RetrogeneDB ID:

retro_eeur_198

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_206553:4504..4983(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IDI1
Ensembl ID:ENSEEUG00000012555
Aliases:None
Description:isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]


Retrocopy-Parental alignment summary:






>retro_eeur_198
AAGCTCTTGTTACAACAGAGATCAGACACTAAAATTACCTTTCCAGGTTGTTTTACCAGTACTTGTTGTAGTCACCCACT
AAGTAATCCAGGAGAGCTTGAAGAAAGTGATGCGATTGGAGTGAAAAGAGCAGTTCAGAGGCGTTTGAAAGTTGATTTAT
GCATTCCCCTGGAAGAGGTTCCTCCAGAAGAAATTAAGTACCTAACACGAATGTAGTACAAGGCTCAATCTGATAGCATT
TGGGGAGAACATGAGATTGATTACATTTTGTTTATGAAGAAGAATCCAGATTCCAATGAGATTAAAAGCTATTGTATGTG
TCAAAGGAAGAAGTAAAAGAACTTTTGAGAAAGGCAGCCACTGGTGAAATTAAGTTAACTCCATGGTTTAAGATTATTAC
AGAGGCTTTTCTCTTTAAATGGTGGGACAGTTTACATAATCTGAATGTGTTTATTGACCATGAGAAAATACACAGAATG

ORF - retro_eeur_198 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.06 %
Parental protein coverage: 69.2 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKLLLQQRSDAKITFPGCFTNTCCSHPLNNPGELEENDAIGVRRAAQRRLKAELGIPLEEVPPEEIQYLTR
KLLLQQRSD.KITFPGCFT.TCCSHPL.NPGELEE.DAIGV.RA.QRRLK..L.IPLEEVPPEEI.YLTR
RetrocopyKLLLQQRSDTKITFPGCFTSTCCSHPLSNPGELEESDAIGVKRAVQRRLKVDLCIPLEEVPPEEIKYLTR
ParentalLYYKAQSDDIWGEHEIDYILFMKKNVTLNPDPNEIKSYC-YVSKEEVKELLRKAATGKIKLTPWFKIITE
..YKAQSD.IWGEHEIDYILFMKKN....PD.NEIKSYC.YVSKEEVKELLRKAATG.IKLTPWFKIITE
RetrocopyM*YKAQSDSIWGEHEIDYILFMKKN----PDSNEIKSYC<YVSKEEVKELLRKAATGEIKLTPWFKIITE
ParentalTFLFKWWDNLHNLDVFIDHEKIHRM
.FLFKWWD.LHNL.VFIDHEKIHRM
RetrocopyAFLFKWWDSLHNLNVFIDHEKIHRM

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 .16 RPM 25 .14 RPM
SRP017611_kidney 0 .00 RPM 12 .19 RPM
SRP017611_liver 0 .48 RPM 27 .33 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_198 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 14 parental genes, and 37 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000084833 retrocopies
Erinaceus europaeus ENSEEUG00000012555 3 retrocopies
retro_eeur_188, retro_eeur_198 , retro_eeur_61,
Homo sapiens ENSG000000670643 retrocopies
Gorilla gorilla ENSGGOG000000009343 retrocopies
Macaca mulatta ENSMMUG000000171153 retrocopies
Monodelphis domestica ENSMODG000000059985 retrocopies
Mus musculus ENSMUSG000000582584 retrocopies
Nomascus leucogenys ENSNLEG000000135943 retrocopies
Oryctolagus cuniculus ENSOCUG000000074931 retrocopy
Ochotona princeps ENSOPRG000000086922 retrocopies
Pongo abelii ENSPPYG000000020392 retrocopies
Pan troglodytes ENSPTRG000000022393 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000232601 retrocopy
Tursiops truncatus ENSTTRG000000111741 retrocopy



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