[Home] | [Total List]

[175836_s_at]

Description g5354165 /REP_DB=GenBank Identifier /GB=AF151640.1 /PROTEIN_GB=AAD42382.1 /CHR=3 /FEA=Mapped Transcript /DEF=ionotropic GABA receptor subunit UNC-49A
Cluster 6grp_total > 33      4grp_total > 47      6grp_cgc > 21      6grp_cgc_sub > De      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 94
1 2 3 4 range
A 141.1
(3)
P 		59.2
(-2.2)
A 		46.8
(-3)
A 		68.4
(-1.6)
P 		94
B 97.5
(1)
P 		79
(-2.8)
A 		107.1
(3)
P 		78.1
(-3)
P 		29
C 137
(3)
P 		70.1
(-1.8)
A 		52.9
(-3)
A 		84.3
(-0.8)
A 		84
avr 125.2
(3) 		69.4
(-2.9) 		68.9
(-3) 		76.9
(-2.1) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 96
1 2 3 4 5 6 range
A 84.7
(2.1)
P 		93.7
(3)
P 		80.7
(1.8)
P 		48.7
(-1.3)
P 		58.8
(-0.3)
P 		30.8
(-3)
A 		63
B 77
(2.1)
P 		84.6
(3)
P 		81.4
(2.6)
A 		33.8
(-2.9)
A 		32.8
(-3)
A 		36.3
(-2.6)
A 		52
C 120.6
(3)
P 		46.2
(-1.6)
P 		89.8
(1.1)
M 		35.5
(-2.3)
A 		45.3
(-1.7)
A 		24.5
(-3)
A 		96
avr 94.1
(3) 		74.8
(1.2) 		84
(2) 		39.3
(-2.2) 		45.6
(-1.6) 		30.5
(-3) 		64
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 41
1 2 3 4 range
A 51.4
(3)
P 		12.9
(-2.6)
A 		12.2
(-2.7)
A 		10
(-3)
P 		41
B 31.1
(3)
P 		19.5
(-1.8)
A 		24.8
(0.4)
P 		16.6
(-3)
P 		15
C 45.3
(3)
P 		20.2
(-1.8)
A 		18.4
(-2.2)
A 		14.2
(-3)
A 		31
avr 42.6
(3) 		17.5
(-2.2) 		18.5
(-2) 		13.6
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 15.6
(-1.1)
P 		33.3
(3)
P 		17.6
(-0.7)
P 		12.4
(-1.9)
P 		17.7
(-0.6)
P 		7.5
(-3)
A 		26
B 26.8
(2.6)
P 		28.2
(3)
P 		19.8
(0.4)
A 		8.9
(-3)
A 		13.3
(-1.6)
A 		13.5
(-1.6)
A 		19
C 44.7
(3)
P 		14.1
(-1.9)
P 		22.9
(-0.5)
M 		7.1
(-3)
A 		14.7
(-1.8)
A 		8.2
(-2.8)
A 		38
avr 29
(3) 		25.2
(1.8) 		20.1
(0.3) 		9.5
(-3) 		15.2
(-1.2) 		9.7
(-2.9) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175836_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19823
Sequence Type Exemplar sequence
Representative Public ID 5354165 NCBI
Target Description g5354165 /REP_DB=GenBank Identifier /GB=AF151640.1 /PROTEIN_GB=AAD42382.1 /CHR=3 /FEA=Mapped Transcript /DEF=ionotropic GABA receptor subunit UNC-49A
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 identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001027611(11), NM_001027610(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027611 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
NM_001027610 NCBI Caenorhabditis elegans UNCoordinated family member (unc-49) (unc-49) mRNA, complete cds. 11/11 None
SNAP00000038796 ENSEMBL cdna:SNAP chromosome:CEL140:III:10520847:10527717:1 11/11 None
GENEFINDER00000038813 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10520847:10527679:1 11/11 None
T21C12.1b ENSEMBL cdna:known chromosome:CEL140:III:10520555:10527840:1 gene:T21C12.1 11/11 A 
T21C12.1a ENSEMBL cdna:known chromosome:CEL140:III:10520681:10532577:1 gene:T21C12.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001027616 7/11 Cross Hyb Matching Probes None
T21C12.1g 7/11 Cross Hyb Matching Probes None
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176472 7 2 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:10520550-10527836(+) 100.0 100.0
Public Domain and Genome References
Ensembl T21C12.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
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 CAA90318 Hypothetical protein T21C12.1a [Caenorhabditis elegans] ref|NP_001022781.1| UNCoordinated family member (unc-49) [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 5.2E-8
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 1.3E-79
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 3.0E-22
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 5.2E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022782.1 4 249-271,278-297,312-334,454-472
NP_001022781.1 8 261-283,290-309,324-346,529-551,592-614,913-935,977-999,1061-1083
T21C12.1b 4 249-271,278-297,312-334,454-472
T21C12.1a 8 261-283,290-309,324-346,529-551,592-614,913-935,977-999,1061-1083
SNAP00000038796 3 249-271,278-297,301-320
GENEFINDER00000038813 4 261-283,290-309,324-346,478-496
Sequence
Target Sequence 
>C. ELEGANS:175836_S_AT
ggatgaagcttgtccgagccagaaaagaatctcgaatgctgacccctttaccacatcttg
agtctcttcctccaaaacgtactctatccgttccctcgtatttcaacaacaccacgtacc
gcccgttttactcgtccaccgatcaaacgtccaacctgtacattccggagtcgcagcgca
cgacgattttctcaaatgaggatgcagtgccgaatgaactaactccaatgctcggacgga
gtaactcacaagcatccgtatttctgtatcaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATGAAGCTTGTCCGAGCCAGAAA 16 489 1314 Antisense
AAAGAATCTCGAATGCTGACCCCTT 603 123 1337 Antisense
GAGTCTCTTCCTCCAAAACGTACTC 549 395 1373 Antisense
TTCCCTCGTATTTCAACAACACCAC 414 697 1404 Antisense
TTTACTCGTCCACCGATCAAACGTC 170 671 1440 Antisense
ACGTCCAACCTGTACATTCCGGAGT 237 93 1460 Antisense
AGTCGCAGCGCACGACGATTTTCTC 14 61 1482 Antisense
GATGCAGTGCCGAATGAACTAACTC 409 413 1514 Antisense
GAACTAACTCCAATGCTCGGACGGA 193 349 1529 Antisense
GAGTAACTCACAAGCATCCGTATTT 619 397 1552 Antisense
CAAGCATCCGTATTTCTGTATCAGA 553 185 1562 Antisense
Sequence Source GenBank