RetrogeneDB ID:

retro_eeur_174

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_143326:214..822(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CD9
Ensembl ID:ENSEEUG00000009313
Aliases:None
Description:CD9 molecule [Source:HGNC Symbol;Acc:1709]


Retrocopy-Parental alignment summary:






>retro_eeur_174
CTGGCTGGGATCGCAGTCCTTGCCATTGGACTATGGTTGTGGTTCGACACTCAGACCAAAAGCATCTTGGAGCAGGACGA
TAACCACTCCAGCTTCCACACAGGAGTGTACATTCTGGTGGGCACTGGTGTTCTCATGACGCTGGTGGGGTTCCTGAGCT
GCTGTGGTGCTGTGCAAGAGTCCTAGTGCATGCTGGGACTGTTCTTCACCTTCCTCTTAGTGATATTCACCATTAAGATA
GTGCGGCCATCTGGGGATACTCTCACAAAGAAGAGGTGATTAAGGAAGTCCAGAAATTCTACCAGGACCCCTATACCAAG
ATGAAGAACAAGGATGAGCTGCAGAAGGAGACATTGAAGGCCATCCACTCCATATTGAACTGCTACAGGATGACCAGAGC
ACTTGAACAATTTCTCACTGACATCTGCCCTGAAAAGAAACTAATGAAAAGCATCACTACAAAGCCCTGCCCTCAAGCCA
TACAGGAGGTCTTCGACAAGTTCCACATCATCCGCGCCCTGGGCATCAGGATCTCTGTGGTGACTATATACGGCATGATC
TTCAGTATGATCCTGTTCTGTGCCATTCATAGAAGCAGAGAGATGGTC

ORF - retro_eeur_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.9 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLAGIAVLAIGLWLRFDTQTKSIFEQENNHSSFYTGVYILIGAGALMMLVGFLGCCGAVQESQCMLGLFFT
LAGIAVLAIGLWL.FDTQTKSI.EQ..NHSSF.TGVYIL.G.G.LM.LVGFL.CCGAVQES.CMLGLFFT
RetrocopyLAGIAVLAIGLWLWFDTQTKSILEQDDNHSSFHTGVYILVGTGVLMTLVGFLSCCGAVQES*CMLGLFFT
ParentalFLLVIFAIEI-AAAIWGYSHKEEVIKEVQKFYQDTYTKLKNKDELQKETLKAIHFALNCCGMTGALEQFL
FLLVIF.I.I..AAIWGYSHKEEVIKEVQKFYQD.YTK.KNKDELQKETLKAIH..LNC..MT.ALEQFL
RetrocopyFLLVIFTIKI<SAAIWGYSHKEEVIKEVQKFYQDPYTKMKNKDELQKETLKAIHSILNCYRMTRALEQFL
ParentalTDICPEKKLMEGITTKPCPQAIQEVFDNKFHIIGAVGIGIAVVMIFGMIFSMILCCAIRRSREMV
TDICPEKKLM..ITTKPCPQAIQEVFD.KFHII.A.GI.I.VV.I.GMIFSMIL.CAI.RSREMV
RetrocopyTDICPEKKLMKSITTKPCPQAIQEVFD-KFHIIRALGIRISVVTIYGMIFSMILFCAIHRSREMV

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 .32 RPM 76 .87 RPM
SRP017611_kidney 0 .56 RPM 138 .22 RPM
SRP017611_liver 0 .16 RPM 57 .08 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_174 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 6 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG00000009313 1 retrocopy
retro_eeur_174 ,
Felis catus ENSFCAG000000068631 retrocopy
Myotis lucifugus ENSMLUG000000069011 retrocopy
Monodelphis domestica ENSMODG000000180533 retrocopies
Mus musculus ENSMUSG000000303421 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000013481 retrocopy



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