RetrogeneDB ID:

retro_eeur_350

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_266976:9333..9660(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM60A
Ensembl ID:ENSEEUG00000012617
Aliases:None
Description:family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]


Retrocopy-Parental alignment summary:






>retro_eeur_350
GTGCATGAGACTCGGTCAGGAGACATTTGTAATGCCTGTGTCTTGCTTGTGAAAAGATGGAAGAAATTACCAGCAGGATC
CAAAAAAAACTGGAATCATGTGGTAGATGCAAGGGCTGGACCCAGTCTAAAGACTACGTTGAAACCAAAGAAAGTGAAAA
CTCTATCTGGAAACAGGATAAAAAGCAACCAGATCAGTAAACTACAGAAGGAATTTAAACGACACAATTCTGATGCTCAC
AGTACCACCTCAAGTGCCTCTCCTGCTCAGTCTCCTTGTTACAGTAACCAGTCAGATGAAGGCTCAGATACAGAAATGGC
TCCTGGC

ORF - retro_eeur_350 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.41 %
Parental protein coverage: 70.32 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLHETRSGDICNACVLLVKRWKKLPAGSKKNWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK
.HETRSGDICNACVLLVKRWKKLPAGS...WNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK
RetrocopyVHETRSGDICNACVLLVKRWKKLPAGSXXXWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK
ParentalEFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMASG
EFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMA.G
RetrocopyEFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMAPG

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 2 .26 RPM
SRP017611_kidney 0 .38 RPM 1 .88 RPM
SRP017611_liver 0 .00 RPM 0 .96 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_350 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 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000106854 retrocopies
Callithrix jacchus ENSCJAG000000012153 retrocopies
Dasypus novemcinctus ENSDNOG000000168732 retrocopies
Equus caballus ENSECAG000000096552 retrocopies
Erinaceus europaeus ENSEEUG00000012617 2 retrocopies
retro_eeur_350 , retro_eeur_372,
Echinops telfairi ENSETEG000000028882 retrocopies
Felis catus ENSFCAG000000089554 retrocopies
Microcebus murinus ENSMICG000000034602 retrocopies
Otolemur garnettii ENSOGAG000000089274 retrocopies
Rattus norvegicus ENSRNOG000000460481 retrocopy
Rattus norvegicus ENSRNOG000000499432 retrocopies
Sarcophilus harrisii ENSSHAG000000062611 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000070971 retrocopy



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