D1037.2 | SeMaPhorin related 2

No description available.

Graphics for smp-2

3'UTR Zoom

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Legend: Blue:ORF, Gray:Updated 3'UTRome V3 dataset.

3'UTR mapped for smp-2

If available, we display here the 3'UTRs sequences we obtained by our analysis (in FASTA format). Putative canonical PAS sites, if found, are highlighted in yellow.

1 ID: 3898 - Tier: 1 - Name: smp-2 - Cosmid: D1037.2 - WBGeneID: WBGene00004890 - Length: 638 - PAS: aatgaa
Cluster Coverage (%): 960 reads (100.00%)
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id Name Chr Strand Start End Length PAS Coverage
3898 smp-2 I - 3666488 3667124 638nt aatgaa (-21nt) 960 reads

This 3'UTR isoform has been detected in the following tissues:
UTRome v31 Intestine2 Pharynx2 Body Muscle2 Arcade cells2 GABA neurons2 NMDA neurons2 Hypodermis2 Seam cells2
1Murari et al., 2023
2Blazie et al., 2016 - Alternative polyadenylation directs tissue specific miRNA targeting in Caenorhabditis elegans somatic tissues. - under review (mixed stages & tissue-specific datasets)
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Updated miRanda Targets for smp-2 (Murari et al., submitted)

smp-2 transcript has been predicted to be targeted by the following miRNAs:

ID miRNA Target Gene Score Energy % Binding (Target) % Binding (miRNA)
3326 cel-miR-36-5p smp-2 174 -23.32 84.21 89.47
110840 cel-miR-4927 smp-2 159 -15.28 85.71 85.71
41549 cel-miR-247-5p smp-2 156 -12.25 68.42 73.68
96348 cel-miR-4805-3p smp-2 154 -13.57 76.92 92.31
30230 cel-miR-86-3p smp-2 152 -19.11 69.57 73.91
123200 cel-miR-5547-5p smp-2 151 -11.91 66.67 72.22
104590 cel-miR-4814-5p smp-2 150 -15.52 100.00 100.00
13332 cel-miR-60-5p smp-2 148 -14.16 70.59 76.47
130206 cel-miR-5551-3p smp-2 147 -9.14 83.33 91.67
8879 cel-miR-48-3p smp-2 146 -17.52 63.16 73.68
72203 cel-miR-800-3p smp-2 145 -15.63 66.67 72.22
79731 cel-miR-1823-3p smp-2 143 -13.46 80.00 90.00
93806 cel-miR-2219-3p smp-2 143 -17.65 68.75 75.00
90692 cel-miR-2209b-5p smp-2 142 -8.27 88.89 88.89
46150 cel-miR-253-5p smp-2 140 -5.62 100.00 100.00
105482 cel-miR-4816-3p smp-2 140 -7.80 100.00 100.00

Predicted or Experimental Interactors for smp-2 (WormBase)

smp-2 has been predicted to interact with the following genes (data from WS200):

  • ced-1 Lee I et al. (2008)
    The ced-1 gene encodes a transmembrane protein on phagocytic cells that is homologous to human CD91, a low density lipoprotein receptor paralog; the cytoplasmic tail of CED-1 contains two motifs important for engulfment.
  • mrck-1 Lee I et al. (2008)
  • plx-1 Lee I et al. (2008)
    plx-1 encodes a C. elegans plexin ortholog; by homology, PLX-1 is predicted to function as a semaphorin receptor whose activity is required for proper positioning of the ray 1 cells in the male tail; genetic analyses indicate that while plx-1 functions in the same genetic pathway as the smp-1 and smp-2 semaphorin-encoding genes to position ray 1 cells, it functions in parallel to unc-73/GEF and the ced-10, mig-2, and rho-1 GTPase genes in affecting ray 1 position; plx-1 reporter gene fusions are expressed in all body wall muscles, male sex-specific muscles, and lateral hypodermal cells during postembryonic development; in the male tail, during the L3 larval stage when ray 1 cells are positioned, the plx-1 reporter is expressed predominantly in cells of the ray 1 and ray 2 lineages, with weaker and transient expression visible in the more posterior 3-9 rays.
  • rho-1 Lee I et al. (2008)
    rho-1 encodes a Rho GTPase; rho-1 activity is required for regulation of a number of actin filament-based processes including embryonic polarity, cell migration, cell shape changes, muscle contraction, and neurite outgrowth; in addition, RHO-1 is required for both DGK-1- and UNC-13-dependent and independent regulation of synaptic signaling at neuromuscular junctions; as RHO-1 binds DGK-1 in vitro, its regulation of DGK-1-mediated signaling may be direct; in vitro RHO-1 GTPase activity is enhanced by the RGA-3 and RGA-4 GAP proteins, consistent with genetic studies showing that, in the early embryo, RHO-1 activity is required for expression of the rga-3/4(RNAi) hypercontractibility phenotype; RHO-1 is ubiquitously expressed throughout development with notably high expression seen in head neurons and asymmetric expression seen in the anterior cortex of one-cell embryos.
  • smp-1 Lee I et al. (2008)
    none available
  • unc-18 Lee I et al. (2008)
    unc-18 encodes the C. elegans ortholog of Saccharomyces cervisiae SEC1 and mammalian Munc18 proteins; UNC-18 function as a chaperone for UNC-64/syntaxin, ensuring its anterograde transport from the endoplasmic reticulum to the plasma membrane; UNC-18 also enables the docking of vesicles to synaptic regions before vesicle priming and fusion, and promotes synaptic vesicle exocytosis; UNC-18 may also inhibit excessive exocytosis; UNC-18 is expressed in ventral cord motor neurons.
  • unc-7 Lee I et al. (2008)
    unc-7 encodes an innexin required for gap junction formation in invertebrates; UNC-7 is also required for normal locomotion, egg-laying, inhibition of feeding by tapping, avermectin sensitivity, and ivermectin sensitivity, as well as for the antagonism of UNC-79 and UNC-80 activity by volatile anesthetics; unc-7 is genetically required, and transcribed in, neurons rather than muscle cells, from larval stages L1 through L4; homologs of UNC-7 include Drosophila OGRE and SHAKING-B, as well as 24 C. elegans paralogs (including EAT-5, UNC-9, and INX-1 through INX-20); UNC-7 genetically interacts with UNC-124, and unc-7 mutants are phenotypically similar to unc-9 and unc-124 mutants; UNC-7 genetically interacts with AVR-14 and GLC-1 in the response to ivermectin.
  • unc-73 Lee I et al. (2008)
    unc-73 encodes a guanine nucleotide exchange factor (GNEF) similar to the Trio protein; UNC-73 is required for vulval morphogenesis, for the migration of QL, QR, CAN, and hypodermal P cells, the commissure outgrowth of D type motoneurons, and amphid axon outgrowth; UNC-73 has GNEF activity for both CED-10 and MIG-2 in vitro; the requirement for UNC-73 in P cell migration can be suppressed by transgenic overexpression of rho-1; UNC-73 activates several small GTPases: RHO-1 in P cell migration, and both CED-10 and MIG-2 in vulval morphogenesis, P cell migration, and axon outgrowth.
  • vps-11 Lee I et al. (2008)


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