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[188002_at]

Description W10C8.2 /REP_DB=WormBase Gene ID /WP=CE26031 /GEN=pop-1 /TR=O45007 /GB=AAK21504.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_total > 39      4grp_total > 19      6grp_cgc > 08      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 66
1 2 3 4 range
A 29.8
(-2.1)
A 		22.8
(-3)
A 		28.4
(-2.3)
A 		70
(3)
A 		47
B 17.5
(0.2)
A 		28.6
(3)
A 		4.4
(-3)
A 		26.7
(2.5)
A 		24
C 26.9
(-0)
A 		31.6
(3)
A 		22.2
(-3)
A 		23.6
(-2.1)
A 		9
avr 24.7
(-1.2) 		27.7
(-0.4) 		18.3
(-3) 		40.1
(3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 35
1 2 3 4 5 6 range
A 35.8
(3)
A 		29.7
(1.9)
A 		1.2
(-3)
A 		5.3
(-2.3)
A 		2.2
(-2.8)
A 		27.9
(1.6)
A 		35
B 13.2
(-0.6)
A 		2.8
(-2.9)
A 		2.8
(-2.9)
A 		2.5
(-3)
A 		28.9
(3)
A 		18.4
(0.6)
A 		26
C 22.4
(2.9)
A 		1.8
(-3)
A 		4.2
(-2.3)
A 		16.9
(1.3)
A 		22.9
(3)
A 		5
(-2.1)
A 		21
avr 23.8
(3) 		11.4
(-0.5) 		2.7
(-3) 		8.2
(-1.4) 		18
(1.4) 		17.1
(1.1) 		21
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 10.9
(3)
A 		4.9
(-3)
A 		7.4
(-0.5)
A 		10.2
(2.3)
A 		6
B 5.6
(1.5)
A 		7.1
(3)
A 		1
(-3)
A 		5.7
(1.6)
A 		6
C 8.9
(2.8)
A 		9.1
(3)
A 		7.7
(1.4)
A 		4
(-3)
A 		5
avr 8.5
(3) 		7
(0.1) 		5.4
(-3) 		6.6
(-0.7) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 11
1 2 3 4 5 6 range
A 6.6
(0.7)
A 		10.6
(3)
A 		0.3
(-3)
A 		1.4
(-2.4)
A 		0.7
(-2.8)
A 		6.8
(0.8)
A 		10
B 4.6
(-0.9)
A 		0.9
(-2.9)
A 		0.7
(-3)
A 		0.7
(-3)
A 		11.7
(3)
A 		6.8
(0.3)
A 		11
C 8.3
(3)
A 		0.6
(-3)
A 		1.1
(-2.6)
A 		3.4
(-0.8)
A 		7.4
(2.3)
A 		1.7
(-2.1)
A 		8
avr 6.5
(2.9) 		4
(0.4) 		0.7
(-3) 		1.8
(-1.9) 		6.6
(3) 		5.1
(1.5) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188002_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.286
Sequence Type Exemplar sequence
Representative Public ID W10C8.2 NCBI
Target Description W10C8.2 /REP_DB=WormBase Gene ID /WP=CE26031 /GEN=pop-1 /TR=O45007 /GB=AAK21504.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=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_058652(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058652 NCBI Caenorhabditis elegans POsterior Pharynx defect family member (pop-1) (pop-1) mRNA, complete cds. 11/11 None
SNAP00000012332 ENSEMBL cdna:SNAP chromosome:CEL140:I:2823469:2830294:-1 11/11 None
GENEFINDER00000012340 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:2823482:2830294:-1 11/11 None
W10C8.2 ENSEMBL cdna:known chromosome:CEL140:I:2823469:2830294:-1 gene:W10C8.2 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:2823468-2830291(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol pop-1
Ensembl W10C8.2
Entrez Gene 171849 Entrez gene
SwissProt Q10666 EMBL-EBI
WormBase CE26031 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1625636_S_AT pangolin dm
DROSGENOME1:151576_S_AT pangolin dm
DROSGENOME1:142459_AT pangolin dm
CHICKEN:GGA.139.1.S1_AT transcription factor 7 (T-cell specific, HMG-box) gga
CHICKEN:GGA.6066.1.S1_AT transcription factor 7 (T-cell specific, HMG-box) gga
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
45944 positive regulation of transcription from RNA polymerase II promoter inferred from direct assay QuickGO AmiGO
6357 regulation of transcription from RNA polymerase II promoter inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
8013 beta-catenin binding inferred from physical interaction QuickGO AmiGO
3702 RNA polymerase II transcription factor activity inferred from direct assay QuickGO AmiGO
3702 RNA polymerase II transcription factor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_491053 POsterior Pharynx defect family member (pop-1) [Caenorhabditis elegans] gb|AAK21504.1| Posterior pharynx defect protein 1 [Caenorhabditis elegans] 0.0
blast Q10666 Pop-1 protein (Posterior pharynx defect protein 1) gb|AAC05308.1| HMG-box protein [Caenorhabditis elegans] 0.0
blast CAE60599 Hypothetical protein CBG04236 [Caenorhabditis briggsae] 1.0E-118
blast CAE60599 Hypothetical protein CBG04236 [Caenorhabditis briggsae] 1.0E-117
Protein Domains
Database ID Description E-Value
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 5.7E-21
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 5.7E-21
Sequence
Target Sequence 
>C. ELEGANS:188002_AT
gaacggtatccggagtggtcggcgcgggaaaattatgcggttaataagaaaaagacgaag
aaacgaagggataagagtattccatcggagaacaacgatcagaagaagtgccgagccaga
ttcggagttaacaacacagaaatgtggtgtaaattctgcaagcggaagaagaagtgcgag
tacgcaactgatcgttcgggcggttccgatataactgacagtcaggatggacgaggtaca
agtggtgcgtatagcagtagctcggagagcccatcaccaaaggcaaacgctggaattgca
ctgaccacacagcagcagcaagcagcaatgatgcatacgatgttgatgcaaatgcgtcta
ggatcgacgacgggagcatcgacgcacgttccatcaccactggcgtcctcgtcggcaggc
aggagtccgctggatgcgaacgcgtcggattcggaatctgatgttgaggaggaggaagac
gagcagattgatccgacggttatgcagcagacac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAACGGTATCCGGAGTGGTCGGCGC 44 349 775 Antisense
GAAGTGCCGAGCCAGATTCGGAGTT 55 337 879 Antisense
GTACGCAACTGATCGTTCGGGCGGT 295 457 954 Antisense
CGGGCGGTTCCGATATAACTGACAG 150 241 971 Antisense
GTGGTGCGTATAGCAGTAGCTCGGA 158 489 1016 Antisense
CTCGGAGAGCCCATCACCAAAGGCA 227 233 1035 Antisense
TGGAATTGCACTGACCACACAGCAG 200 547 1065 Antisense
GGATCGACGACGGGAGCATCGACGC 681 505 1135 Antisense
GCAGGAGTCCGCTGGATGCGAACGC 199 311 1193 Antisense
GATGCGAACGCGTCGGATTCGGAAT 205 415 1207 Antisense
GATCCGACGGTTATGCAGCAGACAC 265 417 1264 Antisense
Sequence Source Affymetrix Proprietary Database