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[192312_s_at]

Description T21C12.1 /REP_DB=WormBase Gene ID /WP=CE02346 /CHR=3 /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor (HINXTON) TR:Q22637 protein_id:CAA90318.1
Cluster 6grp_highest_10_10 > 43      6grp_high1_10_10 > 23      4grp_highest_8_8 > 57      4grp_high_8_8 > 34      6grp_highest_nonorm > 31      6grp_total > 12      4grp_total > 46      6grp_highest_sub > 02      6grp_cgc > 62      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 840
1 2 3 4 range
A 1888.5
(3)
P 		1355
(-0.8)
P 		1078.9
(-2.8)
P 		1053.7
(-3)
P 		835
B 1473.8
(2.8)
P 		1488
(3)
P 		1290.2
(-0.1)
P 		1100.7
(-3)
P 		387
C 1694.9
(3)
P 		1116.9
(-2.4)
P 		1048.9
(-3)
P 		1056.7
(-2.9)
P 		646
avr 1685.7
(3) 		1320
(-0.6) 		1139.3
(-2.3) 		1070.4
(-3) 		615

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1319
1 2 3 4 5 6 range
A 1085.8
(-0.1)
P 		1769.5
(3)
P 		1079.1
(-0.1)
P 		1091.1
(-0.1)
P 		736.1
(-1.7)
P 		450.5
(-3)
P 		1319
B 1063.7
(0.7)
P 		1364.5
(3)
P 		704.4
(-2)
P 		1137
(1.3)
P 		693.6
(-2)
P 		564.6
(-3)
P 		800
C 1303.1
(2.5)
P 		1278.7
(2.4)
P 		1360.6
(3)
P 		689.3
(-2.3)
P 		947
(-0.3)
P 		603.4
(-3)
P 		757
avr 1150.9
(0.9) 		1470.9
(3) 		1048
(0.3) 		972.5
(-0.2) 		792.2
(-1.4) 		539.5
(-3) 		931
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 533
1 2 3 4 range
A 687.6
(3)
P 		294.1
(-1.4)
P 		282.1
(-1.6)
P 		154.2
(-3)
P 		533
B 470
(3)
P 		367.5
(0.4)
P 		299
(-1.4)
P 		234.6
(-3)
P 		235
C 561.1
(3)
P 		321.1
(-0.8)
P 		365.6
(-0.1)
P 		178.2
(-3)
P 		383
avr 572.9
(3) 		327.6
(-0.8) 		315.6
(-1) 		189
(-3) 		384

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 520
1 2 3 4 5 6 range
A 200.2
(-2)
P 		629.3
(3)
P 		235
(-1.6)
P 		276.7
(-1.1)
P 		222.1
(-1.7)
P 		109.7
(-3)
P 		520
B 370.1
(1.2)
P 		454.2
(3)
P 		171
(-3)
P 		301.2
(-0.2)
P 		281.8
(-0.7)
P 		210.5
(-2.2)
P 		283
C 483
(3)
P 		390.2
(1.4)
P 		346.3
(0.6)
P 		138.6
(-3)
P 		306.5
(-0.1)
P 		202
(-1.9)
P 		344
avr 351.1
(0.3) 		491.2
(3) 		250.8
(-1.5) 		238.8
(-1.8) 		270.1
(-1.2) 		174.1
(-3) 		317
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192312_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7206
Sequence Type Exemplar sequence
Representative Public ID T21C12.1 NCBI
Target Description T21C12.1 /REP_DB=WormBase Gene ID /WP=CE02346 /CHR=3 /FEA=Sanger Annotation /DEF=gamma-aminobutyric-acid receptor (HINXTON) TR:Q22637 protein_id:CAA90318.1
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,GenBank identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001027610(11), NM_001027614(11), NM_001027612(11), NM_001027613(11), NM_001027615(11), AF151643(11), AF151645(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027610 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
NM_001027614 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
NM_001027612 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
NM_001027613 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
NM_001027615 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
AF151643 NCBI Caenorhabditis elegans ionotropic GABA receptor subunit UNC-49B.3 (unc-49B) mRNA, complete cds. 11/11 None
AF151645 NCBI Caenorhabditis elegans ionotropic GABA receptor subunit UNC-49Cshort (unc-49C) mRNA, complete cds. 11/11 None
SNAP00000038799 ENSEMBL cdna:SNAP chromosome:CEL140:III:10530455:10533022:1 9/11 None
GENEFINDER00000038811 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10530455:10532432:1 11/11 None
T21C12.1a ENSEMBL cdna:known chromosome:CEL140:III:10520681:10532577:1 gene:T21C12.1 11/11 A 
T21C12.1c.1 ENSEMBL cdna:known chromosome:CEL140:III:10520724:10532580:1 gene:T21C12.1 11/11 A 
T21C12.1d ENSEMBL cdna:known chromosome:CEL140:III:10520724:10532580:1 gene:T21C12.1 11/11 A 
T21C12.1e ENSEMBL cdna:known chromosome:CEL140:III:10520724:10532580:1 gene:T21C12.1 11/11 A 
T21C12.1f ENSEMBL cdna:known chromosome:CEL140:III:10520736:10532584:1 gene:T21C12.1 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176472 7 5 NM_001027610 172061_x_at (11), 175836_s_at (11), 192312_s_at (11)
NM_001027611 175835_at (11), 175836_s_at (11)
NM_001027612 172061_x_at (11), 192312_s_at (11)
NM_001027613 172061_x_at (11), 192312_s_at (11)
NM_001027614 172061_x_at (11), 192312_s_at (11)
NM_001027615 172061_x_at (11), 192312_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10520842-10532428(+) 99.94 100.0
Public Domain and Genome References
Ensembl T21C12.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA90318 Hypothetical protein T21C12.1a [Caenorhabditis elegans] ref|NP_001022781.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] 0.0
blast CAC42346 Hypothetical protein T21C12.1b [Caenorhabditis elegans] ref|NP_001022782.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42382.1| ionotropic GABA receptor subunit UNC-49A [Caenorhabditis elegans] 0.0
blast CAC42349 Hypothetical protein T21C12.1e [Caenorhabditis elegans] ref|NP_001022785.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42385.1| ionotropic GABA receptor subunit UNC-49B.3 [Caenorhabditis elegans] 0.0
blast CAC42347 Hypothetical protein T21C12.1c [Caenorhabditis elegans] ref|NP_001022783.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42383.1| ionotropic GABA receptor subunit UNC-49B.1 [Caenorhabditis elegans] 0.0
blast CAC42348 Hypothetical protein T21C12.1d [Caenorhabditis elegans] ref|NP_001022784.1| UNCoordinated family member (unc-49) [Caenorhabditis elegans] gb|AAD42384.1| ionotropic GABA receptor subunit UNC-49B.2 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 6.6E-39
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-35
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.3E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 2.7E-75
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 0.021
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.6E-35
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.0E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.1E-78
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.0E-8
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.0E-8
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.3E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.7E-75
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.3E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022781.1 8 261-283,290-309,324-346,529-551,592-614,913-935,977-999,1061-1083
NP_001022785.1 4 255-277,284-303,318-340,468-485
NP_001022783.1 4 255-277,284-303,318-340,449-466
NP_001022784.1 4 255-277,284-303,318-340,437-454
NP_001022786.1 3 255-277,319-341,403-425
AAD42385.1 4 255-277,284-303,318-340,468-485
AAD42387.1 3 71-93,135-157,219-241
T21C12.1a 8 261-283,290-309,324-346,529-551,592-614,913-935,977-999,1061-1083
T21C12.1c.1 4 255-277,284-303,318-340,449-466
T21C12.1d 4 255-277,284-303,318-340,437-454
T21C12.1e 4 255-277,284-303,318-340,468-485
T21C12.1f 3 255-277,319-341,403-425
SNAP00000038799 2 71-93,135-157
GENEFINDER00000038811 3 71-93,135-157,219-241
Sequence
Target Sequence 
>C. ELEGANS:192312_S_AT
tttgatcgcgacagcggcttctactttcttcaaatatttttccctgccagcctcgtcgta
gttttatcatggatctcattctggatcaatcgtgactcggcgccttcgcgaaccctaatc
ggtacgatgacggtgctcactgagactcatcttatgaccggaaccaatcgacgtcttcca
ccagttgcctatgtaaaagccgttgatgtattcctcggtttctgctatcttctggttata
ctggcgttgatcgagtacgcctgtgttgcctactcaaaaaagaagaacgaggatcgtcgg
agaagagagaagaagacggagcataaacctgctccgccgacacctgatattcttcacgac
gtccgccttgccgaatgcacatgcaacgcggctccaacctcgatcatcgccgtcatcaag
cagtcgaatcgattctgtgtcagtcacagtcacattgacatcgtcagccgtgccgcgttt
cctcttgttttcatcttgttcaacactctcttctggctgattctactgtacaaatccaag
cgtctgccgtatatta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTGATCGCGACAGCGGCTTCTACT 495 667 2734 Antisense
TGCCAGCCTCGTCGTAGTTTTATCA 394 587 2778 Antisense
GACGGTGCTCACTGAGACTCATCTT 552 377 2862 Antisense
ATGACCGGAACCAATCGACGTCTTC 329 45 2887 Antisense
TCTTCCACCAGTTGCCTATGTAAAA 160 619 2907 Antisense
TGATGTATTCCTCGGTTTCTGCTAT 281 567 2937 Antisense
GACACCTGATATTCTTCACGACGTC 14 369 3072 Antisense
ATCATCGCCGTCATCAAGCAGTCGA 152 29 3136 Antisense
GTCACATTGACATCGTCAGCCGTGC 366 465 3182 Antisense
CTCTTCTGGCTGATTCTACTGTACA 624 229 3241 Antisense
AAATCCAAGCGTCTGCCGTATATTA 13 117 3265 Antisense
Sequence Source Affymetrix Proprietary Database