RetrogeneDB ID:

retro_ocun_830

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:15:43393354..43395449(-)
Located in intron of:ENSOCUG00000008514
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS6KA6
Ensembl ID:ENSOCUG00000006428
Aliases:None
Description:ribosomal protein S6 kinase, 90kDa, polypeptide 6 [Source:HGNC Symbol;Acc:10435]


Retrocopy-Parental alignment summary:






>retro_ocun_830
CAGGATGAAGATGTTAAAGAAATCCCTATTACTCATCACGTTAAAGAAGGATATGAGAAAGCAGATCCTGCACAGTTTGA
GCTGCTCAAGGTGCTTGGTCAGGGATCATTTGGAAAGGTTTTTCTTGTTAGAAAGAAGACTGGTCCTGATGCTGGTCAGC
TCTATGCAATGAAGGTGTTAAAAAAGGCTTCTTTAAAAGTTCGAGACAGAGTTCGGACAAAGATGGAAAGAGATATACTT
GTGGAAGTAAATCATCCATTTATTGTCAAATTGCACTATGCCTTTCAGACTGAAGGGAAGCTGTATTTAATACTGGATTT
TCTCAGGGGAGGAGATGTCTTCACAAGATTATCCAAAGAAGTTCTGTTTACAGAGGAAGATGTGAAATTCTACCTTGCTG
AATTGGCCCTTGCTTTGGATCATCTGCATCGATTAGGGATTGTATATAGAGACCTGAAGCCAGAAAACATTTTGCTTGAT
GAAATAGGACATATCAAGTTAACAGATTTTGGACTCAGCAAAGAGTCAGTAGATCAAGAAAAGAAGGCTTACTCATTTTG
TGGTACAGTAGAGTATATGGCTCCTGAAGTAGTAAATAGGAGAGGCCATTCCCAGAGTGCTGATTGGTGGTCATATGGTG
TACTTATGTTTGAAATGCTTACTGGTACTCTGCCATTTCAAGGTAAAGACAGAAACGAGACCATGAATATGATATTAAAA
GCAAAACTTGGAATGCCTCAGTTTCTTAGTGCTGAAGCACAGAGTCTTCTAAGGATGCTATTCAAAAGGAATCCAGCAAA
TAGATTGGGTTCAGAAGGAGTTGAAGAAATAAAAAGACACCTTTTTTTTTGCAAATATTGACTGGAATAAATTATATAAA
AGAGAAGTTCAACCTCCTTTCAAACCTGCTTCTGGAAAACCAGATGATACTTTTTGTTTTGATCCTGAATTTACTGCAAA
AACACCTAAAGATTCTCCTGGTTTACCAGCCAGTACAAATGCTCATCAACTCTTCAAAGGATTCAGCTTTGTTGCAACGT
CTATTGCAGAAGAATATAAAATAACTCCTATCACAAGTGCAAATGTATTACCAATTGTTCAGATAAATGGAAATGCTGCA
CAATTTGGTGAAGTGTATGAATTGAAAGAGGATATCGGTGTTGGCTCCTATTCCGTTTGCAAGCGATGTGTACATAAAAC
TACCAACATGGAATTTGCAGTGAAGATCATTGACAAAAGTAAATGAGACCCATCAGAAGAAATTGAGATTCTGATGCGCT
ATGGACAGCATCCAAACATTATTACTTTAAAGGATGTCTTTGATGATGGTAGATACATATACCTTGTTACAGATTTGATG
AAAGGAGGAGAACTCCTGGATCGTATTCTCAAACAAAAAAGTTTCTCAGAACAGGAAGCTAGTGATGTACTGTATGTAAT
AACTAAGACAGTTGACTGTCTTCATTGTCAAGGAGTTGTTCATCGTGATCTTAAACCTAGTAATATTTTATACATGGATG
AATCAGCCAATGCAGATTCAATTAGGATCTGTGATTTTGGGTTTGCAAAACAGCTTCGAGGAGAAAATGGACTTCTCTTA
ACTCCATGCTACACTGCAAACTTTGTAGCACCTGAGGTTCTTATGCAACAGGGATATGATGCTGCTTGTGATATTTGGAG
TTTAGGAGTCCTTTTTTACACGATGTTGGCTGGCTACACTCCATTTGCTAATGGCCCCAATGATACTCCTGAAGAGATAC
TACTGCGTATAGGCAATGGAAAGTTCTCCTTGAGTGGTGGAAACTGGGATGGTATTTCAGATGGAGCAAAGGATTTGCTT
TCCCATATGCTTCATGTGGACCCTCATCAACGGTACACTACTGAGCAAATATTAAAGCACTCATGGATAACTCACAGTGA
TCAGTTGCGGAATGATCAGCCAAAGAGAAGTGATGCATCACATGCTGTTAAGGGAGCAGTGGTTGCCACATTTTCTGCCC
TGACTCACAAGACCTTTCAACCAGTTCTTGAGCCTGTTGCTGCTTCAAGCTTAGCTCAGAGACGGAGCATGAAAAAGCGA
ACATCAACTGGCCTG

ORF - retro_ocun_830 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.89 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR
QDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR
RetrocopyQDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR
ParentalVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD
VRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD
RetrocopyVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD
ParentalHLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW
HLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW
RetrocopyHLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW
ParentalSYGVLMVSSIVAIRPFQIQDLAFSVTQEVFVIFGRKQWSLREIEAGLEYLRFMRVPVLAGGSGKKGVEEI
SYGVLM........PFQ..D.............G..Q....E....L..L.F.R.P..A...G..GVEEI
RetrocopySYGVLMFEMLTGTLPFQGKDRNETMNMILKAKLGMPQFLSAEAQSLLRML-FKRNP--ANRLGSEGVEEI
ParentalKRHLFF-ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPASANAHQLFKGFSFVAT
KRHLFF.ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPAS.NAHQLFKGFSFVAT
RetrocopyKRHLFF>ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPASTNAHQLFKGFSFVAT
ParentalSIAEEYKITPITSANVLPIVQQINGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSKR
SIAEEYKITPITSANVLPIVQ.INGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSK.
RetrocopySIAEEYKITPITSANVLPIVQ-INGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSK*
ParentalDPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD
DPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD
RetrocopyDPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD
ParentalYLHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA
.LHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA
RetrocopyCLHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA
ParentalCDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY
CDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY
RetrocopyCDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY
ParentalTTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS
TTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS
RetrocopyTTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS
ParentalTGL
TGL
RetrocopyTGL

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 2 .98 RPM 3 .42 RPM
SRP017611_kidney 4 .87 RPM 3 .34 RPM
SRP017611_liver 0 .15 RPM 0 .00 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_830 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_830 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_830 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Oryctolagus cuniculus ENSOCUG00000006428 1 retrocopy
retro_ocun_830 ,
Oryctolagus cuniculus ENSOCUG000000143671 retrocopy
retro_ocun_1114,




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