RetrogeneDB ID: | retro_itri_1848 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH394084.1:85845..86482(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UBE3C | ||
| Ensembl ID: | ENSSTOG00000001669 | ||
| Aliases: | None | ||
| Description: | ubiquitin protein ligase E3C [Source:HGNC Symbol;Acc:16803] |
Retrocopy-Parental alignment summary:
>retro_itri_1848
AACAGCTCCCTGTTTGTCAAGCAACTGAATGGATCCGAGAGACCGAAATGCTTATTTCAGATAAAGAGGCTCATGAGCCT
CTGTTGCAGGTGGCTGCAGAGCTGTAATGATGACAGTTTGAATGTCGCACTTCCACTGAGAATGCTTGAGGTCTTTTCCT
CTGAGAATACTTCCTTGCCTGTTTACTAGATGCTAGCTATGAGGTGTCAGTAATTGAACAGGTTTTGCACTACATGAAAC
ACAATGGGTATTATAGTCTCTCTATTTGTTGATTAACAGCAAGATTCCATCAAGTATTGAATATTCCGATTTATCTATAG
CAAACATTTTGCTGGGGAGTGTCCTAAACCGTTGCACTTTACCTACAGCTCCTGCCCAGAAGGTGCAAGGCAGCAAGTTT
TTTGAGCCTTCACAGAGGAGTTTTTGGCAGCACCTTTTACAGATCAGATTTTCCGCTTGTCATTCTGGCATTAGCAGATG
TACAGACCGTTTTCCCTTAAGAGCCCTTTCTGAATGCACTATTGTTACTAGAGAGTAGATGTTCAAAAAGGAGTGGTGGA
GCACCTGGCTTTTCTATTTTGTTTTAACTGTTGGCAAAAATGACTTGGGGGTGCTCTCTGAGGAGGGCCTGCTGGTA
ORF - retro_itri_1848 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.59 % |
| Parental protein coverage: | 51.42 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | HSSLFVKQLDGSERPTCLFQIKRLMSLCCRLLQSCNDDSLNVALPMRMLEVFSSENTYLPV-LQDASYVV |
| .SSLFVKQL.GSERP.CLFQIKRLMSLCCR.LQSCNDDSLNVALP.RMLEVFSSENT.LPV.L.DASY.V | |
| Retrocopy | NSSLFVKQLNGSERPKCLFQIKRLMSLCCRWLQSCNDDSLNVALPLRMLEVFSSENTSLPV<LLDASYEV |
| Parental | SVIEQILHYMIHNGYYR-SLYLLINSKLPSSIEYSDLSRVPIAKILLENVL-KPLHFTYSSCPEGARWQV |
| SVIEQ.LHYM.HNGYY..SLYLLINSK.PSSIEYSDLS...IA.ILL..VL.KPLHFTYSSCPEGAR.QV | |
| Retrocopy | SVIEQVLHYMKHNGYYS<SLYLLINSKIPSSIEYSDLS---IANILLGSVL<KPLHFTYSSCPEGARQQV |
| Parental | FSAFTEEFLAAPFTDQIFR-FVIPALADVQTAFPYEPFLNALLLLESRCSKRSRGAP-WLFYFVLTVGEN |
| F.AFTEEFLAAPFTDQIFR..VI.ALADVQT.FP.EPFLNALLLLESRCSKRS.GAP.WLFYFVLTVG.N | |
| Retrocopy | F*AFTEEFLAAPFTDQIFR<LVILALADVQTVFP*EPFLNALLLLESRCSKRSGGAP<WLFYFVLTVGKN |
| Parental | YLGVLSEEGLLV |
| .LGVLSEEGLLV | |
| Retrocopy | DLGVLSEEGLLV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1848 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1848 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Otolemur garnettii | ENSOGAG00000000964 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000001669 | 3 retrocopies |
retro_itri_1547, retro_itri_1817, retro_itri_1848 ,
|