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[187810_at] ligand-gated ionic channel

Description C27H5.8 /REP_DB=WormBase Gene ID /WP=CE06895 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 03      4grp_highest_8_8 > 60      4grp_high_8_8 > 25      6grp_highest_nonorm > 51      6grp_total > 14      4grp_total > 39      6grp_highest_sub > De      6grp_cgc > 23      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1213
1 2 3 4 range
A 1297
(3)
P 		598.2
(-1)
P 		236.5
(-3)
P 		740.2
(-0.2)
P 		1061
B 1449.3
(3)
P 		485.5
(-2.2)
P 		327.3
(-3)
P 		759
(-0.7)
P 		1122
C 1429.9
(3)
P 		462.9
(-2.6)
P 		402.7
(-3)
P 		721.5
(-1.1)
P 		1027
avr 1392.1
(3) 		515.5
(-1.9) 		322.2
(-3) 		740.2
(-0.7) 		1070

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 702
1 2 3 4 5 6 range
A 786.9
(3)
P 		624
(1.1)
P 		515.5
(-0.2)
P 		470.8
(-0.7)
P 		386.2
(-1.7)
P 		275.6
(-3)
P 		511
B 853.1
(3)
P 		744.3
(1.7)
P 		608.2
(0.2)
P 		451.1
(-1.7)
P 		336.8
(-3)
P 		372.1
(-2.6)
P 		516
C 977.3
(3)
P 		783.7
(1.3)
P 		515.6
(-1)
P 		558.1
(-0.6)
P 		282.3
(-3)
P 		413.3
(-1.9)
P 		695
avr 872.4
(3) 		717.3
(1.3) 		546.4
(-0.6) 		493.3
(-1.2) 		335.1
(-3) 		353.7
(-2.8) 		537
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 412
1 2 3 4 range
A 472.2
(3)
P 		129.9
(-2)
P 		61.8
(-3)
P 		108.3
(-2.3)
P 		410
B 462.2
(3)
P 		119.9
(-2.3)
P 		75.8
(-3)
P 		161.7
(-1.7)
P 		386
C 473.3
(3)
P 		133.1
(-2.8)
P 		140.4
(-2.7)
P 		121.6
(-3)
P 		352
avr 469.2
(3) 		127.6
(-2.4) 		92.7
(-3) 		130.5
(-2.4) 		377

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 295
1 2 3 4 5 6 range
A 145.1
(0)
P 		221.9
(3)
P 		112.3
(-1.2)
P 		119.4
(-1)
P 		116.5
(-1.1)
P 		67.1
(-3)
P 		155
B 296.8
(3)
P 		247.8
(1.3)
P 		147.7
(-2)
P 		119.5
(-3)
P 		136.8
(-2.4)
P 		138.8
(-2.3)
P 		177
C 362.2
(3)
P 		239.1
(0.3)
P 		131.2
(-2.1)
P 		112.2
(-2.5)
P 		91.3
(-3)
P 		138.4
(-2)
P 		271
avr 268
(3) 		236.3
(1.8) 		130.4
(-2.4) 		117
(-2.9) 		114.9
(-3) 		114.8
(-3) 		153
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187810_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4682
Sequence Type Exemplar sequence
Representative Public ID C27H5.8 NCBI
Target Description C27H5.8 /REP_DB=WormBase Gene ID /WP=CE06895 /SUBMIT=ST.LOUIS /CHR=2 /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_063088(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063088 NCBI Caenorhabditis elegans Glutamate-gated ChLoride channel family member (glc-4) (glc-4) mRNA, complete cds. 11/11 None
SNAP00000006116 ENSEMBL cdna:SNAP chromosome:CEL140:II:7172286:7175028:-1 11/11 None
GENEFINDER00000006124 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7172286:7175550:-1 11/11 None
C27H5.8 ENSEMBL cdna:known chromosome:CEL140:II:7172161:7174869:-1 gene:C27H5.8 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
chrII:7172281-7175024(-) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel
Gene Symbol glc-4
Ensembl C27H5.8
Entrez Gene 182971 Entrez gene
SwissProt Q95QT7 EMBL-EBI
WormBase CE32152 Wormbase
Functional Annotations
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
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
GO Molecular Function (view graph)
ID Description Evidence Links
4890 GABA-A receptor 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
8068 glutamate-gated chloride channel activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK84494 Glutamate-gated chloride channel protein 4 [Caenorhabditis elegans] ref|NP_495489.2| Glutamate-gated ChLoride channel family member (glc-4) [Caenorhabditis elegans] 0.0
blast CAE67560 Hypothetical protein CBG13087 [Caenorhabditis briggsae] 0.0
blast T15670 hypothetical protein C27H5.5 - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-23
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.4E-42
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-23
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-53
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-23
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.1E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.9E-53
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495489.2 4 266-288,295-314,329-351,470-492
C27H5.8 4 266-288,295-314,329-351,470-492
SNAP00000006116 4 254-276,283-302,317-339,458-480
GENEFINDER00000006124 5 94-116,363-385,392-411,426-448,567-589
Sequence
Target Sequence 
>C. ELEGANS:187810_AT
cagctgcacgtgttccattagcaattgttactcttcttacaatgattacaacttctcatg
caattaattcaaatctaccgccagttagttatgcaaaatcaattgatatctgggttggag
catgtgttgtgttcatttttttctcattgattgagtacgctgtcgtcaattatgtgggaa
ttctggatgagcacagacaaatgaaaaaagcagcatgtaatcgatctcgtctttcgaatg
taattgaaaatgataattttggagaatccttacagtcattgactttcagtccacaagaga
agaaacgtctgatccgccgacgtccaaaaaaaaatatggagatgcaagaaggagattttg
aagcaattgaaatggttgatagaggtcccccacgaagtgctggattaatggaagaaggat
ggacatttcatgatacaactgatttagtttatattggacaacgaaaacgggttgaacttg
tccgttggtgcagtgttctgtcatcacgtggacgagctgaacgtattgatatcatcgcta
gaataatcttccctttagcattcattct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGCTGCACGTGTTCCATTAGCAAT 571 203 1070 Antisense
AAATCTACCGCCAGTTAGTTATGCA 155 117 1140 Antisense
GTGTTGTGTTCATTTTTTTCTCATT 403 485 1193 Antisense
GTACGCTGTCGTCAATTATGTGGGA 240 459 1224 Antisense
AAGCAGCATGTAATCGATCTCGTCT 36 151 1277 Antisense
GAGAAGAAACGTCTGATCCGCCGAC 237 363 1366 Antisense
AAATGGTTGATAGAGGTCCCCCACG 361 119 1439 Antisense
GTCCCCCACGAAGTGCTGGATTAAT 589 475 1454 Antisense
AACTTGTCCGTTGGTGCAGTGTTCT 315 139 1544 Antisense
GCAGTGTTCTGTCATCACGTGGACG 568 311 1559 Antisense
TAATCTTCCCTTTAGCATTCATTCT 661 635 1613 Antisense
Sequence Source Affymetrix Proprietary Database