RetrogeneDB ID: | retro_eeur_583 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_348901:6086..7502(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PIGN | ||
| Ensembl ID: | ENSEEUG00000005812 | ||
| Aliases: | None | ||
| Description: | phosphatidylinositol glycan anchor biosynthesis, class N [Source:HGNC Symbol;Acc:8967] |
Retrocopy-Parental alignment summary:
>retro_eeur_583
ATCTCCCTTTGCAAGGAGCTGATTCGTCTTGCACTGGAAGGATTGTCCTACTACCACACTTACGACAGATTCTTTTTGGG
CATCACTGTTGTTCTTGGTTTTGTGGGATGGACATCTTATGCTTCTCTGTTGATCATCAAGTCTCATTCCAACCTCACCA
GAGGTGGTAGTAACAAAATTAAGAAACCAAATCATCTCCTGACATGTACTTTTGTAGCTGTTGGCATTGCAATAGCATTT
TTCCTGCTGATTCAGTCCTGTCCCTGGACTTACTACGTGTACTGTCTGTTGCCGGTGCCAATATGGCATGCGCTTCTGAG
CGAATTTCCAGTGATTGAGGACCTTGTCAAGTCTCTGCTGACCTTTCCCCCTGGTCAATTTATTGGAAGCCTGTTAGTCT
TTGGTCTGGGACTTGAAATACTAGTTCTCAGTTTTTTCTACCGCTATATGCTTACAGCTGGACTTACAGCATTTGCGGGC
TGGCCATTCGTCACTCAGCTGTGGACTCGAGCAAAGAGCACCTCACTGAGTTGGACTTTGTTCTCTTTGCTCCTGGTAGT
GTTTCCACTGATGCCTGTTGTAGGACAGAAGCCAGACATCTCTGTGGTAATGGGAGCAGGCTTGCTGGTTCTTCTTCTGT
CCCTGTTTGTTGTGACATCATATATAAAAAGAAAAGATAATCTCGATGGAGAACTATTTTTGTATCTGCTACAGATACTG
AGCATCATGCTTTCCATGTACACCGTGTATAGCACGCACAGTAGTCTGCAGCGGAAACAAGGACTACCCTTTCTTAATCA
GACCATTAGCTGGATCATATTAGCCTCTTCCTTCATCCTGCCACTTCTGAGTCCCACCATCCTCTTCGAGCGGTTGTTCA
GCATACTCCTTTCCTTGATGTCCACCTACCTGCTTCTAAGCACAGGGTATGAAGCTCTCTTCCCATTAGTGCTGTCATGT
TTGATGTTCATCTGGATACACATGGAACAAGAAACCCTGCAACAATCTGGCTTTTCCTGTAAACAGAAGGTCAACAGTAT
CCAGTTTGCCTACAATATTGATATAACTCAGTATCGAAAGCTCTATCTCGACGACATCCATAGGGCCTTTTTCCTTGTTT
TCTTCTTACTGACAGCATTTTTTGGAACTGGGAATATAGCTTCTATTAACAGCTTTGATCTTGCTTCAGTCTATTGCTTT
GTGACGGTGTTTAGTCCTTTTGTGATGGGAACCCTGATGATGTGGAAGATTTTAATCCCCTTTGTACTTGTGATGTGTGC
TTTTGAAGCAGTTCAGTTAACTACCCAGCTGTCATCAAAAAGCCTTTTTCTCATGGTTCTCGTCATATCAGACATCATGG
CTTTGCACTTTTTCTTCTTGGTCCAGGATTATGGCAGCTGGCTTGATATTGGAACA
ORF - retro_eeur_583 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.94 % |
| Parental protein coverage: | 53.03 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT |
| ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT | |
| Retrocopy | ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT |
| Parental | FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI |
| FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI | |
| Retrocopy | FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI |
| Parental | LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLLAVFPLMPVVGRKPDISVVMGAGLLV |
| LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLL.VFPLMPVVG.KPDISVVMGAGLLV | |
| Retrocopy | LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLLVVFPLMPVVGQKPDISVVMGAGLLV |
| Parental | LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLPLLNQTISWIILASSFIL |
| LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLP.LNQTISWIILASSFIL | |
| Retrocopy | LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLPFLNQTISWIILASSFIL |
| Parental | PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA |
| PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA | |
| Retrocopy | PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA |
| Parental | YNIDITQYRKLYLDDIRRAFFLVFFLVTAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP |
| YNIDITQYRKLYLDDI.RAFFLVFFL.TAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP | |
| Retrocopy | YNIDITQYRKLYLDDIHRAFFLVFFLLTAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP |
| Parental | FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT |
| FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT | |
| Retrocopy | FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT |
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 | 2 .09 RPM | 9 .99 RPM |
| SRP017611_kidney | 6 .19 RPM | 14 .44 RPM |
| SRP017611_liver | 2 .09 RPM | 7 .56 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_583 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000005812 | 1 retrocopy |
retro_eeur_583 ,
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