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[183997_at]

Description C40D2.4 /REP_DB=WormBase Gene ID /WP=CE19376 /TR=O76560 /GB=AAC26267.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_total > 94      4grp_total > 21      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 57
1 2 3 4 range
A 36.3
(0.4)
A 		28.9
(-0.4)
A 		6.1
(-3)
A 		58.9
(3)
A 		53
B 41.4
(3)
A 		34.1
(1.5)
A 		12.5
(-3)
A 		24.7
(-0.5)
A 		29
C 17.4
(-1)
A 		1.8
(-3)
A 		6.3
(-2.4)
A 		49.7
(3)
A 		48
avr 31.7
(0.9) 		21.6
(-0.8) 		8.3
(-3) 		44.4
(3) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 38
1 2 3 4 5 6 range
A 4.5
(-2.7)
A 		2.6
(-3)
A 		8.4
(-2)
A 		25.6
(0.8)
A 		29.1
(1.3)
A 		39.2
(3)
A 		37
B 2.4
(-2.6)
A 		22.8
(2.5)
A 		2.9
(-2.5)
A 		2.7
(-2.5)
A 		24.7
(3)
A 		0.8
(-3)
A 		24
C 2.6
(-2.8)
A 		8.9
(2.2)
A 		9.9
(3)
A 		3
(-2.4)
A 		2.3
(-3)
A 		5
(-0.9)
A 		8
avr 3.2
(-3) 		11.4
(0.2) 		7.1
(-1.5) 		10.4
(-0.2) 		18.7
(3) 		15
(1.6) 		16
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 13.2
(3)
A 		6.3
(-0.6)
A 		1.6
(-3)
A 		8.6
(0.6)
A 		12
B 13.2
(3)
A 		8.4
(0.2)
A 		2.9
(-3)
A 		5.3
(-1.6)
A 		10
C 5.7
(0.9)
A 		0.5
(-3)
A 		2.2
(-1.7)
A 		8.4
(3)
A 		8
avr 10.7
(3) 		5.1
(-1) 		2.2
(-3) 		7.4
(0.7) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10
1 2 3 4 5 6 range
A 0.8
(-3)
A 		0.9
(-2.9)
A 		1.8
(-2.3)
A 		6.5
(0.9)
A 		8.8
(2.5)
A 		9.6
(3)
A 		9
B 0.8
(-2.7)
A 		7.6
(1.5)
A 		0.7
(-2.8)
A 		0.7
(-2.8)
A 		10
(3)
A 		0.3
(-3)
A 		10
C 1
(-1.9)
A 		2.7
(3)
A 		2.5
(2.4)
A 		0.6
(-3)
A 		0.7
(-2.7)
A 		1.7
(0.1)
A 		2
avr 0.9
(-3) 		3.7
(0) 		1.7
(-2.1) 		2.6
(-1.2) 		6.5
(3) 		3.9
(0.2) 		6
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 183997_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4765
Sequence Type Exemplar sequence
Representative Public ID C40D2.4 NCBI
Target Description C40D2.4 /REP_DB=WormBase Gene ID /WP=CE19376 /TR=O76560 /GB=AAC26267.1 /SUBMIT=ST.LOUIS /CHR=2 /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_061747(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061747 NCBI Caenorhabditis elegans C40D2.4 (C40D2.4) mRNA, complete cds. 11/11 None
SNAP00000024879 ENSEMBL cdna:SNAP chromosome:CEL140:II:1999910:2000821:-1 11/11 None
GENEFINDER00000024882 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:1999910:2002090:-1 9/11 None
C40D2.4 ENSEMBL cdna:known chromosome:CEL140:II:1999910:2000821:-1 gene:C40D2.4 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
chrII:1999908-2000820(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl C40D2.4
Entrez Gene 183364 Entrez gene
SwissProt O76560 EMBL-EBI
WormBase CE19376 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC26267 Hypothetical protein C40D2.4 [Caenorhabditis elegans] ref|NP_494148.1| C40D2.4 [Caenorhabditis elegans] 3.0E-80
blast AAC26267 Hypothetical protein C40D2.4 [Caenorhabditis elegans] ref|NP_494148.1| C40D2.4 [Caenorhabditis elegans] 2.0E-70
blast T19192 hypothetical protein C11E4.5 - Caenorhabditis elegans 4.0E-14
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999987368938E-6
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.0439999997615814
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.0160000007599592
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.0219999998807907
Pfam IPR001356 EMBL-EBI Homeobox 0.0010
Pfam IPR001356 EMBL-EBI Homeobox 0.85
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 1.5E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000024882 3 57-79,92-114,124-146
Sequence
Target Sequence 
>C. ELEGANS:183997_AT
gtagatcactcacttattcttctttattcactttcagcatttgaggagagcaaatatatc
agcagcgaggagcagatgcaaatatcggaatacattaatgtggacgataaaattattcag
agatggtttgaaatccgccgagcaccaacacaggagagctgggaaccagaagtaatttta
ccggaagcgattgcaattttcgagaaagaattcactacaaacccgaatccttgtagtcac
actttggaggaacttcggatgaagactcacgtacaagtagattcgatcaacaaatggttc
gatgaacgtcgatgtgctgccgaacagaatattaaatctgattcggaaggttcggaagcc
agtttctcgttgtgcagctcctggggtgatact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAGATCACTCACTTATTCTTCTTT 187 457 28 Antisense
ATTCTTCTTTATTCACTTTCAGCAT 527 11 43 Antisense
AGATGGTTTGAAATCCGCCGAGCAC 368 65 148 Antisense
CGCCGAGCACCAACACAGGAGAGCT 666 255 163 Antisense
GTAATTTTACCGGAAGCGATTGCAA 245 463 199 Antisense
GAATTCACTACAAACCCGAATCCTT 83 325 235 Antisense
ACCCGAATCCTTGTAGTCACACTTT 193 89 248 Antisense
ACTTCGGATGAAGACTCACGTACAA 467 103 279 Antisense
GATGAACGTCGATGTGCTGCCGAAC 177 413 328 Antisense
GGAAGGTTCGGAAGCCAGTTTCTCG 191 533 372 Antisense
GTTGTGCAGCTCCTGGGGTGATACT 476 437 396 Antisense
Sequence Source Affymetrix Proprietary Database