RetrogeneDB ID: | retro_itri_333 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393284.1:11452329..11453061(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSTOG00000025429 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | VASP | ||
| Ensembl ID: | ENSSTOG00000027705 | ||
| Aliases: | None | ||
| Description: | vasodilator-stimulated phosphoprotein [Source:HGNC Symbol;Acc:12652] |
Retrocopy-Parental alignment summary:
>retro_itri_333
GAGGAGGTGGAGCAGCAGAAAAGGCAGTGGCCCAGCCAGCCCGAGGAAGTGGAGAGGAAGGGATGGGTCACCAAGGCAGG
AAGCCCACCTGTTCACCCAGTGGGGGGACCACCCCCGCCTCCAGGACCTCCCTGTCCTCCGGGTCCCTCCGCACCCCCAG
GATTGCCCTCCTCAGGGGTCCTGGCTTCAAGGCATGGAGTAGGGGGAGGCACATCTCCTGCGATCCCTCTCTCTGCAGCA
CAAGGATGGAATGGTGGAGATGCAGGAGCCCCTGGCTTGGCTGCAGCCATTTGGGGAGCCAAACTTAGAAAAGTCAACAA
GCAGAAGGAGACCTCAGGAAGACCGCTGGGCCCCAAAGCTGAGAACAGTCGAAGCACCGGTCCAGGGTTCATGGAGGAGA
TGGCTGCCTTGCTGGCCCAGAGAAGAAAAGCCACACAGATTGGAGGGAAACCCAAGGAAGAATCTGCTAGTCAGGAGGAG
CCAGGGGCCAGAGGCCCAGCCCAGAGTGAACCTGTGCCAAGACCCTGGGAGAAGAACAGCACAGCCTTGCTGAGGATGAA
GTCCTCTTCTTCGAGGACTGCTTCCAAGGCCCAGCCCTCCAGCCATGGGGAAGAGTCAGACCTGGAGAGGGTGAAAAGGG
AGCTTCTGGAAGAGGTGAGGAAGGAATTACAGAAGGTTAAAGAGGAGATAATTGAAGCCCTTGTCCAGGAGCTGAGGAAT
TGGGGTTCCCCC
ORF - retro_itri_333 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.92 % |
| Parental protein coverage: | 64.83 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EEVEQQKRQQPSQPEYMERERRVSNAGGPPVPPVGGPPPPPGPPPPPGPPPPPGLPPSGVSAAGHGAGGG |
| EEVEQQKRQ.PSQPE..ER...V..AG.PPV.PVGGPPPPPGPP.PPGP..PPGLP.SGV.A..HG.GGG | |
| Retrocopy | EEVEQQKRQWPSQPEEVERKGWVTKAGSPPVHPVGGPPPPPGPPCPPGPSAPPGLPSSGVLASRHGVGGG |
| Parental | PPPAPPLPAAQGPSGGGAGAPGLAAAIAGAKLRKVSKQEEASGGPLAAKAESTRSTGGGLMEEMNAMLAR |
| ..PA.PL.AAQG..GG.AGAPGLAAAI.GAKLRKV.KQ.E.SG.PL..KAE..RSTG.G.MEEM.A.LA. | |
| Retrocopy | TSPAIPLSAAQGWNGGDAGAPGLAAAIWGAKLRKVNKQKETSGRPLGPKAENSRSTGPGFMEEMAALLAQ |
| Parental | RRKATQVGEKPPKEESASQEEPEARVPAQSEPVRRPWEKNSTTLPRMKSSSSITASEAQPSTHSSGEESD |
| RRKATQ.G.K.PKEESASQEEP.AR.PAQSEPV.RPWEKNST.L.RMKSSSS.TAS.AQPS.H..GEESD | |
| Retrocopy | RRKATQIGGK-PKEESASQEEPGARGPAQSEPVPRPWEKNSTALLRMKSSSSRTASKAQPSSH--GEESD |
| Parental | LEKVKQELLEEVRKELQKVKEEIIEAFVQELRKRGSP |
| LE.VK.ELLEEVRKELQKVKEEIIEA.VQELR..GSP | |
| Retrocopy | LERVKRELLEEVRKELQKVKEEIIEALVQELRNWGSP |
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_333 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_333 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012536 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000027705 | 1 retrocopy |
retro_itri_333 ,
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