RetrogeneDB ID:

retro_eeur_171

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_139668:574..942(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSEEUG00000011007
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PAM16
Ensembl ID:ENSEEUG00000007432
Aliases:None
Description:presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]


Retrocopy-Parental alignment summary:






>retro_eeur_171
GCCAGTTACCTCGCCCAGATCATCATGATGGGGGGTGCAGGTGGTGGGCAGGGCCTTCATGTATGGCCTGCAGGAGGAGT
TTGCAGTCAGGCTGGCCACAGCTGATGCTCAGGGGCCGGGCCGGACACCAGTCTGCAACTGCCTCCAACCTCATTTGGCC
TCAGCCTCCAGGAGGCCCAGCAGATTCTCAATGTCTCCAAGCTGAACCTGAGGAGATCCAAAAGAACTGTGAACACTTGT
TCAAGGTGAACATCAAGTCAGTAGGTGGCTCCTTCTACCTGCAGTCAAAGGTGGGCCGGGCAAAGGAGCACCTGGACGAG
GAGCTGAGGATCCAGGCCCAGGAGGACAGAGGAAAAGAACCCAAAACA

ORF - retro_eeur_171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.95 %
Parental protein coverage: 99.19 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalARYLAQIIVMGA-QVVGRAFARALREEFAASRAAADA-RGRAGHQSAAASNLT-GLSLQEAQQILNVSKL
A.YLAQII.MG..QVVGRAF...L.EEFA...A.ADA.RGRAGHQSA.ASNL..GLSLQEAQQILNVSKL
RetrocopyASYLAQIIMMGG>QVVGRAFMYGLQEEFAVRLATADA>RGRAGHQSATASNLI>GLSLQEAQQILNVSKL
ParentalN-PEEIQKNYQHLFKVNDKSVGGSFYLQSKVVRAKERLDEELRIRAQEDRGKEPQT
N.PEEIQKN..HLFKVN.KSVGGSFYLQSKV.RAKE.LDEELRI.AQEDRGKEP.T
RetrocopyN<PEEIQKNCEHLFKVNIKSVGGSFYLQSKVGRAKEHLDEELRIQAQEDRGKEPKT

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 11 .44 RPM
SRP017611_kidney 0 .00 RPM 25 .69 RPM
SRP017611_liver 0 .00 RPM 16 .88 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_171 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 16 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000092001 retrocopy
Canis familiaris ENSCAFG000000192261 retrocopy
Callithrix jacchus ENSCJAG000000197721 retrocopy
Dasypus novemcinctus ENSDNOG000000109212 retrocopies
Dipodomys ordii ENSDORG000000148881 retrocopy
Equus caballus ENSECAG000000193871 retrocopy
Erinaceus europaeus ENSEEUG00000007432 7 retrocopies
Echinops telfairi ENSETEG000000064161 retrocopy
Felis catus ENSFCAG000000279711 retrocopy
Myotis lucifugus ENSMLUG000000089216 retrocopies
Mus musculus ENSMUSG000000143011 retrocopy
Rattus norvegicus ENSRNOG000000046081 retrocopy
Sus scrofa ENSSSCG000000079472 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000034611 retrocopy
Tupaia belangeri ENSTBEG000000013471 retrocopy
Tarsius syrichta ENSTSYG000000093061 retrocopy



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