RetrogeneDB ID:

retro_eeur_484

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_322961:8182..8635(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSEEUG00000014071
Aliases:None
Description:ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]


Retrocopy-Parental alignment summary:






>retro_eeur_484
AAGTTCCTGGGCTTTCTCCGCAAGCAGATGAACACCAACCCCTCCCGCGGCCCCTACCACTTCCGCGCCCCCAGCCGCAT
CTTCTGGAGGACCCTGCGGGGGATGCTGCCCCACAAGACCAAGCGGGGCCAGGCCGCCCTGGACCGGCTGAAGGTGTTTG
ACGGCATCCCGCCCCCGTACGACAAGAAAAAGCGGATGGTGGTGCCGGCTGCCCTCAAGGTCGTGCGTCTGAAGCCAACG
AGGAAGTTTGCCTACCTGGGGCGCCTGGCTCACGAAGTGGGCTGGAAGTACCAGGCGGTGACGGCCACCCTATAGGAGAA
GCGCAAGGAGAAGGCCAAGATGCATTACCGCAGGAAGAAGCAGCTGATGAGGCTACGGAAACAGGCCGAGAAGAACGCCG
AGAAGAAGATCTGCAAGTTCACAGAGGTCCTTAAGACCCACGGACTCCTGGTC

ORF - retro_eeur_484 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.69 %
Parental protein coverage: 74.38 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPA
K.L.FLRK.MNTNPSRGPYHFRAPSRIFWRT.RGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPA
RetrocopyKFLGFLRKQMNTNPSRGPYHFRAPSRIFWRTLRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPA
ParentalALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKMHYRRKKQLMRLRKQAEKNAEKKICKF
ALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATL.EKRKEKAKMHYRRKKQLMRLRKQAEKNAEKKICKF
RetrocopyALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATL*EKRKEKAKMHYRRKKQLMRLRKQAEKNAEKKICKF
ParentalTEVLKTHGLLV
TEVLKTHGLLV
RetrocopyTEVLKTHGLLV

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 2 .26 RPM 88 .15 RPM
SRP017611_kidney 11 .81 RPM 244 .36 RPM
SRP017611_liver 6 .27 RPM 125 .89 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_484 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 20 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052963 retrocopies
Canis familiaris ENSCAFG000000298923 retrocopies
Callithrix jacchus ENSCJAG0000000007216 retrocopies
Cavia porcellus ENSCPOG000000124172 retrocopies
Erinaceus europaeus ENSEEUG00000014071 6 retrocopies
Echinops telfairi ENSETEG000000170762 retrocopies
Felis catus ENSFCAG000000091944 retrocopies
Gorilla gorilla ENSGGOG0000000293211 retrocopies
Myotis lucifugus ENSMLUG0000000494510 retrocopies
Macaca mulatta ENSMMUG0000000755114 retrocopies
Mus musculus ENSMUSG000000741293 retrocopies
Oryctolagus cuniculus ENSOCUG000000252589 retrocopies
Otolemur garnettii ENSOGAG000000046257 retrocopies
Ochotona princeps ENSOPRG000000011943 retrocopies
Pongo abelii ENSPPYG000000102511 retrocopy
Pan troglodytes ENSPTRG000000112981 retrocopy
Rattus norvegicus ENSRNOG0000002061810 retrocopies
Sus scrofa ENSSSCG000000031664 retrocopies
Tarsius syrichta ENSTSYG000000087914 retrocopies
Tursiops truncatus ENSTTRG000000054857 retrocopies



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