RetrogeneDB ID:

retro_eeur_199

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_207085:3833..4172(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UCK2
Ensembl ID:ENSEEUG00000013484
Aliases:None
Description:uridine-cytidine kinase 2 [Source:HGNC Symbol;Acc:12562]


Retrocopy-Parental alignment summary:






>retro_eeur_199
TACCGTGTCCTCACCTCTGAGCAGAAGGCCAAAGCCCTCAAGGGCCAGTTCAACTTTGATCACCCAGATGCCTTTGACAA
TGAACTCATCTTCAAGATGCTCAAAGAAATTATGGACGGGAAGACAGTGCAGATCCCAGTGTATGACTCTGTCTCTAATT
GCGGAAGGAGGAGACTTTCACCGTGTTATCCTGCCGACGTGGTGCCCTTTGAGAGGATCCTGGCCTTCTACTCCCAGGAA
GTGCAAAACCTGATCCAGATGAAGCTTTTTGTGGACAGAGATGCTGATACCCTGCTGTCCCGCAGAGTATTGGCGGACAT
CAGTGAACCAGGGAGGGAC

ORF - retro_eeur_199 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.87 %
Parental protein coverage: 73.2 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYRVLTSEQK-KALKGQFNFDHPDAFDNELIFMTLKEIMEGKTVQIPVYDFVSHS-RKEETVTV-YPADVV
YRVLTSEQK.KALKGQFNFDHPDAFDNELIF..LKEIM.GKTVQIPVYD.VS...RKEET.TV.YPADVV
RetrocopyYRVLTSEQKAKALKGQFNFDHPDAFDNELIFKMLKEIMDGKTVQIPVYDSVSNC<RKEETFTV>YPADVV
ParentalLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRELRDISCKGPD
.FE.ILAFYSQEV..L.QMKLFVD.DADT.LSRR.L.DIS..G.D
RetrocopyPFERILAFYSQEVQNLIQMKLFVDRDADTLLSRRVLADISEPGRD

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 .32 RPM 4 .67 RPM
SRP017611_kidney 0 .00 RPM 0 .94 RPM
SRP017611_liver 0 .00 RPM 0 .96 RPM
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
retro_eeur_199 was not experimentally validated.

Retrocopy orthology:
Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG00000013484 1 retrocopy
retro_eeur_199 ,
Myotis lucifugus ENSMLUG000000160121 retrocopy
Oryctolagus cuniculus ENSOCUG000000084461 retrocopy
Pteropus vampyrus ENSPVAG000000076941 retrocopy



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