RetrogeneDB ID:

retro_ocun_1807

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:GL018974:282148..283076(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000000203
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_1807
TTGGATTCTGCCCAAAGAAAGACGGAGATGGTGTTATCTGAAAAGGTTAGTCAGCTGATGGAATGGACCAATAAAAGACC
TGTAATAAGAATGAATGCAGACAAGTTTTGTCATCTTGTTAAAGCTCCACCAAGAAATTACTCCGTTATTGTCATGTTCA
CTGCTCTCCAACTTCATAGACAGTGTGTTGTTTGCAAACAAGCTGATGAAGAATTCCAGATCCTGGCAAACTTGGCGATA
TTCCAGTGCATTTACCAACAGGATATTTTTTTGCCATGGTAGATTTTGATGAAGGTTCTGATGTATTTCAAATGCTAAAC
ATGAACTCGGCTCCAACTTTCATCAACTTTCCTGCAACAGGGAAACCCAAATGGGGCGATACATATGAGTTGCAGGTGCG
TGGTTTTTCAGCTGAGCAGATTGCCTGGTGGATTGCAGACAGAACTGATGTCAATATTAGAGTAATAGACCCCCAAATTA
TGCTGGTCCCCTTTTGTTGGGATTACTTTTGGCTGTTATTGGTGGACTTGTGTATCTTCGAAGAAGCAATATGGAATTTA
TCTTTAATAAAACTGGATGGGCTTTTGAAGCTTTGTGTTTTGTGCTTGCTATGACATCTGGTCAAATGTGGAACCATATA
AGAGGACCACCATATGCTCATAAGAATCCTCACATAGGACATGTGAATTATGTCCATGGAAGCAGCCAAGCCCAGTGTGT
GGCTGAAACACACATCGTTCTTCTGTTCAATGATGGGATTACCTTAGGGATGGTACTTTTATGTGAAGCTGCTACTTCTG
ACATGGATATTGGAAAGCAAAAGATAATGTGCGTAGCTGGTATTGCATTGGTTGTGTTATTCTTCAGTTGGATGCTGTCC
ATTTTCAGATCTAAATATCATGGGTATCCATACAGCTTTCTGATGAGT

ORF - retro_ocun_1807 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.38 %
Parental protein coverage: 92.54 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLASAQRKKEMVLSEKVSQLMEWTNKRPVIRMNGDKFRRLVKAPPRNYSVIVMFTALQLHRQCVVCKQADE
L.SAQRK.EMVLSEKVSQLMEWTNKRPVIRMN.DKF..LVKAPPRNYSVIVMFTALQLHRQCVVCKQADE
RetrocopyLDSAQRKTEMVLSEKVSQLMEWTNKRPVIRMNADKFCHLVKAPPRNYSVIVMFTALQLHRQCVVCKQADE
ParentalEFQILANSWRYSSAFTNRI-FFAMVDFDEGSDVFQMLNMNSAPTFINFPAKGKPKRGDTYELQVRGFSAE
EFQILAN...........I.FFAMVDFDEGSDVFQMLNMNSAPTFINFPA.GKPK.GDTYELQVRGFSAE
RetrocopyEFQILANLAIFQCIYQQDI<FFAMVDFDEGSDVFQMLNMNSAPTFINFPATGKPKWGDTYELQVRGFSAE
ParentalQIARWIADRTDVNIRVI-RPPNYAGPLMLGLLLAVIGGLVYLRRSNMEFLFNKTGWAFAALCFVLAMTSG
QIA.WIADRTDVNIRVI.RPPNYAGPL.LGLLLAVIGGLVYLRRSNMEF.FNKTGWAF.ALCFVLAMTSG
RetrocopyQIAWWIADRTDVNIRVI<RPPNYAGPLLLGLLLAVIGGLVYLRRSNMEFIFNKTGWAFEALCFVLAMTSG
ParentalQMWNHIRGPPYAHKNPHTGHVNYIHGSSQAQFVAETHIVLLFNGGVTLGMVLLCEAATSDMDIGKRKIMC
QMWNHIRGPPYAHKNPH.GHVNY.HGSSQAQ.VAETHIVLLFN.G.TLGMVLLCEAATSDMDIGK.KIMC
RetrocopyQMWNHIRGPPYAHKNPHIGHVNYVHGSSQAQCVAETHIVLLFNDGITLGMVLLCEAATSDMDIGKQKIMC
ParentalVAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS
VAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS
RetrocopyVAGIALVVLFFSWMLSIFRSKYHGYPYSFLMS

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






(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 .00 RPM 30 .52 RPM
SRP017611_kidney 0 .00 RPM 111 .09 RPM
SRP017611_liver 0 .00 RPM 71 .37 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1807 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1807 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1807 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Gorilla gorilla ENSGGOG000000103421 retrocopy
Loxodonta africana ENSLAFG000000128861 retrocopy
Oryctolagus cuniculus ENSOCUG00000000203 1 retrocopy
retro_ocun_1807 ,
Pongo abelii ENSPPYG000000204931 retrocopy



Copyright © RetrogeneDB 2014-2017