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[179991_s_at]

Description F31A3.4 /REP_DB=WormBase Gene ID /WP=CE07161 /TR=Q19917 /GB=AAB36858.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_total > 54      4grp_total > 0      6grp_cgc > 65      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 5.1
(-2.5)
A 		2.2
(-3)
A 		35
(3)
A 		33.4
(2.7)
A 		33
B 9.1
(-1)
A 		5.2
(-2.4)
A 		20.1
(3)
A 		3.5
(-3)
A 		17
C 23.5
(-1.5)
A 		3.8
(-3)
A 		3.7
(-3)
A 		85.4
(3)
P 		82
avr 12.6
(-1.6) 		3.7
(-3) 		19.6
(-0.4) 		40.8
(3) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 2
(-3)
A 		4.8
(-2.2)
A 		21.4
(2.4)
A 		3.6
(-2.6)
A 		23.6
(3)
A 		3
(-2.7)
A 		22
B 3.6
(-0.9)
A 		4.1
(-0.4)
A 		8
(3)
A 		1.2
(-3)
A 		4.3
(-0.3)
A 		6.4
(1.6)
A 		7
C 3.6
(-3)
A 		13.8
(0.9)
A 		4.8
(-2.5)
A 		5.4
(-2.3)
A 		5.8
(-2.1)
A 		19.1
(3)
A 		16
avr 3.1
(-3) 		7.6
(0.3) 		11.4
(3) 		3.4
(-2.8) 		11.2
(2.9) 		9.5
(1.6) 		8
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 1.8
(-2.1)
A 		0.5
(-3)
A 		9.2
(3)
A 		4.9
(0)
A 		9
B 2.9
(0.3)
A 		1.3
(-2.2)
A 		4.6
(3)
A 		0.8
(-3)
A 		4
C 7.8
(0)
A 		1.1
(-3)
A 		1.3
(-2.9)
A 		14.4
(3)
P 		13
avr 4.2
(0.4) 		1
(-3) 		5
(1.2) 		6.7
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7
1 2 3 4 5 6 range
A 0.4
(-3)
A 		1.7
(-1.8)
A 		4.7
(0.9)
A 		0.9
(-2.6)
A 		7.1
(3)
A 		0.7
(-2.7)
A 		7
B 1.2
(-0.4)
A 		1.4
(0.1)
A 		1.9
(1.6)
A 		0.3
(-3)
A 		1.7
(1)
A 		2.4
(3)
A 		2
C 1.4
(-2.7)
A 		4.2
(0.5)
A 		1.2
(-2.9)
A 		1.1
(-3)
A 		1.9
(-2.1)
A 		6.4
(3)
A 		5
avr 1
(-2.6) 		2.4
(0.4) 		2.6
(0.9) 		0.8
(-3) 		3.6
(3) 		3.2
(2.1) 		3
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 179991_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17660
Sequence Type Exemplar sequence
Representative Public ID F31A3.4 NCBI
Target Description F31A3.4 /REP_DB=WormBase Gene ID /WP=CE07161 /TR=Q19917 /GB=AAB36858.1 /SUBMIT=ST.LOUIS /CHR=X /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_078437(11), NM_078436(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078437 NCBI Caenorhabditis elegans Helix Loop Helix family member (hlh-28) (hlh-28) mRNA, complete cds. 11/11 None
NM_078436 NCBI Caenorhabditis elegans Helix Loop Helix family member (hlh-29) (hlh-29) mRNA, complete cds. 11/11 None
SNAP00000018622 ENSEMBL cdna:SNAP chromosome:CEL140:X:17547727:17548547:-1 11/11 None
GENEFINDER00000018630 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:17547727:17548547:-1 11/11 None
SNAP00000018623 ENSEMBL cdna:SNAP chromosome:CEL140:X:17550967:17551787:1 11/11 None
GENEFINDER00000018626 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:17550967:17551787:1 11/11 None
F31A3.4 ENSEMBL cdna:known chromosome:CEL140:X:17547727:17548547:-1 gene:F31A3.4 11/11 None
F31A3.2 ENSEMBL cdna:known chromosome:CEL140:X:17549634:17551787:1 gene:F31A3.2 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
chrX:17550965-17551786(+) 99.58 99.58
chrX:17547725-17548546(-) 100.0 100.0
Public Domain and Genome References
Gene Title

Gene Symbol hlh-28
hlh-29
Ensembl F31A3.4
F31A3.2
Entrez Gene 185134 Entrez gene
185136 Entrez gene
SwissProt Q19918 EMBL-EBI
Q19917 EMBL-EBI
WormBase CE07159 Wormbase
CE07161 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB36855 Helix loop helix protein 28 [Caenorhabditis elegans] ref|NP_510838.1| Helix Loop Helix family member (hlh-28) [Caenorhabditis elegans] 1.0E-147
blast AAB36858 Helix loop helix protein 29 [Caenorhabditis elegans] ref|NP_510837.1| Helix Loop Helix family member (hlh-29) [Caenorhabditis elegans] 1.0E-133
blast AAB36855 Helix loop helix protein 28 [Caenorhabditis elegans] ref|NP_510838.1| Helix Loop Helix family member (hlh-28) [Caenorhabditis elegans] 1.0E-133
blast AAB36858 Helix loop helix protein 29 [Caenorhabditis elegans] ref|NP_510837.1| Helix Loop Helix family member (hlh-29) [Caenorhabditis elegans] 1.0E-132
blast AAB36855 Helix loop helix protein 28 [Caenorhabditis elegans] ref|NP_510838.1| Helix Loop Helix family member (hlh-28) [Caenorhabditis elegans] 1.0E-132
Protein Domains
Database ID Description E-Value
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 5.6E-9
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 5.6E-9
Sequence
Target Sequence 
>C. ELEGANS:179991_S_AT
aattgtgcaaaatccttctgacagcaatgagaagatttcacacgaaactattctattccg
tgtgtttgaacgggtttctggagttgatttggaaacaaaattcaactcaaccgttgatat
ccctaaagctgagggaaatacaaaagaggagaagcagaaagtgaagacaaaaagagaaca
aatcagaagaagtaagcaagatatctgttacaccgaacttggaaatttcgttcacaaaaa
ccgacttggcaatactgagcaaaggaacaaattggaacgcgtaacagttttgcaaataat
tctcgaatacatctgtcaaatgccagaacaatcagaagcaatagaaaaggaaaactcacc
gatgtaccaagtgtatctagaaccaactaaatgtatttctccagaacaatccgtcgcttc
tcccagccctttccttctttcaaacacgttggcattcttcaatcaggttgcacagctcca
ttttatcgcgaaacttcaagctatgctcccaccgacgccagttcaaacaccagaagcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATTGTGCAAAATCCTTCTGACAGC 435 179 144 Antisense
ACGAAACTATTCTATTCCGTGTGTT 527 91 185 Antisense
TCAACCGTTGATATCCCTAAAGCTG 485 629 250 Antisense
AGATATCTGTTACACCGAACTTGGA 604 63 342 Antisense
AAAACCGACTTGGCAATACTGAGCA 305 129 380 Antisense
ATAATTCTCGAATACATCTGTCAAA 681 25 439 Antisense
AACACGTTGGCATTCTTCAATCAGG 616 135 586 Antisense
CTTCAATCAGGTTGCACAGCTCCAT 356 221 600 Antisense
ACAGCTCCATTTTATCGCGAAACTT 102 109 615 Antisense
GCGAAACTTCAAGCTATGCTCCCAC 395 289 631 Antisense
GACGCCAGTTCAAACACCAGAAGCC 128 381 657 Antisense
Sequence Source Affymetrix Proprietary Database