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Table 3 Gene annotation of 19 adaptive outlier loci against the Ciona robusta genome

From: Rapid microevolution during recent range expansion to harsh environments

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
  1. 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