RetrogeneDB ID: | retro_eeur_480 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_322007:1014..1410(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TPD52L1 | ||
| Ensembl ID: | ENSEEUG00000013289 | ||
| Aliases: | None | ||
| Description: | tumor protein D52-like 1 [Source:HGNC Symbol;Acc:12006] |
Retrocopy-Parental alignment summary:
>retro_eeur_480
ATGGAGACACAGGCACAAGGTTTGTTGGAGAGTGAACCATTGCAAGGAGTAAATGACGACTCTGTAGCCAGCACGGACTT
CTCTAGCATGCTCTCTGAGGAGGAAAAAGAAGAGTTAAAGGCAGAATTAGTTCAGCTGGAAGACGAAATTACAACTTTAC
GACAAGTTTTATCAGCAAAAGAAAGGTATCTGGTTGAGATCAAACAAAAACTCGGCATGAATTTGATGAATGAATTAAAA
CAGAACTTCAGCAAAAGCTGGCATGATATGCAGACTACTACTGCCTATAAGAAGACACATGAAACTCTGAGTCATGCCGG
GCAGAAAGCAACTGCAGCTTTCAGCAAAGTTGGAACAGCCATCAGCAAGAAGTTTGGAGATATGAGCTACTCCATT
ORF - retro_eeur_480 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.21 % |
| Parental protein coverage: | 64.08 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | METQAQGLLESEPLQGVDDDSVASADFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKERHLVEIKQK |
| METQAQGLLESEPLQGV.DDSVAS.DFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKER.LVEIKQK | |
| Retrocopy | METQAQGLLESEPLQGVNDDSVASTDFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKERYLVEIKQK |
| Parental | LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFSNVGTAISKKFGDMSDSI |
| LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFS.VGTAISKKFGDMS.SI | |
| Retrocopy | LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFSKVGTAISKKFGDMSYSI |
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 .26 RPM | 11 .60 RPM |
| SRP017611_kidney | 10 .69 RPM | 47 .45 RPM |
| SRP017611_liver | 0 .64 RPM | 4 .82 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_480 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 | ENSEEUG00000013289 | 1 retrocopy |
retro_eeur_480 ,
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