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[193898_at] Helix-loop-helix DNA-binding domain (2 domains)

Description T01E8.2 /REP_DB=WormBase Gene ID /WP=CE02306 /GEN=ref-1 /TR=Q22069 /GB=CAA88744.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Helix-loop-helix DNA-binding domain (2 domains)
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 76      4grp_high_8_8 > 45      6grp_highest_nonorm > 90      6grp_total > 67      4grp_total > 50      6grp_highest_sub > Da      6grp_cgc > 48      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 116
1 2 3 4 range
A 77.9
(-1.4)
P 		130.2
(2.3)
P 		140.7
(3)
P 		55.5
(-3)
A 		85
B 86
(-1.2)
P 		168.2
(3)
P 		156
(2.4)
P 		52.1
(-3)
P 		116
C 83.7
(-3)
P 		165
(3)
P 		138.6
(1.1)
P 		88.9
(-2.6)
P 		81
avr 82.5
(-1.9) 		154.5
(3) 		145.1
(2.4) 		65.5
(-3) 		89

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 103
1 2 3 4 5 6 range
A 145.1
(-0.3)
P 		113.1
(-3)
P 		115.3
(-2.8)
P 		140.3
(-0.7)
P 		116.3
(-2.7)
P 		184.4
(3)
P 		71
B 106.1
(-2.4)
P 		114.4
(-1.5)
P 		100.6
(-3)
P 		120.4
(-0.8)
P 		121.1
(-0.8)
P 		155.6
(3)
P 		55
C 81.9
(-3)
P 		157.2
(2.8)
P 		103.4
(-1.3)
P 		104.7
(-1.2)
P 		115.7
(-0.4)
P 		159.2
(3)
P 		77
avr 111
(-2.5) 		128.2
(-0.8) 		106.4
(-3) 		121.8
(-1.5) 		117.7
(-1.9) 		166.4
(3) 		60
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 28.4
(1.2)
P 		28.3
(1.2)
P 		36.8
(3)
P 		8.1
(-3)
A 		29
B 27.4
(0.2)
P 		41.5
(3)
P 		36.2
(2)
P 		11.1
(-3)
P 		30
C 27.7
(-0.7)
P 		47.4
(2.8)
P 		48.3
(3)
P 		15
(-3)
P 		33
avr 27.8
(0.4) 		39.1
(2.7) 		40.4
(3) 		11.4
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 37
1 2 3 4 5 6 range
A 26.7
(-2.5)
P 		40.2
(1.6)
P 		25.1
(-3)
P 		35.6
(0.2)
P 		35.1
(0)
P 		44.9
(3)
P 		20
B 36.9
(-0.8)
P 		38.1
(-0.6)
P 		24.4
(-3)
P 		31.9
(-1.7)
P 		49.2
(1.4)
P 		58
(3)
P 		34
C 30.3
(-1.3)
P 		48
(2)
P 		26.3
(-2)
P 		21
(-3)
P 		37.4
(0)
P 		53.3
(3)
P 		32
avr 31.3
(-1.7) 		42.1
(0.8) 		25.3
(-3) 		29.5
(-2.1) 		40.6
(0.4) 		52.1
(3) 		27
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193898_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3397
Sequence Type Exemplar sequence
Representative Public ID T01E8.2 NCBI
Target Description T01E8.2 /REP_DB=WormBase Gene ID /WP=CE02306 /GEN=ref-1 /TR=Q22069 /GB=CAA88744.1 /SUBMIT=HINXTON /CHR=2 /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_063803(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063803 NCBI Caenorhabditis elegans REgulator of Fusion family member (ref-1) (ref-1) mRNA, complete cds. 11/11 None
SNAP00000042898 ENSEMBL cdna:SNAP chromosome:CEL140:II:10218383:10219646:1 11/11 None
GENEFINDER00000042914 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10218383:10219646:1 11/11 None
T01E8.2 ENSEMBL cdna:known chromosome:CEL140:II:10218381:10219935:1 gene:T01E8.2 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
chrII:10218379-10219643(+) 100.0 100.0
Public Domain and Genome References
Gene Title Helix-loop-helix DNA-binding domain (2 domains)
Gene Symbol ref-1
Ensembl T01E8.2
Entrez Gene 174585 Entrez gene
SwissProt Q22069 EMBL-EBI
WormBase CE02306 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA88744 Hypothetical protein T01E8.2 [Caenorhabditis elegans] ref|NP_496204.1| REgulator of Fusion family member (ref-1) [Caenorhabditis elegans] gb|AAK52772.1| REF-1 [Caenorhabditis elegans] 1.0E-145
blast CAE57858 Hypothetical protein CBG00896 [Caenorhabditis briggsae] 1.0E-111
blast CAE65517 Hypothetical protein CBG10491 [Caenorhabditis briggsae] 1.0E-15
Protein Domains
Database ID Description E-Value
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 1.8E-10
Pfam IPR001092 EMBL-EBI Basic helix-loop-helix dimerization domain bHLH 5.4E-4
Sequence
Target Sequence 
>C. ELEGANS:193898_AT
aacgcttgaacaccctggatatcataattgcctacattcaaaacaagaagcacaattttg
ttagtcgaagcgaccaggagcagtcactctatgcacatgcaattgcagagggaaagaaga
ctgcaaaaaacattgccttccaatttttcaagagcgaccgtcacctcgttgtccgatgcg
cagaccttgaaaagttcttcgaattctccttatcaccaaagccactctttggattcccat
ccatgcccatcccaattccaccaccatcattcccaatcttcccattccggccattcccat
tcttcccaatgccaatggcaccaatggcaacaagtccaaaatctcaacagtctccatcat
attcactggattctccaccaccatcatccgatacttcttcgtcatcaatcgaaacaccat
ccactccaaatgagaactcgaattccaatcctaaagct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACGCTTGAACACCCTGGATATCAT 642 145 623 Antisense
GGAGCAGTCACTCTATGCACATGCA 646 519 699 Antisense
ATTTTTCAAGAGCGACCGTCACCTC 125 13 765 Antisense
TTGTCCGATGCGCAGACCTTGAAAA 183 709 791 Antisense
TCGAATTCTCCTTATCACCAAAGCC 415 601 821 Antisense
CAAAGCCACTCTTTGGATTCCCATC 153 193 839 Antisense
TTCCCATTCTTCCCAATGCCAATGG 357 697 916 Antisense
ATCTCAACAGTCTCCATCATATTCA 236 33 963 Antisense
TCATATTCACTGGATTCTCCACCAC 124 621 979 Antisense
CATCATCCGATACTTCTTCGTCATC 547 213 1004 Antisense
GAACTCGAATTCCAATCCTAAAGCT 465 349 1056 Antisense
Sequence Source Affymetrix Proprietary Database