLTVLTQDSMTVEDVETIISETTYS
ADA.G.EGIY.AHI.LNGYPFL..K.EF.H.TLA.DVM.PRR..P.L.VLTQD.MTVEDVE..I..T.Y.
RetrocopyADAFGKEGIYEAHIHLNGYPFLDVKDEFTHRTLATDVMRPRRGEPPLSVLTQDGMTVEDVEALIKDTDYN
ParentalGFPVVVSRESQRLVGFVLRRDLIISIENARKKQDGVVSTSIIYFTEHSPPMPPYTPPTLKLRNILDLSPF
GFPVVVSR.S.RL.GF..RR.LI..I.NAR..QDGVVS.S..YFTE..P..P...P..LKLR.I..LSPF
RetrocopyGFPVVVSRDSERLIGFAQRRELILAIKNARQRQDGVVSSSVTYFTEEPPELPANSPQPLKLRRIVNLSPF
ParentalTVTDLTPMEIVVDIFRKLGLRQCLVTHNGRLLGIITKKDVLKHIAQMANQDPDSILFN
TVTD.TPME.VVDIFRKLGLRQCLVT..GRLLGIITKKDVL.H.AQMANQDP.SI.FN
RetrocopyTVTDHTPMETVVDIFRKLGLRQCLVTRSGRLLGIITKKDVLRHMAQMANQDPESIMFN

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 .11 RPM 2 .87 RPM
SRP017611_kidney 0 .00 RPM 42 .77 RPM
SRP017611_liver 0 .00 RPM 4 .47 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_700 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_700 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_700 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 ENSOCUG00000017336 1 retrocopy
retro_ocun_700 ,


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