RetrogeneDB ID:

retro_eeur_298

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_246801:7766..8146(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZCRB1
Ensembl ID:ENSEEUG00000000397
Aliases:None
Description:zinc finger CCHC-type and RNA binding motif 1 [Source:HGNC Symbol;Acc:29620]


Retrocopy-Parental alignment summary:






>retro_eeur_298
ATGAGTGGCGGGTTGGCCCCAAGCAAAAGCACCGTGTATGTATACAACTTGCCCTTTTCTCTGATCATCAATGACTTATT
CTGGATATTTTCCAAATATGACCAAGTTGTAAAGGTTACTATAATGAAAGACAACAATACCAGGAGGAGTAAAGGGGTTG
TGTTTATTTTGCTTTTGGATAAAGACTCTATGCAAAACTGTATCAGAACAATAAAAATAAGCAGTTATTTGGTAGAGTGG
TAAAAGCAAGCATTACTATTGACAGTAGAAGAGCAGCTGAGTTTTTCCAAAGATGGAACTACTTTGATAAGTATAAGTGT
TATAAATGTGGGGAAAGTGGCCACTTAAGTTATGCCTATCCTAAAAATATGCATGGAGAA

ORF - retro_eeur_298 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.44 %
Parental protein coverage: 59.07 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGGLAPSKSTVYVSNLPFSLTNNDLFRXXXXXXXXXXVTIMKDKDTRRSKGVAFILFLDKDSAQNCTRA
MSGGLAPSKSTVYV.NLPFSL..NDLF...........VTIMKD..TRRSKGV.FIL.LDKDS.QNC.R.
RetrocopyMSGGLAPSKSTVYVYNLPFSLIINDLFWIFSKYDQVVKVTIMKDNNTRRSKGVVFILLLDKDSMQNCIRT
ParentalI-NNKQLFGRVIKASIAIDNGRAAEFIRRRNYFDKSKCYECGESGHLSYACPKNMLGE
I..NKQLFGRV.KASI.ID..RAAEF..R.NYFDK.KCY.CGESGHLSYA.PKNM.GE
RetrocopyI<KNKQLFGRVVKASITIDSRRAAEFFQRWNYFDKYKCYKCGESGHLSYAYPKNMHGE

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 28 .04 RPM
SRP017611_kidney 0 .00 RPM 17 .63 RPM
SRP017611_liver 0 .00 RPM 12 .86 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_298 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 20 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000191192 retrocopies
Choloepus hoffmanni ENSCHOG000000044901 retrocopy
Callithrix jacchus ENSCJAG000000177493 retrocopies
Cavia porcellus ENSCPOG000000145541 retrocopy
Dasypus novemcinctus ENSDNOG0000001010711 retrocopies
Equus caballus ENSECAG000000121741 retrocopy
Erinaceus europaeus ENSEEUG00000000397 1 retrocopy
retro_eeur_298 ,
Echinops telfairi ENSETEG000000193021 retrocopy
Gorilla gorilla ENSGGOG000000156471 retrocopy
Loxodonta africana ENSLAFG000000088472 retrocopies
Microcebus murinus ENSMICG000000174223 retrocopies
Myotis lucifugus ENSMLUG000000013323 retrocopies
Monodelphis domestica ENSMODG000000088931 retrocopy
Mus musculus ENSMUSG000000226351 retrocopy
Oryctolagus cuniculus ENSOCUG000000136642 retrocopies
Otolemur garnettii ENSOGAG000000131782 retrocopies
Ochotona princeps ENSOPRG000000110952 retrocopies
Procavia capensis ENSPCAG000000117492 retrocopies
Pan troglodytes ENSPTRG000000048381 retrocopy
Pteropus vampyrus ENSPVAG000000066512 retrocopies



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