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[193262_at] ligand-gated ionic channel

Description F21F3.5 /REP_DB=WormBase Gene ID /WP=CE24908 /GEN=unc-38 /TR=SW:Q23022 /GB=AAB42282.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster 6grp_highest_10_10 > 50      6grp_high1_10_10 > 06      4grp_highest_8_8 > 59      4grp_high_8_8 > 25      6grp_highest_nonorm > 50      6grp_total > 07      4grp_total > 38      6grp_highest_sub > De      6grp_cgc > 20      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 408
1 2 3 4 range
A 631.5
(3)
P 		312.7
(-3)
P 		350.7
(-2.3)
P 		322.7
(-2.8)
P 		319
B 563.7
(3)
P 		484.1
(1.3)
P 		280.8
(-3)
P 		509.2
(1.8)
P 		283
C 688.6
(3)
P 		361.4
(-2.8)
P 		396.4
(-2.2)
P 		352.8
(-3)
P 		336
avr 627.9
(3) 		386.1
(-2.1) 		342.6
(-3) 		394.9
(-1.9) 		285

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 425
1 2 3 4 5 6 range
A 646.9
(3)
P 		500.1
(0.6)
P 		454
(-0.2)
P 		440.4
(-0.4)
P 		394.8
(-1.1)
P 		280.5
(-3)
P 		366
B 705.8
(3)
P 		491.8
(-0.6)
P 		483.3
(-0.7)
P 		455.2
(-1.2)
P 		373.2
(-2.6)
P 		349.3
(-3)
P 		357
C 642.5
(3)
P 		539.4
(0.8)
P 		436.6
(-1.4)
P 		501.5
(-0)
P 		362.1
(-3)
P 		416.4
(-1.8)
P 		280
avr 665.1
(3) 		510.4
(0.1) 		458
(-0.9) 		465.7
(-0.8) 		376.7
(-2.5) 		348.7
(-3) 		316
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 183
1 2 3 4 range
A 229.9
(3)
P 		67.9
(-2.3)
P 		91.7
(-1.5)
P 		47.2
(-3)
P 		183
B 179.7
(3)
P 		119.6
(-0.1)
P 		65.1
(-3)
P 		108.5
(-0.7)
P 		115
C 227.9
(3)
P 		103.9
(-1.4)
P 		138.1
(-0.2)
P 		59.5
(-3)
P 		168
avr 212.5
(3) 		97.1
(-1.9) 		98.3
(-1.9) 		71.7
(-3) 		141

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 177
1 2 3 4 5 6 range
A 119.2
(-0.2)
P 		177.9
(3)
P 		98.9
(-1.3)
P 		111.7
(-0.6)
P 		119.1
(-0.2)
P 		68.3
(-3)
P 		110
B 245.6
(3)
P 		163.7
(-0.8)
P 		117.4
(-3)
P 		120.6
(-2.9)
P 		151.6
(-1.4)
P 		130.3
(-2.4)
P 		128
C 238.1
(3)
P 		164.6
(-0.2)
P 		111.1
(-2.6)
P 		100.9
(-3)
P 		117.2
(-2.3)
P 		139.4
(-1.3)
P 		137
avr 201
(3) 		168.7
(0.9) 		109.1
(-3) 		111.1
(-2.9) 		129.3
(-1.7) 		112.7
(-2.8) 		92
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193262_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2089
Sequence Type Exemplar sequence
Representative Public ID F21F3.5 NCBI
Target Description F21F3.5 /REP_DB=WormBase Gene ID /WP=CE24908 /GEN=unc-38 /TR=SW:Q23022 /GB=AAB42282.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_059071(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059071 NCBI Caenorhabditis elegans UNCoordinated family member (unc-38) (unc-38) mRNA, complete cds. 11/11 None
GENEFINDER00000035681 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4897692:4900901:-1 11/11 None
SNAP00000035672 ENSEMBL cdna:SNAP chromosome:CEL140:I:4897823:4900901:-1 9/11 None
F21F3.5 ENSEMBL cdna:known chromosome:CEL140:I:4897641:4900978:-1 gene:F21F3.5 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:4897691-4900901(-) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel
Gene Symbol unc-38
Ensembl F21F3.5
Entrez Gene 172105 Entrez gene
WormBase CE24908 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.3473.1.S1_AT similar to cholinergic receptor, nicotinic, alpha polypeptide 3 cfa
CANINE_2:CFAAFFX.3473.1.S1_S_AT similar to cholinergic receptor, nicotinic, alpha polypeptide 3 cfa
CANINE_2:CFAAFFX.3505.1.S1_S_AT similar to cholinergic receptor, nicotinic, alpha polypeptide 3 cfa
CANINE_2:CFAAFFX.3509.1.S1_AT similar to cholinergic receptor, nicotinic, alpha polypeptide 3 cfa
DROSOPHILA_2:1632060_AT nicotinic Acetylcholine Receptor alpha 96Aa dm
DROSGENOME1:143056_AT nicotinic Acetylcholine Receptor alpha 96Aa dm
CHICKEN:GGA.5095.1.S1_AT cholinergic receptor, nicotinic, alpha polypeptide 3 gga
HG-U133_PLUS_2:211587_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A:211587_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A_2:211587_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133_PLUS_2:211772_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A:211772_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A_2:211772_X_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133_PLUS_2:210221_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A:210221_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-FOCUS:210221_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U133A_2:210221_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HU35KSUBA:U62432_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HUGENEFL:U62432_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HU35KSUBC:RC_R85529_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HUGENEFL:M86383_S_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HUGENEFL:M37981_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
U133_X3P:G13543945_3P_S_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
U133_X3P:G12653482_3P_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U95AV2:34019_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
HG-U95C:54403_AT cholinergic receptor, nicotinic, alpha polypeptide 3 hs
MOE430A:1452010_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MOUSE430A_2:1452010_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MOUSE430_2:1452010_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MOE430A:1455931_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MOUSE430A_2:1455931_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MOUSE430_2:1455931_AT cholinergic receptor, nicotinic, alpha polypeptide 3 mm
MG-U74BV2:108337_AT Cholinergic receptor, nicotinic, alpha polypeptide 3 (Chrna3), mRNA mm
MOE430B:1444368_AT Cholinergic receptor, nicotinic, alpha polypeptide 3 (Chrna3), mRNA mm
MOUSE430_2:1444368_AT Cholinergic receptor, nicotinic, alpha polypeptide 3 (Chrna3), mRNA mm
MU11KSUBB:MSA.31159.0_S_AT Cholinergic receptor, nicotinic, alpha polypeptide 3 (Chrna3), mRNA mm
RN-U34:L31621_S_AT cholinergic receptor, nicotinic, alpha polypeptide 3 rn
RG-U34A:L31621_S_AT cholinergic receptor, nicotinic, alpha polypeptide 3 rn
RAE230A:1369001_AT cholinergic receptor, nicotinic, alpha polypeptide 3 rn
RAT230_2:1369001_AT cholinergic receptor, nicotinic, alpha polypeptide 3 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
6811 ion transport inferred from electronic annotation QuickGO AmiGO
7274 neuromuscular synaptic transmission inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
45211 postsynaptic membrane inferred from electronic annotation QuickGO AmiGO
45202 synapse inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4889 nicotinic acetylcholine-activated cation-selective channel activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5230 extracellular ligand-gated ion channel activity inferred from electronic annotation QuickGO AmiGO
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
15464 acetylcholine receptor activity inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB42282 Uncoordinated protein 38 [Caenorhabditis elegans] emb|CAA67197.1| alpha nicotinic acetylcholine receptor subunit [Caenorhabditis elegans] emb|CAA67196.1| alpha nicotinic acetylcholine receptor subunit [Caenorhabditis elegans] ref|NP_491472.1| UNCoordinated family member (unc-38) [Caenorhabditis elegans] sp|Q23022|ACH5_CAEEL Acetylcholine receptor, alpha-type subunit unc-38 precursor (Uncoordinated protein 38) 0.0
blast T25720 hypothetical protein F21F3.5 - Caenorhabditis elegans 0.0
blast CAE73110 Hypothetical protein CBG20491 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 9.8E-64
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 4.8E-23
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.8E-99
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491472.1 4 260-282,289-311,324-346,465-487
F21F3.5 4 260-282,289-311,324-346,465-487
GENEFINDER00000035681 4 260-282,289-311,324-346,465-487
SNAP00000035672 5 4-21,258-280,295-317,324-346,461-483
Sequence
Target Sequence 
>C. ELEGANS:193262_AT
ctgctcactgaaatcattccggccacatcgatcacgttgccactgattggaaaatatcta
ctgttcacaatggtgatggttacactttctgtcgtggttactgttatttcattaaacttg
catttccgtactccaacaacccatttgatgcctaattgggtgaagaaagtattcctaaaa
tggcttccaaaacttcttttcatgagacgaccaatcgatgattacgaggaaaaattcgat
gataaaaagaagccgaaagacgggaaaattgcattgagcgttcatgcacatcgagtttca
aatgttggaaataacattaggaatgcaacaattgatgacacaattcaaaaaatgtattat
tctccgccagttgtaaaagctttcgaaaatatttgctttatcgccgaactgctgaaaaag
aaagatcgagacgataaaatcgatgaggattggaaatacgtggcaatggtccttgatcga
cttttccttcttattttctcaattgcttgttttgtaggaacagttataattcttttgagg
gcaccaacactgtatgacacacgacaacccatcgatttgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGCTCACTGAAATCATTCCGGCCA 33 239 925 Antisense
ACATCGATCACGTTGCCACTGATTG 470 105 949 Antisense
GGTTACACTTTCTGTCGTGGTTACT 607 501 1002 Antisense
TTAAACTTGCATTTCCGTACTCCAA 341 683 1036 Antisense
GTACTCCAACAACCCATTTGATGCC 704 457 1052 Antisense
GAGCGTTCATGCACATCGAGTTTCA 263 387 1200 Antisense
AAATGTATTATTCTCCGCCAGTTGT 599 119 1274 Antisense
AATATTTGCTTTATCGCCGAACTGC 627 173 1312 Antisense
AATGGTCCTTGATCGACTTTTCCTT 603 153 1389 Antisense
GGGCACCAACACTGTATGACACACG 608 493 1463 Antisense
GACACACGACAACCCATCGATTTGC 43 367 1480 Antisense
Sequence Source Affymetrix Proprietary Database