RetrogeneDB ID:

retro_eeur_231

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_215002:4908..5175(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GCSH
Ensembl ID:ENSEEUG00000009653
Aliases:None
Description:glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]


Retrocopy-Parental alignment summary:






>retro_eeur_231
AGCATGTAACCCGCACTATGCAGCCTGCTCACAGCCTGGCTCCTGGAGAGCTGCGGCCTCTGCTGCCCTGCAGGCTGCAT
GCCGGCACCTTGTGCATGCTGAGCCCTGCTCTGCTCTGCTCTCTGTAGGTGAGTTCAAGGCAAACATGAATGGATAATAA
AAGAAAATTGTATTGAAACTGTGAGTATCAGCAGCGTTGCACAGGAAGCTTTGGGAGATGGGGTTTAATGTCGGCTACCT
GAAGCTGGGACAGAATGGAACAAAGAG

ORF - retro_eeur_231 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.99 %
Parental protein coverage: 52.02 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalNMRAALCSLRAA-SAPAAQSPLRPRRLHAGAVRTLCTG-SALLSVRKFT-DKHEWITTENGIGTVGISNF
.M..ALCSL..A..AP....PL.P.RLHAG....L....SALLSV..F...KHEWI..EN.I.TV.IS..
RetrocopySM*PALCSLLTA<LAPGELRPLLPCRLHAGTLCMLSPA<SALLSVGEFK<GKHEWIIKENCIETVSISSV
ParentalAQEALGDVVYCSLPEVGTKLNKQ
AQEALGD.V.C.LPE.GT..NK.
RetrocopyAQEALGDGV*CRLPEAGTEWNKE

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 4 .19 RPM
SRP017611_kidney 0 .00 RPM 18 .19 RPM
SRP017611_liver 0 .00 RPM 13 .34 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_231 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 21 parental genes, and 175 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000089051 retrocopy
Ailuropoda melanoleuca ENSAMEG000000139595 retrocopies
Bos taurus ENSBTAG000000067958 retrocopies
Canis familiaris ENSCAFG000000200145 retrocopies
Choloepus hoffmanni ENSCHOG0000000243437 retrocopies
Erinaceus europaeus ENSEEUG00000009653 2 retrocopies
retro_eeur_189, retro_eeur_231 ,
Felis catus ENSFCAG000000130388 retrocopies
Homo sapiens ENSG0000014090510 retrocopies
Gorilla gorilla ENSGGOG0000000023210 retrocopies
Loxodonta africana ENSLAFG000000155863 retrocopies
Myotis lucifugus ENSMLUG0000000578312 retrocopies
Macaca mulatta ENSMMUG000000130885 retrocopies
Mustela putorius furoENSMPUG000000096774 retrocopies
Nomascus leucogenys ENSNLEG000000268441 retrocopy
Procavia capensis ENSPCAG000000058201 retrocopy
Pongo abelii ENSPPYG0000000758515 retrocopies
Pan troglodytes ENSPTRG0000000838610 retrocopies
Sarcophilus harrisii ENSSHAG000000055291 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000164332 retrocopies
Tupaia belangeri ENSTBEG0000000005627 retrocopies
Tursiops truncatus ENSTTRG000000079928 retrocopies



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