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[189952_at]

Description R08B4.1 /REP_DB=WormBase Gene ID /WP=CE28245 /GEN=grd-1 /TR=Q21835 /GB=CAA92000.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=groundhog
Cluster 6grp_high1_10_10 > 80      6grp_total > 82      4grp_total > 49      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 421
1 2 3 4 range
A 10.2
(-3)
A 		318
(2.4)
P 		351.6
(3)
P 		10.6
(-3)
A 		341
B 73.1
(-2.5)
A 		347.5
(2.7)
P 		361.1
(3)
P 		45.2
(-3)
A 		316
C 37.5
(-3)
A 		431.5
(3)
P 		414.6
(2.7)
P 		45
(-2.9)
P 		394
avr 40.3
(-2.9) 		365.7
(2.8) 		375.8
(3) 		33.6
(-3) 		342

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 275
1 2 3 4 5 6 range
A 100.1
(-3)
A 		331.1
(3)
P 		240.9
(0.7)
P 		295.7
(2.1)
P 		246.3
(0.8)
P 		132.3
(-2.2)
P 		231
B 142.8
(-0.8)
P 		281.2
(2.7)
P 		292.8
(2.9)
P 		295.1
(3)
P 		231.1
(1.4)
P 		55.9
(-3)
P 		239
C 57.7
(-3)
P 		273.4
(2.1)
P 		288.5
(2.4)
P 		299.6
(2.7)
P 		312.7
(3)
P 		71.2
(-2.7)
P 		255
avr 100.2
(-2.6) 		295.2
(3) 		274.1
(2.4) 		296.8
(3) 		263.4
(2) 		86.5
(-3) 		210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 143
1 2 3 4 range
A 3.7
(-2.9)
A 		69
(1.5)
P 		91.9
(3)
P 		1.5
(-3)
A 		90
B 23.3
(-1.9)
A 		85.8
(3)
P 		83.7
(2.8)
P 		9.6
(-3)
A 		76
C 12.4
(-2.8)
A 		124
(2.1)
P 		144.5
(3)
P 		7.6
(-3)
P 		137
avr 13.1
(-2.6) 		92.9
(2.2) 		106.7
(3) 		6.2
(-3) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 99
1 2 3 4 5 6 range
A 18.4
(-3)
A 		117.7
(3)
P 		52.5
(-0.9)
P 		75
(0.4)
P 		74.3
(0.4)
P 		32.2
(-2.2)
P 		99
B 49.7
(-0.6)
P 		93.6
(3)
P 		71.1
(1.1)
P 		78.2
(1.7)
P 		93.9
(3)
P 		20.8
(-3)
P 		73
C 21.4
(-3)
P 		83.4
(1.7)
P 		73.4
(0.9)
P 		60.3
(-0.1)
P 		101.2
(3)
P 		23.8
(-2.8)
P 		80
avr 29.8
(-2.7) 		98.2
(3) 		65.7
(0.3) 		71.2
(0.8) 		89.8
(2.3) 		25.6
(-3) 		73
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189952_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16391
Sequence Type Exemplar sequence
Representative Public ID R08B4.1 NCBI
Target Description R08B4.1 /REP_DB=WormBase Gene ID /WP=CE28245 /GEN=grd-1 /TR=Q21835 /GB=CAA92000.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=groundhog
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_001029673(11), NM_001029672(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029673 NCBI Caenorhabditis elegans R08B4.1b (groundhog) mRNA, complete cds. 11/11 None
NM_001029672 NCBI Caenorhabditis elegans R08B4.1a (groundhog) mRNA, complete cds. 11/11 None
GENEFINDER00000019873 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11108833:11115592:1 11/11 None
SNAP00000019866 ENSEMBL cdna:SNAP chromosome:CEL140:X:11111672:11115592:1 11/11 None
R08B4.1a ENSEMBL cdna:known chromosome:CEL140:X:11109548:11115649:1 gene:R08B4.1 11/11 A 
R08B4.1b ENSEMBL cdna:known chromosome:CEL140:X:11109548:11115763:1 gene:R08B4.1 11/11 A 
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:11108586-11115592(+) 88.54 100.0
Public Domain and Genome References
Ensembl R08B4.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA92000 Hypothetical protein R08B4.1a [Caenorhabditis elegans] ref|NP_001024843.1| R08B4.1a [Caenorhabditis elegans] 0.0
blast CAD91696 Hypothetical protein R08B4.1b [Caenorhabditis elegans] ref|NP_001024844.1| R08B4.1b [Caenorhabditis elegans] 0.0
blast CAE70701 Hypothetical protein CBG17433 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.1E-15
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.2E-33
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.8E-32
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 4.3E-28
Pfam IPR001767 EMBL-EBI Peptidase C46, hedgehog protein, hint region 9.4E-107
Pfam IPR001767 EMBL-EBI Peptidase C46, hedgehog protein, hint region 9.4E-107
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.1E-15
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.2E-33
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.8E-32
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 4.3E-28
Pfam IPR001767 EMBL-EBI Peptidase C46, hedgehog protein, hint region 9.4E-107
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.2E-33
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 6.8E-32
Pfam IPR007284 EMBL-EBI Protein of unknown function DUF398 4.3E-28
Pfam IPR001767 EMBL-EBI Peptidase C46, hedgehog protein, hint region 3.3E-95
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000019873 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:189952_AT
caggagcatgtttctcactggacacctgggtcacaacacccactggtaaaaagagaatgg
atcaaattgacattggcgattatgttctgacagccgatctagaaaagacctatttcacac
ccattactctttggattcaccgcgagccggaaaaagtccaagaattccttacaattatga
cggaatatgggaaaactctccgaatcacctcgcgtcactttatgtatcggaacaaatgtg
gaaaatcatatccgcaatatatcaaaatgctccctcatgacggagaagcaatattcgcat
cagaccttgaagttggagactgtgttgttgtactgtacaagggaaaatatcgccaacaga
aaattgaaactatcaccagatctgtgagaacgggaatttattcaccgctgacaaacaatg
ggagaataattgtaaacgatatgctagcctcttgttatagtgagatacagcaaaacacac
tgcaaacaactttcttctgggcatatgacaaacttcgtagtgttctcgttgaattctttg
gagatctgtacaacaacaagatcgaactcccaaccgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGGAGCATGTTTCTCACTGGACAC 237 209 3065 Antisense
TCACTGGACACCTGGGTCACAACAC 275 625 3079 Antisense
ATTTCACACCCATTACTCTTTGGAT 45 17 3176 Antisense
CTTTGGATTCACCGCGAGCCGGAAA 694 217 3193 Antisense
ATGGGAAAACTCTCCGAATCACCTC 51 51 3251 Antisense
ACCTCGCGTCACTTTATGTATCGGA 366 87 3271 Antisense
GAACGGGAATTTATTCACCGCTGAC 194 311 3452 Antisense
AAACGATATGCTAGCCTCTTGTTAT 433 127 3498 Antisense
GCAAACAACTTTCTTCTGGGCATAT 176 319 3546 Antisense
GACAAACTTCGTAGTGTTCTCGTTG 129 365 3571 Antisense
ACAACAAGATCGAACTCCCAACCGG 349 111 3617 Antisense
Sequence Source Affymetrix Proprietary Database