RetrogeneDB ID:

retro_eeur_657

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_377024:78641..78932(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPE1
Ensembl ID:ENSEEUG00000005040
Aliases:None
Description:heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]


Retrocopy-Parental alignment summary:






>retro_eeur_657
CGCCAGGAATTTAGGAAGTTCCTTCCTCTCTTAGACCGAGTGCTGGTTGAGAGGAGAGCAGCTGAAACTGTGACCAAAGG
AGGCATCGTGCTTCCAGAGAAGTCTCAGGGGAAGGTGTTGCAAGCAACGGTGGTGGCTGTCTGCTCTGGCTCCAAAGGAA
AGACTGGAGATATGCGTGTGAAAGTTGGAGATAAAGTTCTTCTGTCAGAATATGGAGGCGCCAAAGTGGTTCGAGATGAC
AAGGGTTATTTCTTTTTTTGAGACGGAGATATTCTTGGAAAATATGTAGAC

ORF - retro_eeur_657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60. %
Parental protein coverage: 99. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRQALGKFFPLFDQVLAEWSAGETVTEEGIMLPEKCQ-RVLLTAVAAXXXXXXXXTGEIQPVSVKVGDKVL
RQ...KF.PL.D.VL.E..A.ETVT..GI.LPEK.Q..VL...V.A........TG......VKVGDKVL
RetrocopyRQEFRKFLPLLDRVLVERRAAETVTKGGIVLPEKSQGKVLQATVVAVCSGSKGKTGDMR---VKVGDKVL
ParentalLPEYGGTKVVLDDKDYFLFRDGDILGKYVD
L.EYGG.KVV.DDK.YF.F.DGDILGKYVD
RetrocopyLSEYGGAKVVRDDKGYFFF*DGDILGKYVD

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 13 .21 RPM
SRP017611_kidney 0 .00 RPM 58 .32 RPM
SRP017611_liver 0 .00 RPM 43 .09 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_657 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 13 parental genes, and 116 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001376918 retrocopies
Canis familiaris ENSCAFG000000108904 retrocopies
Callithrix jacchus ENSCJAG000000040081 retrocopy
Dasypus novemcinctus ENSDNOG0000001324627 retrocopies
Erinaceus europaeus ENSEEUG00000005040 6 retrocopies
Felis catus ENSFCAG000000144559 retrocopies
Gorilla gorilla ENSGGOG0000002794417 retrocopies
Loxodonta africana ENSLAFG000000000571 retrocopy
Macaca mulatta ENSMMUG000000104911 retrocopy
Oryctolagus cuniculus ENSOCUG000000103601 retrocopy
Otolemur garnettii ENSOGAG0000003443424 retrocopies
Pongo abelii ENSPPYG000000258761 retrocopy
Rattus norvegicus ENSRNOG000000148686 retrocopies



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