RetrogeneDB ID: | retro_eeur_342 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_264593:620..960(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSEEUG00000000428 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSPAN31 | ||
| Ensembl ID: | ENSEEUG00000006647 | ||
| Aliases: | None | ||
| Description: | tetraspanin 31 [Source:HGNC Symbol;Acc:10539] |
Retrocopy-Parental alignment summary:
>retro_eeur_342
CTGGCTATTAACCATAGCACACAGACAGATGTCATCAGTGCTTCTTGGCGGGTTATGAGCAACAAAAACCCAGCATGAAC
TTGAAAGAAGTTTTGATTGTTGTGGCTTGTTCAAACTCACAACCCTACATCAACAAGATTATGCTTTCTGCGCGGCAAGC
TGCAAAAAGTGGAACATGTGCCGATTGTGTGGAGAGAAGCTTCTGAGACATTCAGATGAAGCCCTGAAAATCCTGGGAGG
TGTCAGACTCTTCTTTAGCTTTACAGAGATCTTTGGTGTTTGGGTAGCAATGAGATTCTGGAATCAGAAGGATCCTCACG
CCAACCCCAGTGCCTTTCTA
ORF - retro_eeur_342 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.96 % |
| Parental protein coverage: | 54.07 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LAINQNTQTDVINASWRVMSN-KTQHELERSFDCCGLFNLTTLHQQDYAFCAASCRKWKTCQLCGEKFLK |
| LAIN..TQTDVI.ASWRVMSN.KTQHELERSFDCCGLF.LTTLHQQDYAFCAASC.KW..C.LCGEK.L. | |
| Retrocopy | LAINHSTQTDVISASWRVMSN>KTQHELERSFDCCGLFKLTTLHQQDYAFCAASCKKWNMCRLCGEKLLR |
| Parental | HSDEALKILGGVGLFFSFTEILGVWLAMRFRNQKDPRANPSAFL |
| HSDEALKILGGV.LFFSFTEI.GVW.AMRF.NQKDP.ANPSAFL | |
| Retrocopy | HSDEALKILGGVRLFFSFTEIFGVWVAMRFWNQKDPHANPSAFL |
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 .81 RPM | 30 .62 RPM |
| SRP017611_kidney | 0 .38 RPM | 41 .82 RPM |
| SRP017611_liver | 0 .16 RPM | 20 .10 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_342 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000006647 | 1 retrocopy |
retro_eeur_342 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000001138 | 1 retrocopy |