Table 3.
Gene annotation of 19 adaptive outlier loci against the Ciona robusta genome
| Loci | Location | E-value | Gene annotation (NCBI BLASTN) | Uniprot GO/AmiGo2 GO |
|---|---|---|---|---|
| Cin10 | Chromosome 1: 4,135,583-4,136,208 |
0 | no hit | no |
| Cin19 | Chromosome 1: 6,677,358-6,678,040 |
0 | uncharacterized LOC108949898 | no |
| Cin20 | Scaffold HT001144.1: 27,547-27,960 |
0 | protein MB21D2 (MB21D2 gene) | protein-containing complex binding; cadherin binding |
| Cin36 | Scaffold HT000030.1: 142,799-143,299 |
0 | no hit | no |
| Cin59 | Scaffold HT000127.1: 84,997-85,135 |
1.00E-53 | uncharacterized LOC104266650 | no |
| Cin66 | Chromosome 3: 2,342,118-2,342,780 |
0 | uncharacterized LOC104265511 | no |
| Cin74 |
Chromosome 3:
5,106,446-5,106,970 |
0 | polyadenylate-binding protein 2 (PABP2 gene) |
RNA binding; mRNA polyadenylation;
poly(A) binding; nucleus; cytoplasm |
| Cin95 |
Chromosome 5:
3,787,692-3,787,983 |
6.00E-122 | S-phase kinase-associated protein 2 (SKP2 gene) |
G1/S transition of mitotic cell cycle;
G2/M transition of mitotic cell cycle; protein polyubiquitination; protein binding ubiquitin-protein transferase activity |
| Cin98 |
Chromosome 5:
4,569,724-4,570,072 |
3.00E-170 | low-density lipoprotein receptor-related protein 6 (LRP6 gene) |
negative regulation of protein phosphorylation;
low-density lipoprotein particle receptor activity; signaling receptor binding; frizzled binding; protein binding |
| Cin106 | Chromosome 6: 1,498,836-1,499,402 |
0 | inositol polyphosphate 5-phosphatase OCRL-1 (OCRL gene) | GTPase activator activity; in utero embryonic development; photoreceptor outer segment; phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity; trans-Golgi network; signal transduction; nucleus; clathrin-coated vesicle |
| Cin138 | Chromosome 1: 1,567,428-1,567,684 |
6.00E-88 | no hit | no |
| Cin153 | Scaffold HT000103.1: 128,876-129,440 |
0 | IST1 homolog (IST1 gene) | protein binding |
| Cin162 |
Chromosome 9:
4,578,790-4,579,144 |
2.00E-152 | mitochondrial uncoupling protein 3 (UCP3 gene) |
response to cold; adaptive thermogenesis; response to nutrient;
lipid metabolic process; fatty acid metabolic process; aging; response to superoxide; response to hypoxia; respiratory gaseous exchange; oxidative phosphorylation uncouple activity; mitochondrial inner; transporter activity membrane |
| Cin182 | Chromosome 12: 1,101,323-1,101,594 |
2.00E-94 | no hit | no |
| Cin189 | Chromosome 13: 1,255,212-1,255,526 |
6.00E-144 | no hit | no |
| Cin193 |
Chromosome 14:
244,529-244,945 |
0 | histone acetyltransferase p300 (EP300 gene) |
negative regulation of transcription by RNA polymerase II;
response to hypoxia; somitogenesis; stimulatory C-type lectin receptor signaling pathway; RNA polymerase II activating transcription factor binding; RNA polymerase II proximal promoter sequence-specific DNA binding; p53 binding; histone acetyltransferase complex |
| Cin211 |
Chromosome 5:
2,499,390-2,499,700 |
8.00E-126 |
AP-3 complex subunit mu-1
(AP3M1 gene) |
anterograde axonal transport; anterograde synaptic vesicle transport |
| Cin225 | Chromosome 10: 293,070-293,590 |
0 | persulfide dioxygenase ETHE1 (ETHE1 gene) | glutathione metabolic process; hydrogen sulfide metabolic process; oxidation-reduction process; sulfur dioxygenase activity; iron ion binding; mitochondrion; nucleoplasm |
| Cin229 | Scaffold HT000276.1: 9605-10,133 |
0 | no hit | No |
Gene annotation was performed using BLASTN search in the NCBI website and gene ontology (GO) terms were against UniProt database and AmiGO 2 GO browser. Microsatellite loci in bold are located in genes putatively involved in temperature and salinity adaptation