RetrogeneDB ID: | retro_itri_1883 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH394580.1:9084..9720(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM120A | ||
| Ensembl ID: | ENSSTOG00000021804 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 120A [Source:HGNC Symbol;Acc:13247] |
Retrocopy-Parental alignment summary:
>retro_itri_1883
TTTCCACCAGAATTTTCACTAGTGATCATTAAGTAATGGGCAGCTTACAAGGAAAAATCTCCTCAAACCCCGTCTCAGGG
CAGGGGCAGAGGCTTTGCAGGAATCTGTGGATTTGGCAGCCCTTATGGGAAAACCGTAGCAACTTGCCCTTACGGTGCCT
TCTGGGTGGTGGCAGCATTGGGACACTGTGGAGCCTTCTCAGGTAGTGACAGCAGTAGGACTAGCAAGTCCCAGGATGGA
GTCCAAACTATACCTTCTCAGGGAGGGAAACGAGAAATCACTGGCACTGTGGTTGGCAGCTGGGCAGAAAGCAAGCAGAA
CCATGGAGGCTGAGGGCCCTTCCCACTGCAAGTTGTCTCAGTGGGAGGACCAGCAAGAGGGCGTCCAAGAGGCATTATTT
ACACCATAGGGATATGGAGGTTTGGTAGAGGTGGAAGGCACCATGGCTGAGGTTATAAAAGCCAGGGAGCAATTTAGGGC
AGACCTACTTATGCTGCTTCAGCAGAAGAAGTGGCCAAAGAGCTGAAGTCAAAATCCGGGGAATCAAAGTTCACTGCCAT
GTCTTCACATGGGTCCCTGGCTGAAAATGGAGTGATGGCCTACGAGAAGACAGTGCCCCAGATGAATGAAAGTGCC
ORF - retro_itri_1883 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.58 % |
| Parental protein coverage: | 52.22 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FPPPPALPFYPASVYPRHFGPVPPSQGRGRGFAGVCGFGGPYGETVASGPYRAFRVAAASGHCGAFSGSD |
| FPP...L.............P..PSQGRGRGFAG.CGFG.PYG.TVA..PY.AF.V.AA.GHCGAFSGSD | |
| Retrocopy | FPPEFSLVIIK*WAAYKEKSPQTPSQGRGRGFAGICGFGSPYGKTVATCPYGAFWVVAALGHCGAFSGSD |
| Parental | SSRTSKSQGGVQPIPSQGGKLEIAGTVVGHWAGSRRGRGGRGPFPLQVVSVGGPARGRPRGVISTPVIRT |
| SSRTSKSQ.GVQ.IPSQGGK.EI.GTVVG.WA.S....GG.GPFPLQVVSVGGPARGRPRG.I.T..I.. | |
| Retrocopy | SSRTSKSQDGVQTIPSQGGKREITGTVVGSWAESKQNHGG*GPFPLQVVSVGGPARGRPRGIIYTIGIWR |
| Parental | FGRGGRYYGRGYKSQGAIQGRPPYAASAEEVAKELKSKSGESKSSAVSSDGSLAENGVMAEEKPVPQMNG |
| FGRGGR..G.GYKSQGAI.GRP.YAASAEEVAKELKSKSGESK..A.SS.GSLAENGVMA.EK.VPQMN. | |
| Retrocopy | FGRGGRHHG*GYKSQGAI*GRPTYAASAEEVAKELKSKSGESKFTAMSSHGSLAENGVMAYEKTVPQMNE |
| Parental | SA |
| SA | |
| Retrocopy | SA |
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_1883 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1883 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 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000021804 | 2 retrocopies |
retro_itri_1835, retro_itri_1883 ,
|