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[172061_x_at]

Description g5354175 /REP_DB=GenBank Identifier /GB=AF151645.1 /PROTEIN_GB=AAD42387.1 /CHR=3 /FEA=Mapped Transcript /DEF=ionotropic GABA receptor subunit UNC-49Cshort
Cluster 6grp_highest_10_10 > 43      6grp_high1_10_10 > 23      4grp_highest_8_8 > 56      4grp_high_8_8 > 35      6grp_highest_nonorm > 31      6grp_total > 12      4grp_total > 45      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.
4 662
1 2 3 4 range
A 1379
(3)
P 		1366.8
(2.9)
P 		1054.4
(0.1)
P 		717.1
(-3)
P 		662
B 1266
(3)
P 		1161
(1.4)
P 		861
(-3)
P 		1064.9
(0)
P 		405
C 1316.4
(3)
P 		1179.8
(1.2)
P 		858.9
(-3)
P 		927.6
(-2.1)
P 		458
avr 1320.5
(3) 		1235.9
(1.8) 		924.8
(-2.7) 		903.2
(-3) 		417

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 938
1 2 3 4 5 6 range
A 1093.7
(1)
P 		1400.2
(3)
P 		857.4
(-0.5)
P 		934.5
(-0)
P 		761.2
(-1.1)
P 		471.4
(-3)
P 		929
B 885
(-0.6)
P 		1409
(3)
P 		1023
(0.3)
P 		1012
(0.3)
P 		688.4
(-2)
P 		540.1
(-3)
P 		869
C 963.4
(0)
P 		1391.8
(3)
P 		1045.2
(0.6)
P 		728.8
(-1.6)
P 		751
(-1.5)
P 		529.5
(-3)
P 		862
avr 980.7
(0.2) 		1400.3
(3) 		975.2
(0.1) 		891.8
(-0.4) 		733.5
(-1.5) 		513.7
(-3) 		887
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 397
1 2 3 4 range
A 502.1
(3)
P 		296.7
(-0.1)
P 		275.6
(-0.4)
P 		105
(-3)
P 		397
B 403.7
(3)
P 		286.7
(-0.4)
P 		199.5
(-3)
P 		226.9
(-2.2)
P 		204
C 435.8
(3)
P 		339.2
(0.9)
P 		299.4
(0.1)
P 		156.4
(-3)
P 		279
avr 447.2
(3) 		307.5
(0.1) 		258.2
(-1) 		162.8
(-3) 		284

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 383
1 2 3 4 5 6 range
A 201.6
(-1.6)
P 		498
(3)
P 		186.7
(-1.9)
P 		237
(-1.1)
P 		229.7
(-1.2)
P 		114.8
(-3)
P 		383
B 307.9
(-0.6)
P 		469
(3)
P 		248.4
(-1.9)
P 		268
(-1.5)
P 		279.7
(-1.2)
P 		201.4
(-3)
P 		268
C 357.1
(1.5)
P 		424.7
(3)
P 		266
(-0.4)
P 		146.6
(-3)
P 		243
(-0.9)
P 		177.2
(-2.3)
P 		278
avr 288.9
(-0.5) 		463.9
(3) 		233.7
(-1.6) 		217.2
(-1.9) 		250.8
(-1.3) 		164.5
(-3) 		299
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172061_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19805
Sequence Type Exemplar sequence
Representative Public ID 5354175 NCBI
Target Description g5354175 /REP_DB=GenBank Identifier /GB=AF151645.1 /PROTEIN_GB=AAD42387.1 /CHR=3 /FEA=Mapped Transcript /DEF=ionotropic GABA receptor subunit UNC-49Cshort
Cluster Evidence This cluster is supported by a Mapped Transcript.
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
GENEFINDER00000038811 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10530455:10532432:1 9/11 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
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000038799 6/11 Cross Hyb Matching Probes None
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:10530296-10532579(+) 100.0 100.0
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
GENEFINDER00000038811 3 71-93,135-157,219-241
Sequence
Target Sequence 
>C. ELEGANS:172061_X_AT
gacggtgctcactgagactcatcttatgaccggaaccaatcgacgtcttccaccagttgc
ctatgtaaaagccgttgatgtattcctcggtttctgctatcttctggttatactggcgtt
gatcgagtacgcctgtgttgcctactcaaaaaagaagaacgaggatcgtcggagaagaga
gaagaagacggagcataaacctgctccgccgacacctgatattcttcacgacgtccgcct
tgccgaatgcacatgcaacgcggctccaacctcgatcatcgccgtcatcaagcagtcgaa
tcgattctgtgtcagtcacagtcacattgacatcgtcagccgtgccgcgtttcctcttgt
tttcatcttgttcaacactctcttctggctgattctactgtacaaatccaagcgtctgcc
gtatattagtgaacacgagggtgaccgttgcgatgctccagaccttcattaatctcaatc
caacttcctcatcattttccatttcgaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGGTGCTCACTGAGACTCATCTT 557 377 490 Antisense
ATGACCGGAACCAATCGACGTCTTC 334 45 515 Antisense
TCTTCCACCAGTTGCCTATGTAAAA 165 619 535 Antisense
TGATGTATTCCTCGGTTTCTGCTAT 286 567 565 Antisense
GACACCTGATATTCTTCACGACGTC 19 369 700 Antisense
ATCATCGCCGTCATCAAGCAGTCGA 157 29 764 Antisense
CTCTTCTGGCTGATTCTACTGTACA 629 229 869 Antisense
AAATCCAAGCGTCTGCCGTATATTA 9 117 893 Antisense
ACACGAGGGTGACCGTTGCGATGCT 625 109 922 Antisense
ATGCTCCAGACCTTCATTAATCTCA 119 43 942 Antisense
CTTCCTCATCATTTTCCATTTCGAA 545 219 973 Antisense
Sequence Source GenBank