RetrogeneDB ID:

retro_eeur_253

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_224423:198..517(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2C
Ensembl ID:ENSEEUG00000010643
Aliases:None
Description:ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]


Retrocopy-Parental alignment summary:






>retro_eeur_253
ATATATGATGACCTGAAGTATAAGCTCTCCCTGCAGTTCCCTGCTGACTACCCCTACAACGCACCCACTATGAAGTTCCT
CACACACTGCTACCACCCCAGTGTACACACCCAGAGCAACATCTGCCTGGACATCTTGAAAGACAAGTGGTCTGCCCTGT
ATGAGGTCAGGACTATCCTGCTCTCCATCCAGAGCCTTCCTGGAGAACCCAATATCAACAGCCCTTTGAACACATGCTGC
TGAGCTCTGGAAAAATCCCACAGCCTTTAAGAAGTACCTACAAGAAACCTACTCAAAGCGGGTCTCCAGTTAAGAACCC

ORF - retro_eeur_253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.7 %
Parental protein coverage: 59.78 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKDKWSALYDVRTILLSIQSL-LGE
.Y.DL.YKLSL.FP..YPYNAPT.KFLT.CYHP.V.TQ.NICLDILKDKWSALY.VRTILLSIQSL.L..
RetrocopyIYDDLKYKLSLQFPADYPYNAPTMKFLTHCYHPSVHTQSNICLDILKDKWSALYEVRTILLSIQSL>LEN
ParentalPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVASQEP
P.I...L.THAAELWKNPTAFKKYLQETYSK.V.S.EP
RetrocopyP-ISTAL*THAAELWKNPTAFKKYLQETYSKRVSS*EP

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 .16 RPM 0 .32 RPM
SRP017611_kidney 0 .00 RPM 0 .19 RPM
SRP017611_liver 0 .00 RPM 0 .16 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_253 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 16 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000167461 retrocopy
Canis familiaris ENSCAFG000000097456 retrocopies
Equus caballus ENSECAG000000146192 retrocopies
Erinaceus europaeus ENSEEUG00000010643 14 retrocopies
Erinaceus europaeus ENSEEUG000000118861 retrocopy
Felis catus ENSFCAG000000018854 retrocopies
Loxodonta africana ENSLAFG000000031641 retrocopy
Macropus eugenii ENSMEUG0000000717714 retrocopies
Microcebus murinus ENSMICG000000112182 retrocopies
Macaca mulatta ENSMMUG000000210234 retrocopies
Monodelphis domestica ENSMODG000000136616 retrocopies
Mustela putorius furoENSMPUG000000176192 retrocopies
Oryctolagus cuniculus ENSOCUG000000121763 retrocopies
Otolemur garnettii ENSOGAG000000049893 retrocopies
Pan troglodytes ENSPTRG000000135641 retrocopy
Sus scrofa ENSSSCG000000074231 retrocopy



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