RetrogeneDB ID:

retro_eeur_277

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_235277:2497..3172(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POLR3D
Ensembl ID:ENSEEUG00000007632
Aliases:None
Description:polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]


Retrocopy-Parental alignment summary:






>retro_eeur_277
AAAAGCGGGAGAGAGAGAGATCGCCAGAGAGATGGCCATGGATGGGGTAGAGGTCGCCCAGAGCTGATCCAGTCCCATTC
CATCTTTGAGCAAGGCCCTGCAGAAATGATGAGGAAAACAGGGAACTGGGATAAGACAGTGGATATGTTGGACGTGGGAC
CCTCTCATATCATCAGCATCAAAAAAGAAACGAGGGAGACGGATGAAGAGACCAAACAGATCCTGCGCATGCTAGAGAAG
GATGACTTCATCGATGATCCGGACTGAGGAAAGACACTCGGAACATCTGTGCAGCTGCCACTGCCTCACTCAGGGTGGCT
TTTCAAGGAAGAAAACGAGGAGGCAGATGAGAAGCCTTCGCTGAGCAGCCCCAAGGAAGAGGATATGGATGTGGACATCC
CTCCTGTGGAAAGAGGAGCCACGTGATGAGGATGATGAGACTAAGGTGAAGGCTCCTCCCAGAGTAGCCAAGAAGACCCC
TGGCCTCCTAAGGATGTGTCTGTGGCTGAGTTGCTCAGAGAGCTGAGCGTCACCCAGGAAGAGGAGTTGTTGTTCCTCCA
GCTGCCTGACACGCTTCCTGACCAGCCACCTACTCAGGACATCAAGCCTGTCAAGACAGAGGTGCAGAATGAGGATGGAC
AGATGGTGGTGATAAAGCAAGAAAAAGACGGAGAG

ORF - retro_eeur_277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.22 %
Parental protein coverage: 57.29 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKRERDRDRQRDGHGRGRGRPELIQSHSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHIINIKKEKRETDEE
K..R.RDRQRDGHG.GRGRPELIQSHSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHII.IKKE.RETDEE
RetrocopyKSGRERDRQRDGHGWGRGRPELIQSHSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHIISIKKETRETDEE
ParentalTKQILRMLEKDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEESEEADEKPSLSNPKEEDMDVDIPPVKV-
TKQILRMLEKDDFIDDP.....T....VQLPL.HSGWLFKEE.EEADEKPSLS.PKEE..D.D.....V.
RetrocopyTKQILRMLEKDDFIDDPD*-GKTLGTSVQLPLPHSGWLFKEENEEADEKPSLSSPKEE--DMDVDIPPV>
ParentalKEEPRDDDEETKVKAPPRVAKKTPGL-PKDVSVSELLRELSLTQEEELLFLQLPDTLPGQPPTQDIKPVK
KEEPRD.D.ETKVKAPPRVAKKTPGL.PKDVSV.ELLRELS.TQEEELLFLQLPDTLP.QPPTQDIKPVK
RetrocopyKEEPRDEDDETKVKAPPRVAKKTPGL<PKDVSVAELLRELSVTQEEELLFLQLPDTLPDQPPTQDIKPVK
ParentalTEVQNEDGQMVVIKQEKDRE
TEVQNEDGQMVVIKQEKD.E
RetrocopyTEVQNEDGQMVVIKQEKDGE

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 23 .53 RPM
SRP017611_kidney 0 .00 RPM 13 .13 RPM
SRP017611_liver 0 .00 RPM 8 .20 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_277 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 12 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000134881 retrocopy
Equus caballus ENSECAG000000250901 retrocopy
Erinaceus europaeus ENSEEUG00000007632 2 retrocopies
retro_eeur_277 , retro_eeur_705,
Homo sapiens ENSG000001684951 retrocopy
Macropus eugenii ENSMEUG000000004651 retrocopy
Myotis lucifugus ENSMLUG000000021091 retrocopy
Macaca mulatta ENSMMUG000000232261 retrocopy
Monodelphis domestica ENSMODG000000094911 retrocopy
Nomascus leucogenys ENSNLEG000000155021 retrocopy
Pongo abelii ENSPPYG000000184191 retrocopy
Pan troglodytes ENSPTRG000000200561 retrocopy
Tursiops truncatus ENSTTRG000000127451 retrocopy



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