RetrogeneDB ID:

retro_eeur_148

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_102830:3173..3368(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FXYD4
Ensembl ID:ENSEEUG00000010030
Aliases:None
Description:FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]


Retrocopy-Parental alignment summary:






>retro_eeur_148
CTTCCTGCCCTGGAAGCCAGTGAGTCCATAGATGAGAGCAGTCCCTTCTACTATGACTGAGAGACCCTGCAGCTGGCAGG
AGTCATCTGCTTGGTCAGCATAGCCTTCGCCCTGAGCAACAAATGTAAATGCAAAACTAAAAAGGAGTAGAGCCTGATAC
CTGAGAGAGCTGTCCCATTCATTATGCCAGGGTCT

ORF - retro_eeur_148 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.97 %
Parental protein coverage: 95.95 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLPALEADEATADESSPFYYDWETLQLAGTICAGVLCLVGIAFALSNKCKCKTKKEQSPVPESAIPFIVPG
LPALEA.E...DESSPFYYD.ETLQLAG.IC...L.....A.....KC..KTKKE.S..PE.A.PFI.PG
RetrocopyLPALEASESI-DESSPFYYD*ETLQLAGVIC---LVSIAFALSNKCKC--KTKKE*SLIPERAVPFIMPG
ParentalS
S
RetrocopyS

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 0 .64 RPM
SRP017611_kidney 0 .00 RPM 5 .06 RPM
SRP017611_liver 0 .00 RPM 0 .32 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_148 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 8 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000249231 retrocopy
Dasypus novemcinctus ENSDNOG000000173851 retrocopy
Erinaceus europaeus ENSEEUG00000010030 4 retrocopies
Felis catus ENSFCAG000000224172 retrocopies
Monodelphis domestica ENSMODG000000275781 retrocopy
Oryctolagus cuniculus ENSOCUG000000067221 retrocopy
Tupaia belangeri ENSTBEG000000160331 retrocopy
Tarsius syrichta ENSTSYG000000144603 retrocopies



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