RetrogeneDB ID:

retro_ocun_393

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:139175185..139177198(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NEDD4L
Ensembl ID:ENSOCUG00000014471
Aliases:None
Description:neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:7728]


Retrocopy-Parental alignment summary:






>retro_ocun_393
GACTCCCTGGGGCTGGCCGTGCCCCCGCCACCCGCCTCCCCTGTGTCCCGGACCAGCCCCCAGGAGCTGACAGAGGAGCT
GAGCAGGCGGCTTCAGGTCACTCTGGACGCCAACGGGGAGCAGTTCAGTTCCCTCATCAGAGAGCCCTCCTCCAGGCTGC
GTTCCTGCAGTGTCACCGACGCCGTCGCCGAGCAGGCCCATCTGCCACCGCCGTCAGTGGCCTATGTACACACCACGCCG
GGCCTTCCTTCAGGCTGGGAAGAAAGGAAAGATGCTAAGTGACGCACATACTATGTCAATCATAACAATCGAACCACAAC
TTGGACTCGGCCCATCATGCAGCTTGCAGAAGACGGCGCCGCCTCCGGATCGGCCACAAACAGTAGCAACCACCTAATCG
AGCCTCAGATCCGCCGGCCTCGTAGCCTCAGCTCGCCAACAGTAACTTTATCTGCCCCGCTGGAGGGTGCCAAGGACTCC
CCCGTGCGTCGGGCTGTGAAAGACACCCTTTCCAACCCACAGTCCCCACAGCCGTCCCCCTACAACTCCCCCAAACCTCA
GCACAGAGTCACCCAGAGCTTCCTGCCGCCCGGCTGGGAGATGAGGATCGCGCCCAACGGCCGGCCCTTCTTCATTGACC
ACAACACAAAGACGACGACGTGGGAAGATCCACGCCTTAAGTTCCCAGTTCATATGCGGTCAAAGGCATCTTTAAACCCC
AATGACCTCGGCCCTCTCCCGCCTGGCTGGGAAGAAAGGATTCACTTGGACGGCCGGATGTTCTACATCGATCACAACAG
CAAAATCACCCAGTGGGAAGACCCAAGACTGCAGAACCCAGCCATCACCGGTCCGGCCGTTCCTTATTCCAGAGAATTTA
AGCAGAAATACGACTACTTCAGGAAGAAGCTGAAGAAGCCGGCTGATATTCCAAACAGATTTGAAATGAAGCTCCACAGG
AACAACATATTCGAAGAATCCTACCGGAGGATCATGTCGGTGAAAAGACCAGATGTCCTGAAAGCCAGACTCTGGATAGA
ATTCGAGTCGGAGAAAGGCCTGGACTATGGGGGCGTGGCCAGAGAATGGTTCTTCCTACTGTCCAAAGAGATGTTCAACC
CTTACTATGGTCTCTTTGAGTACTCTGCCACGGACAACTACACACTTCAAATCAACCCCAATTCAGGCCTCTGTAATGAA
GACCACTTGTCCTATTTCACGTTTATCGGGAGAGTCGCGGGTCTGGCTGTATTTCATGGGAAGCTCTTGGATGGTTTCTT
CATCCGCCCGTTTTACAAAATGATGCTGGGGAAGCAGATAACCCTGAACGACATGGAGTCCGTGGACAGTGAATACTACA
ACTCTTTGAAGTGGATCTTAGAAAATGACCCCACCGAACTGGACCTCATGTTCTGCATAGATGAGGAGAACTTCGGGCAG
ACATACCAAGTGGACCTGAAGCCCAATGGCTCAGAGATAATGGTGACGAATGAAAACAAAAGGGAATATATCGACTTGGT
CATCCAGTGGAGGTTTGTGAACCGGGTCCAGAAGCAGATGAACGCCTTCCTGGAGGGATTCACAGAACTCCTTCCCATTG
ACCTGATTAAAATTTTTGATGAAAATGAGCTGGAGTTGCTGATGTGTGGTCTCGGGGATGTGGACGTGAACGACTGGAGA
CAGCATTCTATCTACAAGAATGGCTACTGCCCAAACCACCCGGTCATCCAGTGGTTCTGGAAGGCTGTGCTTCTGATGGA
CGCCGAGAAGCGCATCCGGTTACTGCAGTTTGTCACGGGCACGTCCCGGGTACCTATGAATGGATTTGCCGAACTTTATG
GTTCCAGTGGTCCTCAGCTGTTTACAATAGAGCAATGGGGAAGTCCTGAAAAGCTGCCCAGAGCTCACACATGCTTTAAT
CGCCTCGACTTACCTCCGTACGAAACCTTCGAAGATTTACGGGAGAAACTGCTCATGGCCGTGGAGAACGCCCAGGGCTT
CGAAGGGGTGGAT

ORF - retro_ocun_393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.26 %
Parental protein coverage: 71.41 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDSLGLAVPPPPASPVSRTSPQELTEELSRRLQVTPDANGEQFSSLIQREPSSRLRSCSVTDAVAEQAHLP
DSLGLAVPPPPASPVSRTSPQELTEELSRRLQVT.DANGEQFSSLI.REPSSRLRSCSVTDAVAEQAHLP
RetrocopyDSLGLAVPPPPASPVSRTSPQELTEELSRRLQVTLDANGEQFSSLI-REPSSRLRSCSVTDAVAEQAHLP
ParentalPPSVAYVHTTPGLPSGWEERKDAKGRTYYVNHNNRTTTWTRPIMQLAEDGAASGSATNSSNHLIEPQIRR
PPSVAYVHTTPGLPSGWEERKDAK.RTYYVNHNNRTTTWTRPIMQLAEDGAASGSATNSSNHLIEPQIRR
RetrocopyPPSVAYVHTTPGLPSGWEERKDAK*RTYYVNHNNRTTTWTRPIMQLAEDGAASGSATNSSNHLIEPQIRR
ParentalPRSLSSPTVTLSAPLEGAKDSPVRRAVKDTLSNPQSPQPSPYNSPKPQHRVTQSFLPPGWEMRIAPNGRP
PRSLSSPTVTLSAPLEGAKDSPVRRAVKDTLSNPQSPQPSPYNSPKPQHRVTQSFLPPGWEMRIAPNGRP
RetrocopyPRSLSSPTVTLSAPLEGAKDSPVRRAVKDTLSNPQSPQPSPYNSPKPQHRVTQSFLPPGWEMRIAPNGRP
ParentalFFIDHNTKTTTWEDPRLKFPVHMRSKASLNPNDLGPLPPGWEERIHLDGRTFYIDHNSKITQWEDPRLQN
FFIDHNTKTTTWEDPRLKFPVHMRSKASLNPNDLGPLPPGWEERIHLDGR.FYIDHNSKITQWEDPRLQN
RetrocopyFFIDHNTKTTTWEDPRLKFPVHMRSKASLNPNDLGPLPPGWEERIHLDGRMFYIDHNSKITQWEDPRLQN
ParentalPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFE
PAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFE
RetrocopyPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFE
ParentalSEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFH
SEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFH
RetrocopySEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFH
ParentalGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPN
GKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPN
RetrocopyGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPN
ParentalGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDW
GSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDW
RetrocopyGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDW
ParentalRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSP
RQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGS.GPQLFTIEQWGSP
RetrocopyRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSSGPQLFTIEQWGSP
ParentalEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD
EKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD
RetrocopyEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD

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 .37 RPM 34 .99 RPM
SRP017611_kidney 2 .64 RPM 69 .23 RPM
SRP017611_liver 1 .77 RPM 34 .14 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_393 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_393 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_393 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
Callithrix jacchus ENSCJAG000000035971 retrocopy
retro_cjac_3021,
Oryctolagus cuniculus ENSOCUG00000014471 1 retrocopy
retro_ocun_393 ,


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