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[192331_at] Helix-loop-helix DNA-binding domain

Description DY3.3 /REP_DB=WormBase Gene ID /WP=CE15747 /TR=O45320 /GB=CAB09412.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain
Cluster 6grp_total > 38      4grp_total > 0      6grp_cgc > 18      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 69
1 2 3 4 range
A 15.1
(-2.2)
A 		6.5
(-3)
A 		40.4
(-0)
A 		74.8
(3)
A 		68
B 24.8
(0.2)
A 		23.3
(-0.1)
A 		11.2
(-3)
A 		36.6
(3)
A 		25
C 5.6
(-3)
A 		7.4
(-2.7)
A 		37.1
(1.9)
A 		44
(3)
A 		38
avr 15.2
(-2.6) 		12.4
(-3) 		29.6
(-0.4) 		51.8
(3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 47
1 2 3 4 5 6 range
A 5
(-3)
A 		12.4
(-1.8)
A 		30.6
(1.3)
A 		15.6
(-1.2)
A 		40.8
(3)
A 		19.6
(-0.6)
A 		36
B 33.6
(1.2)
A 		26.9
(0.3)
A 		4.1
(-3)
A 		9.5
(-2.2)
A 		12.4
(-1.8)
A 		45.8
(3)
A 		42
C 44
(2.1)
A 		51.2
(3)
A 		5.2
(-2.9)
A 		4.6
(-3)
A 		5.7
(-2.9)
A 		18.6
(-1.2)
A 		47
avr 27.5
(2.2) 		30.2
(3) 		13.3
(-2) 		9.9
(-3) 		19.6
(-0.1) 		28
(2.3) 		20
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 5.5
(-0.4)
A 		1.4
(-3)
A 		10.6
(2.8)
A 		10.9
(3)
A 		10
B 7.9
(3)
A 		5.7
(0.5)
A 		2.6
(-3)
A 		7.8
(2.9)
A 		5
C 1.8
(-3)
A 		2.1
(-2.8)
A 		12.9
(3)
A 		7.4
(0)
A 		11
avr 5.1
(-0.9) 		3.1
(-3) 		8.7
(3) 		8.7
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 16
1 2 3 4 5 6 range
A 0.9
(-3)
A 		4.4
(-1.2)
A 		6.7
(0.1)
A 		4
(-1.4)
A 		12.3
(3)
A 		4.8
(-0.9)
A 		11
B 11.7
(1)
A 		9
(-0)
A 		1
(-3)
A 		2.5
(-2.4)
A 		5
(-1.5)
A 		17.1
(3)
A 		16
C 16.3
(3)
A 		15.6
(2.7)
A 		1.3
(-2.8)
A 		0.9
(-3)
A 		1.8
(-2.6)
A 		6.2
(-0.9)
A 		15
avr 9.6
(2.9) 		9.7
(3) 		3
(-2.6) 		2.5
(-3) 		6.4
(0.3) 		9.4
(2.8) 		7
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192331_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.902
Sequence Type Exemplar sequence
Representative Public ID DY3.3 NCBI
Target Description DY3.3 /REP_DB=WormBase Gene ID /WP=CE15747 /TR=O45320 /GB=CAB09412.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain
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_059971(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059971 NCBI Caenorhabditis elegans Helix Loop Helix family member (hlh-16) (hlh-16) mRNA, complete cds. 11/11 None
SNAP00000022834 ENSEMBL cdna:SNAP chromosome:CEL140:I:8775152:8776155:-1 9/11 None
GENEFINDER00000022848 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8775152:8776155:-1 9/11 None
DY3.3 ENSEMBL cdna:known chromosome:CEL140:I:8774796:8776131:-1 gene:DY3.3 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:8774726-8776062(-) 100.0 100.0
Public Domain and Genome References
Gene Title Helix-loop-helix DNA-binding domain
Gene Symbol hlh-16
Ensembl DY3.3
Entrez Gene 183973 Entrez gene
SwissProt O45320 EMBL-EBI
WormBase CE15747 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB09412 Hypothetical protein DY3.3 [Caenorhabditis elegans] ref|NP_492372.1| Helix Loop Helix family member (hlh-16) [Caenorhabditis elegans] 1.0E-108
blast CAB09412 Hypothetical protein DY3.3 [Caenorhabditis elegans] ref|NP_492372.1| Helix Loop Helix family member (hlh-16) [Caenorhabditis elegans] 4.0E-73
blast CAE66969 Hypothetical protein CBG12364 [Caenorhabditis briggsae] 1.0E-68
blast CAE66969 Hypothetical protein CBG12364 [Caenorhabditis briggsae] 3.0E-62
blast XP_585626 PREDICTED: similar to basic helix-loop-helix domain containing, class B, 4 [Bos taurus] 1.0E-12
Protein Domains
Database ID Description E-Value
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 1.8E-16
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 1.8E-16
Sequence
Target Sequence 
>C. ELEGANS:192331_AT
tcaccgcctggagccgaggaagaattcgagccatatgtgagaagaaaacgatcggaagca
ggaggccggaagaaaatgcaaggcttgaatgagcaagaacaaaatctgttgagaaactca
attaacagtcgagaacgtcgtcgaatgcacgagttgaacgatgaattcgagactctacgt
gaatgtcttccttatccgaatgaagcgaacagtcgacgaatgagcaaagcgaatacattg
ttactagcttccaattggattaagcaacttgcaaatgcaaatcacaagcttcaaatggaa
ttaaacatggcaaatgcaaagatcgactccctcatggtgcaacttaaaaaagtggaaaaa
ccatcttcaaaatgctcaaagtgtcaacaaaactttctattttttattaaattaagaaat
ttgaataaaatctgttttgggtacattattgaacgaagttttcggaaaatcgtcttacaa
gtagctaacagagatatgaaaaattcattactctatcttaaactctatcatattttgaaa
atttgcactttctgcagttgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCACCGCCTGGAGCCGAGGAAGAAT 615 625 25 Antisense
GGAAGAATTCGAGCCATATGTGAGA 476 531 42 Antisense
AACGTCGTCGAATGCACGAGTTGAA 14 125 158 Antisense
GAATTCGAGACTCTACGTGAATGTC 44 323 187 Antisense
ACGTGAATGTCTTCCTTATCCGAAT 60 95 201 Antisense
GCGAATACATTGTTACTAGCTTCCA 87 289 253 Antisense
GCAAATGCAAAGATCGACTCCCTCA 90 319 334 Antisense
GACTCCCTCATGGTGCAACTTAAAA 173 375 349 Antisense
GAAAAACCATCTTCAAAATGCTCAA 422 355 379 Antisense
ATTACTCTATCTTAAACTCTATCAT 368 13 531 Antisense
GAAAATTTGCACTTTCTGCAGTTGT 386 353 561 Antisense
Sequence Source Affymetrix Proprietary Database