WormBase Tree Display for Variation: WBVar00000109
expand all nodes | collapse all nodes | view schema
WBVar00000109 | Evidence | Paper_evidence | WBPaper00004836 | ||||||
---|---|---|---|---|---|---|---|---|---|
Name | Public_name | ak4 | |||||||
Other_name | CE30128:p.Glu352_Ter750delextTer? | ||||||||
F07F6.6.1:c.1054_2250del | |||||||||
HGVSg | CHROMOSOME_II:g.5443296_5445175del | ||||||||
Sequence_details | SMap | S_parent | Sequence | F07F6 | |||||
Flanking_sequences | tttaatgataaatgtgaacgaattggagtc | atatgggattcaactcgactggaatttgaa | |||||||
Mapping_target | F07F6 | ||||||||
Type_of_mutation | Deletion | ||||||||
SeqStatus | Sequenced | ||||||||
Variation_type | Allele | ||||||||
Origin | Species | Caenorhabditis elegans | |||||||
Strain | WBStrain00040168 | ||||||||
WBStrain00040171 | |||||||||
WBStrain00040666 | |||||||||
WBStrain00040796 | |||||||||
WBStrain00048048 | |||||||||
WBStrain00048049 | |||||||||
WBStrain00048050 | |||||||||
WBStrain00048052 | |||||||||
WBStrain00048074 | |||||||||
WBStrain00048082 | |||||||||
WBStrain00048083 | |||||||||
WBStrain00054658 | |||||||||
WBStrain00054659 | |||||||||
Laboratory | VM | ||||||||
Status | Live | ||||||||
Affects | Gene | WBGene00003774 | |||||||
Transcript | F07F6.6.1 | VEP_consequence | splice_acceptor_variant,splice_donor_variant,stop_lost,inframe_deletion,intron_variant | ||||||
VEP_impact | HIGH | ||||||||
HGVSc | F07F6.6.1:c.1054_2250del | ||||||||
HGVSp | CE30128:p.Glu352_Ter750delextTer? | ||||||||
cDNA_position | 1056-2252 | ||||||||
CDS_position | 1054-2250 | ||||||||
Protein_position | 352-750 | ||||||||
Intron_number | 8-15/20 | ||||||||
Exon_number | 8-16/21 | ||||||||
Codon_change | GAATATGATATTATTAATTTTCATATGGAGAGGAAACAAGTTGGAAATATGGTTGGTTTAGTTGTATAAATCTTGAAATCCAAATACAGTACACCTATTCTCAAAGTAGTGCTCATTAATTCTGAGCTCTGCATCGGTGTTGCATAATACTATTCAAGCTTTTACATTTCAATTCTTCAGCGCCATTTTATAGAAACTGAAAAATCAACACCAAAAATTTTTACTGCATCTTCAACCCCAAAAATTAAAAATGTACAGAATTCGTAGTAACAATTTTCAAGTTTTTTAAAATTATATTTCCAATAAACATCCTGATTGATATTCCCCATAGAATGTGTAGTTTTCCAGGTTGGTGATATCCTTAGACTTGATGAAGATTCGATTGAATGGGCTGGTGGTACGAAACCTCTAGAAATATCTCTTCCAAAACATCTTCGCGTGGTTACTGTAGCTGATCCTCCATTCGTTTATACAACTCCAATTGGCTCACCGTCTCAGTGTGCAGAGCTAGGAAATACTGTAGTCGAATGGTCGATATTCGATAAAATTGTTGTGGTGAGGAAGTTTTACTTGAAACTTGAAAGTTTACAGCTATTTTCAGAGTGGACCTTGGTACTCTTGCCCGTTGACTTTGGAAAATTCAACTGAATATTTTTGCTGTGCAGGATTAGCGATTGACCTTTTATCAAATTTGTCACTTCCTGAGGTACTGATTATAATTTATTATATGCATTTAATGTTGTGCTTTTCAAGGCAAATAACTCAATCGATACAAGTTTCACTTTTTCCCTCCATCTCAATGAATCCTATGGAGTTGTACAAGCCTCAGAGACAGTGAGTTTTTATTTAAATATTTGTTTTTAAATTCAAAATAGATTCTCTAATTAATTTCAGACCGGAATAACTATAAGTGGAGTGATTGGCGAGTTGGATGGTGATACGGCTGACATGGCAATTGGTGGAATTACAATCAATCCTGAAAGAGAGAGAATTGTAGATTTTACTGAACCTTGGCTTTATCATGGTATCAGGATTTTAGAGAAAAATGTGAGTACTATGTTTTGATGTTACCGGGAAAGTTTTTCAAATCCTTTTCTGTTGTTCAAAAAAAGATAATACTTGAAAAAAATTATTTCCAGATTCCCAGAGACTCTCCAATGCAATCATTTCTTCAACCTCTACAATCCTCCCTCTGGACTGCACTCTTCATTTCTGTGATACTTGTTGGCCTTGCCATCTACTGTTTGGATTTCAAATCACCATTTGAAAGATTCTATCAAGCTGATAAGGAAATGGAGCAGGACCTGAAAAAAGAGTTCGAGCTTTGGATTGGGAAGGATGCTGATGAAAACGTGAATTTTGGAGAAGCAATGTGGTTTGTTTGGGGAGTTCTGTTGAACAGCGGAGTTTCAGAAAGTGAGTGGGTTTTCCAAGGAAAGAAAACTAAAATTTAACAATTGAAAACTTCAGAGACTCCAAGAAGTTGCTCGGCTCGTGTTCTGGGGATAGTTTGGTGCGGATTTTGCATGATTATGGTTGCATCATACACTGCAAACCTCGCAGCTTTTCTGGTTTTAGATCAACCTGAAAAAGGTTTAACAGGAGTCACTGATCCACGGGTAAGATTGATAGCGGTGTTTTTAAGTTTTGTCCATTTTCAGCTCCGAAATCCATCTGCAAACTTTTCATTTGGAACGGTTTTGAACTCAAATGTCTATCAATACTTCAAAAGACATGTGGAATTATCATCCATGTTTCGAAAAATGGAACCTCATAACGTGCGGCGAGCTTCAGAGGTGAGCACTAGTGATTGATAACCTTGTAAAAAATATTTAATTCAGGCTGTGCACTCTCTTCTCAATGGTTCATTGGATGCATTT/- | ||||||||
Amino_acid_change | EYDIINFHMERKQVGNMVGLVV*ILKSKYSTPILKVVLINSELCIGVA*YYSSFYISILQRHFIETEKSTPKIFTASSTPKIKNVQNS**QFSSFLKLYFQ*TS*LIFPIECVVFQVGDILRLDEDSIEWAGGTKPLEISLPKHLRVVTVADPPFVYTTPIGSPSQCAELGNTVVEWSIFDKIVVVRKFYLKLESLQLFSEWTLVLLPVDFGKFN*IFLLCRISD*PFIKFVTS*GTDYNLLYAFNVVLFKANNSIDTSFTFSLHLNESYGVVQASETVSFYLNICF*IQNRFSN*FQTGITISGVIGELDGDTADMAIGGITINPERERIVDFTEPWLYHGIRILEKNVSTMF*CYRESFSNPFLLFKKR*YLKKIISRFPETLQCNHFFNLYNPPSGLHSSFL*YLLALPSTVWISNHHLKDSIKLIRKWSRT*KKSSSFGLGRMLMKT*ILEKQCGLFGEFC*TAEFQKVSGFSKERKLKFNN*KLQRLQEVARLVFWG*FGADFA*LWLHHTLQTSQLFWF*INLKKV*QESLIHG*D**RCF*VLSIFSSEIHLQTFHLERF*TQMSINTSKDMWNYHPCFEKWNLITCGELQR*ALVIDNLVKNI*FRLCTLFSMVHWMHX/- | ||||||||
Interactor | WBInteraction000501705 | ||||||||
Genetics | Interpolated_map_position | II | -1.51326 | ||||||
Mapping_data | In_multi_point | 4538 | |||||||
Description | Phenotype | WBPhenotype:0000016 | Paper_evidence | WBPaper00060924 | |||||
Curator_confirmed | WBPerson557 | ||||||||
Remark | VM487 strain used: nmr-1(ak4) | Paper_evidence | WBPaper00060924 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
Phenotype_assay | Treatment | One day old adult worms were placed on Aldicarb (0.1 mM) plates. | Paper_evidence | WBPaper00060924 | |||||
Curator_confirmed | WBPerson557 | ||||||||
Temperature | 20 | Paper_evidence | WBPaper00060924 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
WBPhenotype:0000420 | Paper_evidence | WBPaper00060924 | |||||||
Curator_confirmed | WBPerson557 | ||||||||
Remark | VM487 strain used: nmr-1(ak4) | Paper_evidence | WBPaper00060924 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
Phenotype_assay | Treatment | Levamisole assays were carried out on NGM plates with 200 M Levamisole. | Paper_evidence | WBPaper00060924 | |||||
Curator_confirmed | WBPerson557 | ||||||||
Temperature | 20 | Paper_evidence | WBPaper00060924 | ||||||
Curator_confirmed | WBPerson557 | ||||||||
WBPhenotype:0001182 | Paper_evidence | WBPaper00032082 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Fat levels were not reduced when compared to daf-7(e1375), as determined by Sudan Black assay (described in Kimura et al., 1997). | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Treatment | To minimize staining variability, which allowed for quantitative comparisons between various genotypes: animals from one genotype were labeled with fluorescein isothiocyanate (FITC) and then fixed and stained in the same tube as unlabeled animals from another genotype. | Paper_evidence | WBPaper00032082 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Temperature | 22 | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001265 | Paper_evidence | WBPaper00042154 | |||||||
Curator_confirmed | WBPerson1455 | ||||||||
Remark | In free locomotion, irregular head swing is infrequent (Fig. 8D, E and Table 3), and coordination between head movement and body center movement is higher than the wild type (Fig. 7 and Table 3). | Paper_evidence | WBPaper00042154 | ||||||
Curator_confirmed | WBPerson1455 | ||||||||
WBPhenotype:0001444 | Paper_evidence | WBPaper00032335 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals showed defects in gustatory plasticity to NaCl compared to wild type. | Paper_evidence | WBPaper00032335 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003571 | Paper_evidence | WBPaper00032335 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Treatment | Animals were tested for response to 25 mM NaCl after various pre-treatments: a 15-min wash in CTX buffer with or without 100 mM NaCl (liquid), or 30 min on a CTX plate with or without 100 mM NaCl, and in the presence or absence of bacteria, 500 mM glycerol, or 3 uL of benzaldehyde. | Paper_evidence | WBPaper00032335 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001524 | Paper_evidence | WBPaper00035944 | |||||||
Curator_confirmed | WBPerson2776 | ||||||||
WBPerson10038 | |||||||||
Remark | Quoted from paper: "The median quiescent bout durations of nmr-1(ak4); egl-4 (ks60) were similar to egl-4(ks60) indicating egl-4 acts downstream of or within command interneurons in maintenance of quiescence (Figure 1A)." | Paper_evidence | WBPaper00035944 | ||||||
Curator_confirmed | WBPerson10038 | ||||||||
WBPhenotype:0001785 | Paper_evidence | WBPaper00031974 | |||||||
WBPaper00040253 | |||||||||
WBPaper00041586 | |||||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPerson1251 | |||||||||
WBPerson10038 | |||||||||
Remark | Animals were unable to fully retain NaCl avoidance; animals recovered from the avoidance state more rapidly than either wild-type animals or AMPAR mutants. Memory retention was restored in animals expressing wild-type NMR under the control of the glr-1 or tdc-1promoter, but not under the promoter for rig-3, tol-1, or odr-2. | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Table 1. Quoted from paper "nmr-1 is required for associative but not non-associative learning." | Paper_evidence | WBPaper00041586 | |||||||
Curator_confirmed | WBPerson10038 | ||||||||
Phenotype_assay | Control_strain | WBStrain00000001 | Paper_evidence | WBPaper00041586 | |||||
Curator_confirmed | WBPerson10038 | ||||||||
Treatment | Animals were subjected to a salt-chemotaxis-learning assay, in which starvation is paired with NaCl. | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0002114 | Paper_evidence | WBPaper00035944 | |||||||
Curator_confirmed | WBPerson2776 | ||||||||
WBPhenotype:0002346 | Paper_evidence | WBPaper00004836 | |||||||
Curator_confirmed | WBPerson2301 | ||||||||
WBPhenotype:0004017 | Paper_evidence | WBPaper00042154 | |||||||
Curator_confirmed | WBPerson1455 | ||||||||
Remark | In free locomotion, irregular head swing is infrequent (Fig. 8D, E and Table 3), and coordination between head movement and body center movement is higher than the wild type (Fig. 7 and Table 3). | Paper_evidence | WBPaper00042154 | ||||||
Curator_confirmed | WBPerson1455 | ||||||||
WBPhenotype:0004029 | Paper_evidence | WBPaper00064660 | |||||||
Curator_confirmed | WBPerson51549 | ||||||||
Phenotype_not_observed | WBPhenotype:0000006 | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | All these animals retained a similar number of eggs when compared to wild-type animals (~10 eggs). | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Treatment | Young well-fed animals were scored | Paper_evidence | WBPaper00032082 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Temperature | 25 | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000019 | Paper_evidence | WBPaper00032082 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals did not exhibit reduced pharyngeal pumping when compared with daf-7(e1375). | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Treatment | Pumping rates were assayed for well-fed , pheromone-untreated; food-deprived, pheromone-untreated; and well-fed, pheromone-treated animals. Pheromone treatment consisted of transfer of animals grown under well-fed conditions to plates containing 30 ul/ml of a dauer-pheromone prep (Golden and Riddle, 1982) and 30 ml of OP50 E. coli food. | Paper_evidence | WBPaper00032082 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Temperature | 20 | Paper_evidence | WBPaper00032082 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000062 | Paper_evidence | WBPaper00031974 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000147 | Paper_evidence | WBPaper00031974 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Starved animals showed an enhanced slowing in response to food (data not shown). | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0000643 | Paper_evidence | WBPaper00031974 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals showed no gross locomotion defect (data not shown). | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001072 | Paper_evidence | WBPaper00031974 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals moved more slowly in response to food (data not shown). | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001084 | Paper_evidence | WBPaper00031974 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals showed normal chemotaxis to NaCl in mock-conditioned assays and avoided NaCl just after conditioning. | Paper_evidence | WBPaper00031974 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001462 | Paper_evidence | WBPaper00032335 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals did not show defects in chemotaxis to NaCl compared to wild type. | Paper_evidence | WBPaper00032335 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003571 | Paper_evidence | WBPaper00032335 | |||||
Curator_confirmed | WBPerson712 | ||||||||
Phenotype_assay | Treatment | Animals were tested for response to 25 mM NaCl. | Paper_evidence | WBPaper00032335 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0001765 | Paper_evidence | WBPaper00031936 | |||||||
Curator_confirmed | WBPerson2021 | ||||||||
Remark | Mutants defective in the synthesis and reception of nonessential excitatory neurotransmitters respond normally to CO2 | Paper_evidence | WBPaper00031936 | ||||||
Curator_confirmed | WBPerson2021 | ||||||||
EQ_annotations | Life_stage | WBls:0000057 | PATO:0000460 | Paper_evidence | WBPaper00031936 | ||||
Curator_confirmed | WBPerson2021 | ||||||||
Phenotype_assay | Treatment | 10% CO2 | Paper_evidence | WBPaper00031936 | |||||
Curator_confirmed | WBPerson2021 | ||||||||
WBPhenotype:0001817 | Paper_evidence | WBPaper00032335 | |||||||
Curator_confirmed | WBPerson712 | ||||||||
Remark | Animals exhibited enhanced-gustatory plasticity, i.e. strong avoidance to NaCl after starvation, similar to that observed for wild type. | Paper_evidence | WBPaper00032335 | ||||||
Curator_confirmed | WBPerson712 | ||||||||
Affected_by | Molecule | WBMol:00003571 | Paper_evidence | WBPaper00032335 | |||||
Curator_confirmed | WBPerson712 | ||||||||
WBPhenotype:0002370 | Paper_evidence | WBPaper00059155 | |||||||
Curator_confirmed | WBPerson10038 | ||||||||
Remark | Quote from paper: "The results illustrated in Figure 3 suggest that mutants associated with glutamate receptor glr-1, glr-2, nmr-1, nmr-2 thermal avoidance was not affected." | Paper_evidence | WBPaper00059155 | ||||||
Curator_confirmed | WBPerson10038 | ||||||||
Phenotype_assay | Strain | WBStrain00040168 | Paper_evidence | WBPaper00059155 | |||||
Curator_confirmed | WBPerson10038 | ||||||||
Control_strain | WBStrain00000001 | Paper_evidence | WBPaper00059155 | ||||||
Curator_confirmed | WBPerson10038 | ||||||||
Disease_info | Models_disease | DOID:1289 | |||||||
Models_disease_in_annotation | WBDOannot00000907 | ||||||||
WBDOannot00000908 | |||||||||
Reference | WBPaper00040253 | ||||||||
WBPaper00032082 | |||||||||
WBPaper00031936 | |||||||||
WBPaper00032335 | |||||||||
WBPaper00026195 | |||||||||
WBPaper00025273 | |||||||||
WBPaper00031974 | |||||||||
WBPaper00004836 | |||||||||
WBPaper00035944 | |||||||||
WBPaper00012348 | |||||||||
WBPaper00042154 | |||||||||
WBPaper00041586 | |||||||||
WBPaper00059155 | |||||||||
WBPaper00060161 | |||||||||
WBPaper00060924 | |||||||||
WBPaper00064660 | |||||||||
Method | Deletion_allele |