RetrogeneDB ID:

retro_eeur_60

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:GeneScaffold_3172:33129..33468(+)
Located in intron of:ENSEEUG00000009975
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22L1
Ensembl ID:ENSEEUG00000011941
Aliases:None
Description:ribosomal protein L22-like 1 [Source:HGNC Symbol;Acc:27610]


Retrocopy-Parental alignment summary:






>retro_eeur_60
AAGCAGGTTCTGAAGTTCACCCTTGATTACACACACCCTGTTGAAGATGGAATCATGGATGCTGCTAATTTTGAGCAGTT
TCTTCAAGAGAGAATCAAAGTGAATGGCAAAGCTGGGAATCTTGGTGGTGGAGTTGTCACCATTGAAGGAAGCAAGAGCA
AGATCACTGTGACTTCTGAGGTGCCTTTCTCTAAAAGGTATTTGAAATATCTCACCAAAAAATATCTGAAGAAGAATAAT
CTACGTGATTGGTTATGCGTAGTTGCTAACAGCAAAGACAGCTATGAATTGCGTTACTTCCAGATTAACCAAAATGAAGA
AGAGGAGGAAGATGAAGAT

ORF - retro_eeur_60 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.8 %
Parental protein coverage: 85.5 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKATWKFNLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGN-VVHIERFKNKITVVSEKQFSKRYLKY
K...KF.LD.THPVEDGI.D..NFEQFL.E..KVNGK.GNLG..VV.IE..K.KITV.SE..FSKRYLKY
RetrocopyKQVLKFTLDYTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIEGSKSKITVTSEVPFSKRYLKY
ParentalLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDDDGSESED
LTKKYLKKNNLRDWL.VVA..K..YELRYFQI.Q.....E.ED
RetrocopyLTKKYLKKNNLRDWLCVVANSKDSYELRYFQINQNEEEEEDED

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 9 .02 RPM 20 .79 RPM
SRP017611_kidney 22 .88 RPM 19 .69 RPM
SRP017611_liver 12 .70 RPM 21 .38 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_60 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 27 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000047301 retrocopy
Canis familiaris ENSCAFG000000149552 retrocopies
Callithrix jacchus ENSCJAG000000024271 retrocopy
Cavia porcellus ENSCPOG000000092151 retrocopy
Equus caballus ENSECAG000000188941 retrocopy
Erinaceus europaeus ENSEEUG00000011941 5 retrocopies
Echinops telfairi ENSETEG000000106589 retrocopies
Homo sapiens ENSG000001635841 retrocopy
Gorilla gorilla ENSGGOG000000017341 retrocopy
Gadus morhua ENSGMOG000000040771 retrocopy
Loxodonta africana ENSLAFG000000132202 retrocopies
Macropus eugenii ENSMEUG000000094841 retrocopy
Myotis lucifugus ENSMLUG000000230522 retrocopies
Myotis lucifugus ENSMLUG000000276838 retrocopies
Macaca mulatta ENSMMUG000000228812 retrocopies
Mus musculus ENSMUSG000000392214 retrocopies
Nomascus leucogenys ENSNLEG000000052872 retrocopies
Oryctolagus cuniculus ENSOCUG000000149622 retrocopies
Otolemur garnettii ENSOGAG000000126422 retrocopies
Procavia capensis ENSPCAG000000087041 retrocopy
Pongo abelii ENSPPYG000000259001 retrocopy
Pteropus vampyrus ENSPVAG000000115241 retrocopy
Rattus norvegicus ENSRNOG000000118172 retrocopies
Sus scrofa ENSSSCG000000274415 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000229723 retrocopies
Tupaia belangeri ENSTBEG0000000035717 retrocopies
Tursiops truncatus ENSTTRG000000070353 retrocopies



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