RetrogeneDB ID:

retro_eeur_386

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_279755:5427..6028(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCNB1
Ensembl ID:ENSEEUG00000005724
Aliases:None
Description:cyclin B1 [Source:HGNC Symbol;Acc:1579]


Retrocopy-Parental alignment summary:






>retro_eeur_386
CCTGGGAAAAGGGAAAAGCAACCCATGCCTTTGGAGTGAGAGTCCAAACCTGAGCTAGAACCTGAGCCTCTGAGAAAAGA
AAAGCTCTCACTTGAGCCTATTTTGGTGGATGCTCCCTCTGTAAGCTCCAATGGAGACATCCGGGTGTGCTCCAGCAGAA
GATGATCTGTGCCAAGCTTTCTCTGATATAATTCTTGCTATGAGTGATGTGCATGCAGAAGATGGAGCTGACCCAAACCT
CTGTAGTGAATGTGTGAAAGATATCTATGTTTACCTGAGACAACTTGAGGAAGAGCAAGCAGTTAAGCCAAAATACCTAC
TGGGTCGATAAGTCACTGAAAACATGAGAGCCATCTTAATTGACTGGCTAGTGCAGGTTCAAATGAAATTCAGGTTGCTG
CAGAAGACTATGTATATGATTGTTTCTATTATTGATTGGTTCATGCAGAACAATCTTGTGCCCAAGAAGATGCTGCAGCT
GGTTGTTACTGCTATGTTAGTTGCAAGCAAATATGAAGAGATGTGCCCTCCAGAAATTGGCGACTTTGCCTTTGTGATTG
ATAATGCCTATACTAAGCACCAAATCAGACAGATGGAAATT

ORF - retro_eeur_386 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.14 %
Parental protein coverage: 51.02 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPKPVEKEPMPLERESKPELEPEPPREEKLSPEPILVDTPSAS-PMETSGCAPAEEDLCQAFSDVILAVSD
P...EK.PMPLE.ESKPELEPEP.R.EKLS.EPILVD.PS.S.PMETSGCAPAE.DLCQAFSD.ILA.SD
RetrocopyPGKREKQPMPLE*ESKPELEPEPLRKEKLSLEPILVDAPSVS>PMETSGCAPAEDDLCQAFSDIILAMSD
ParentalVDAEDGADPNLCSEYVKDIYVYLRQLEEEQAVKPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYM
V.AEDGADPNLCSE.VKDIYVYLRQLEEEQAVKPKYLLGR.VT.NMRAILIDWLVQVQMKFRLLQ.TMYM
RetrocopyVHAEDGADPNLCSECVKDIYVYLRQLEEEQAVKPKYLLGR*VTENMRAILIDWLVQVQMKFRLLQKTMYM
ParentalTVSIIDRFMQNNCVPKKMLQLVGVTAMFVASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEM
.VSIID.FMQNN.VPKKMLQLV.VTAM.VASKYEEM.PPEIGDFAFV.DN.YTKHQIRQME.
RetrocopyIVSIIDWFMQNNLVPKKMLQLV-VTAMLVASKYEEMCPPEIGDFAFVIDNAYTKHQIRQMEI

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 1 .61 RPM
SRP017611_kidney 0 .00 RPM 0 .94 RPM
SRP017611_liver 0 .00 RPM 0 .16 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_386 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 10 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000142392 retrocopies
Canis familiaris ENSCAFG000000077051 retrocopy
Callithrix jacchus ENSCJAG000000160751 retrocopy
Cavia porcellus ENSCPOG000000146291 retrocopy
Erinaceus europaeus ENSEEUG00000005724 2 retrocopies
retro_eeur_386 , retro_eeur_548,
Mustela putorius furoENSMPUG000000146481 retrocopy
Procavia capensis ENSPCAG000000024511 retrocopy
Sarcophilus harrisii ENSSHAG000000076851 retrocopy
Tupaia belangeri ENSTBEG000000118174 retrocopies
Tarsius syrichta ENSTSYG000000089281 retrocopy



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