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[172921_x_at]

Description F38C2.2 /REP_DB=WormBase Gene ID /WP=CE16002 /TR=O45489 /GB=CAB05189.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain (2 domains)
Cluster 6grp_total > 11      4grp_total > 02      6grp_cgc > 44      6grp_cgc_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 563
1 2 3 4 range
A 42.1
(-2.8)
A 		69.5
(-2.4)
A 		25.9
(-3)
A 		434.6
(3)
P 		409
B 48.1
(-2.8)
A 		57.7
(-2.7)
A 		38.5
(-3)
A 		378.4
(3)
P 		340
C 14
(-3)
A 		36.1
(-2.8)
A 		40.2
(-2.7)
A 		577.4
(3)
P 		563
avr 34.7
(-3) 		54.4
(-2.7) 		34.9
(-3) 		463.5
(3) 		429

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 82
1 2 3 4 5 6 range
A 67.2
(2.1)
A 		66.4
(2)
A 		78.6
(3)
P 		8.8
(-2.8)
A 		34.2
(-0.7)
A 		6.2
(-3)
A 		72
B 34.5
(-0.8)
A 		86.3
(3)
A 		63
(1.3)
A 		4.7
(-3)
A 		48.3
(0.2)
A 		11.5
(-2.5)
A 		82
C 45.5
(-0.9)
A 		75.9
(3)
A 		54.1
(0.2)
A 		38.6
(-1.8)
A 		28.8
(-3)
A 		32.5
(-2.5)
A 		47
avr 49.1
(0.3) 		76.2
(3) 		65.2
(1.9) 		17.4
(-2.9) 		37.1
(-0.9) 		16.7
(-3) 		60
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 93
1 2 3 4 range
A 15.3
(-2.1)
A 		15.1
(-2.1)
A 		6.8
(-3)
A 		63.6
(3)
P 		57
B 15.3
(-2.5)
A 		14.2
(-2.6)
A 		8.9
(-3)
A 		80.6
(3)
P 		72
C 4.6
(-3)
A 		10.4
(-2.6)
A 		14
(-2.4)
A 		97.4
(3)
P 		93
avr 11.7
(-2.8) 		13.2
(-2.7) 		9.9
(-3) 		80.5
(3) 		71

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27
1 2 3 4 5 6 range
A 12.4
(-0)
A 		23.6
(3)
A 		17.1
(1.2)
P 		2.2
(-2.8)
A 		10.3
(-0.6)
A 		1.5
(-3)
A 		22
B 12
(-0.7)
A 		28.7
(3)
A 		15.3
(0.1)
A 		1.3
(-3)
A 		19.6
(1)
A 		4.3
(-2.3)
A 		27
C 16.9
(0.5)
A 		23.2
(3)
A 		13.8
(-0.7)
A 		7.8
(-3)
A 		9.3
(-2.4)
A 		10.9
(-1.8)
A 		15
avr 13.8
(-0.2) 		25.2
(3) 		15.4
(0.3) 		3.8
(-3) 		13.1
(-0.4) 		5.6
(-2.5) 		21
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172921_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9971
Sequence Type Exemplar sequence
Representative Public ID F38C2.2 NCBI
Target Description F38C2.2 /REP_DB=WormBase Gene ID /WP=CE16002 /TR=O45489 /GB=CAB05189.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain (2 domains)
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 identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001028022(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028022 NCBI Caenorhabditis elegans F38C2.8 (F38C2.8) mRNA, complete cds. 10/11 None
SNAP00000039184 ENSEMBL cdna:SNAP chromosome:CEL140:IV:16257629:16259378:1 10/11 None
F38C2.8 ENSEMBL cdna:known chromosome:CEL140:IV:16257629:16259019:1 gene:F38C2.8 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_070527 6/11 Cross Hyb Matching Probes None
NM_001028259 3/11 Cross Hyb Matching Probes None
SNAP00000018411 3/11 Cross Hyb Matching Probes None
SNAP00000039183 6/11 Cross Hyb Matching Probes None
GENEFINDER00000039191 6/11 Cross Hyb Matching Probes None
GENEFINDER00000039195 6/11 Cross Hyb Matching Probes None
Y105C5B.29 3/11 Cross Hyb Matching Probes None
F38C2.2 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:16254741-16259025(+) 98.71 100.0
Public Domain and Genome References
Gene Title
Ensembl F38C2.8
Entrez Gene 3565632 Entrez gene
SwissProt Q86D08 EMBL-EBI
WormBase CE33779 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAD89743 Hypothetical protein F38C2.8 [Caenorhabditis elegans] ref|NP_001023193.1| F38C2.8 [Caenorhabditis elegans] 8.0E-67
blast CAD89743 Hypothetical protein F38C2.8 [Caenorhabditis elegans] ref|NP_001023193.1| F38C2.8 [Caenorhabditis elegans] 5.0E-49
blast CAB05189 Hypothetical protein F38C2.2 [Caenorhabditis elegans] ref|NP_502928.2| Helix Loop Helix family member (hlh-17) [Caenorhabditis elegans] 7.0E-30
blast CAE17962 Hypothetical protein Y105C5B.29 [Caenorhabditis elegans] ref|NP_001023430.1| Y105C5B.29 [Caenorhabditis elegans] 6.0E-26
blast CAB05190 Hypothetical protein F38C2.4 [Caenorhabditis elegans] ref|NP_502929.1| F38C2.4 [Caenorhabditis elegans] 3.0E-22
blast CAB05189 Hypothetical protein F38C2.2 [Caenorhabditis elegans] ref|NP_502928.2| Helix Loop Helix family member (hlh-17) [Caenorhabditis elegans] 6.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 2.0E-10
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 1.0E-10
Sequence
Target Sequence 
>C. ELEGANS:172921_X_AT
acgaggcacttgacgatctgcgagctgtaattccatatgctcacgggggttccgtgagga
agttgagcaagattgctacgttgcttttggccaaaaatcatattatcatgcagatgaaca
actacaaaatgagaattgaagatcaaaaagtacaaataactgaaattcttcaaatcttta
tgtctgcccgcgaaaatgattctggaaaatggaaagattgcggattagatatgatacgca
acaagataaatgagaaatatatggcccaatcagggcttggatctcaagttaaattgtccg
gtttattgagtaaggacggcaagctgtcgagtcggaaaatgaaatcgtcaaagctcttga
aaagatgccgaatgcatgacttaaacgaggcacttgacgatctgcgagctgtaattccat
atgctcacgggggttccgtgaggaagttgagcaagattgctacgttgcttttggctaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGAGGCACTTGACGATCTGCGAGC 43 95 200 Antisense
GTAATTCCATATGCTCACGGGGGTT 388 463 226 Antisense
AAGATTGCTACGTTGCTTTTGGCCA 38 157 268 Antisense
TCTTCAAATCTTTATGTCTGCCCGC 145 617 366 Antisense
GTCTGCCCGCGAAAATGATTCTGGA 493 471 381 Antisense
ATGGCCCAATCAGGGCTTGGATCTC 562 53 460 Antisense
TAAGGACGGCAAGCTGTCGAGTCGG 107 635 510 Antisense
AACGAGGCACTTGACGATCTGCGAG 355 145 583 Antisense
GATCTGCGAGCTGTAATTCCATATG 268 419 598 Antisense
TAATTCCATATGCTCACGGGGGTTC 181 575 611 Antisense
AGATTGCTACGTTGCTTTTGGCTAA 445 65 653 Antisense
Sequence Source Affymetrix Proprietary Database