RetrogeneDB ID:

retro_eeur_685

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_69435:3412..3890(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL15
Ensembl ID:ENSEEUG00000011286
Aliases:None
Description:ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]


Retrocopy-Parental alignment summary:






>retro_eeur_685
CCACATTCCACCTGGCCAGATAAAGCCCACAGGCTGGATTACAAGGCCAAGCAAGGGTACATCATGTATTGGAATCATGT
CCGCCATAGTGGCCCCAAATGTCCAGTTCCTAAGGGTGCAGCCTATAGTAAGCCTGTCCATCATGGTGCTAACCAGCTGA
AGTTTTTATGGAGCCTTCCGTCTATTGCTGTGGAGCAAGCTGGATGCCACTGTGGGGGCTCTGAGAGTCCTGAATTCTCA
CTGGATGAAGTCCACATACAGGTTCTTTGAGATAATCTTCATTAAACCATTTCATGAAGCTATCAGAAGAAATCCCAATA
TCCATTGGTTCACCAAACCAGTCCACAAACACAGGGAGATGCGAGGGATGACATCCCCAAGCCACAAGTGCTGTGACCTT
GGAAAGGGCCACAAATTCCACCATACTATTGGTGGTTCTCTCCATGTAGCTTGGAGAAGGTACAACATTCTTCAGCTC

ORF - retro_eeur_685 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.52 %
Parental protein coverage: 75.94 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRH
P..T.PDKA.RL.YKAKQGY..Y...VR..G.K.PVPKGA.Y.KPVHHG.NQLKF..SL.S.A.E.AG.H
RetrocopyPHSTWPDKAHRLDYKAKQGYIMYWNHVRHSGPKCPVPKGAAYSKPVHHGANQLKFLWSLPSIAVEQAGCH
ParentalCG-ALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGH
CG.ALRVLNS.W....STY.FFE.I.I.PFH.AIRRNP...W.TKPVHKHREMRG.TS...K...LGKGH
RetrocopyCG>ALRVLNSHWM--KSTYRFFEIIFIKPFHEAIRRNPNIHWFTKPVHKHREMRGMTSPSHKCCDLGKGH
ParentalKFHHTIGGSRRAAWRRRNTLQL
KFHHTIGGS...AWRR.N.LQL
RetrocopyKFHHTIGGSLHVAWRRYNILQL

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 48 .99 RPM
SRP017611_kidney 0 .00 RPM 131 .28 RPM
SRP017611_liver 0 .00 RPM 73 .31 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_685 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 99 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000330802 retrocopies
Erinaceus europaeus ENSEEUG00000011286 5 retrocopies
Echinops telfairi ENSETEG000000150444 retrocopies
Macropus eugenii ENSMEUG000000145223 retrocopies
Macaca mulatta ENSMMUG000000063531 retrocopy
Mustela putorius furoENSMPUG000000121487 retrocopies
Mus musculus ENSMUSG000000124052 retrocopies
Otolemur garnettii ENSOGAG0000001305613 retrocopies
Procavia capensis ENSPCAG000000119951 retrocopy
Rattus norvegicus ENSRNOG0000000814017 retrocopies
Sus scrofa ENSSSCG000000280795 retrocopies
Tupaia belangeri ENSTBEG0000000984334 retrocopies
Tursiops truncatus ENSTTRG000000072445 retrocopies



Copyright © RetrogeneDB 2014-2017