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[189993_at] C-type lectin domain

Description F08H9.8 /REP_DB=WormBase Gene ID /WP=CE09272 /TR=Q19226 /GB=CAB01145.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=C-type lectin domain
Cluster 6grp_high1_10_10 > 12      4grp_high_8_8 > 50      6grp_total > 23      4grp_total > 53      6grp_cgc > 70      6grp_high1_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 446
1 2 3 4 range
A 503.9
(3)
P 		348.8
(0.7)
P 		307.4
(0)
P 		105.7
(-3)
P 		398
B 485.5
(3)
P 		328.5
(0.8)
P 		288.3
(0.2)
P 		57.5
(-3)
A 		428
C 455.3
(3)
P 		358.2
(1.4)
P 		308.6
(0.6)
P 		85.7
(-3)
P 		370
avr 481.6
(3) 		345.2
(0.9) 		301.4
(0.3) 		83
(-3) 		399

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 572
1 2 3 4 5 6 range
A 537.2
(2)
P 		467.7
(1.3)
P 		632.7
(3)
P 		322.4
(-0.3)
P 		183.7
(-1.7)
P 		60.9
(-3)
A 		572
B 542.4
(3)
P 		472.6
(2.1)
P 		542.6
(3)
P 		276.4
(-0.3)
P 		175.7
(-1.6)
P 		65.4
(-3)
P 		477
C 548.2
(3)
P 		452.9
(1.7)
P 		472.7
(2)
P 		348.3
(0.4)
P 		176.7
(-1.9)
P 		94.6
(-3)
P 		454
avr 542.6
(2.9) 		464.4
(1.9) 		549.3
(3) 		315.7
(0.1) 		178.7
(-1.7) 		73.6
(-3) 		476
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 171
1 2 3 4 range
A 183.5
(3)
P 		75.7
(-0.9)
P 		80.4
(-0.7)
P 		15.5
(-3)
P 		168
B 154.8
(3)
P 		81.1
(-0.1)
P 		66.8
(-0.7)
P 		12.3
(-3)
A 		143
C 150.7
(3)
P 		103
(0.9)
P 		107.6
(1.1)
P 		14.5
(-3)
P 		136
avr 163
(3) 		86.6
(-0.1) 		84.9
(-0.1) 		14.1
(-3) 		149

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 188
1 2 3 4 5 6 range
A 99
(0.3)
P 		166.3
(3)
P 		137.8
(1.9)
P 		81.8
(-0.3)
P 		55.4
(-1.4)
P 		14.8
(-3)
A 		152
B 188.7
(3)
P 		157.3
(1.9)
P 		131.8
(0.9)
P 		73.2
(-1.2)
P 		71.4
(-1.3)
P 		24.4
(-3)
P 		164
C 203.2
(3)
P 		138.2
(0.7)
P 		120.3
(0.1)
P 		70
(-1.7)
P 		57.2
(-2.1)
P 		31.7
(-3)
P 		172
avr 163.6
(3) 		153.9
(2.6) 		130
(1.6) 		75
(-0.8) 		61.3
(-1.4) 		23.6
(-3) 		140
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189993_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14112
Sequence Type Exemplar sequence
Representative Public ID F08H9.8 NCBI
Target Description F08H9.8 /REP_DB=WormBase Gene ID /WP=CE09272 /TR=Q19226 /GB=CAB01145.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=C-type lectin 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_074189(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074189 NCBI Caenorhabditis elegans C-type LECtin family member (clec-54) (clec-54) mRNA, complete cds. 10/11 None
SNAP00000029734 ENSEMBL cdna:SNAP chromosome:CEL140:V:14479527:14481500:1 10/11 None
GENEFINDER00000029743 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:14477108:14481500:1 11/11 None
F08H9.8 ENSEMBL cdna:known chromosome:CEL140:V:14479527:14481500:1 gene:F08H9.8 10/11 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
chrV:14479526-14481500(+) 100.0 100.0
Public Domain and Genome References
Gene Title C-type lectin domain
Gene Symbol clec-54
Ensembl F08H9.8
Entrez Gene 184217 Entrez gene
SwissProt Q19226 EMBL-EBI
WormBase CE35853 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5529 sugar binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB01145 Hypothetical protein F08H9.8 [Caenorhabditis elegans] ref|NP_506590.2| C-type LECtin family member (clec-54) [Caenorhabditis elegans] 0.0
blast CAB01151 Hypothetical protein F08H9.7 [Caenorhabditis elegans] ref|NP_506589.2| C-type LECtin family member (clec-56) [Caenorhabditis elegans] 0.0
blast CAB01438 Hypothetical protein F08H9.9 [Caenorhabditis elegans] emb|CAB01152.1| Hypothetical protein F08H9.9 [Caenorhabditis elegans] ref|NP_506591.1| C-type LECtin family member (clec-55) [Caenorhabditis elegans] 1.0E-178
blast CAB01438 Hypothetical protein F08H9.9 [Caenorhabditis elegans] emb|CAB01152.1| Hypothetical protein F08H9.9 [Caenorhabditis elegans] ref|NP_506591.1| C-type LECtin family member (clec-55) [Caenorhabditis elegans] 1.0E-156
blast CAE60888 Hypothetical protein CBG04603 [Caenorhabditis briggsae] 1.0E-138
Protein Domains
Database ID Description E-Value
Pfam IPR000859 EMBL-EBI CUB 6.5E-21
Pfam IPR000859 EMBL-EBI CUB 2.5E-14
Pfam IPR001304 EMBL-EBI C-type lectin 5.3E-6
Pfam IPR000859 EMBL-EBI CUB 1.1E-7
Pfam IPR000859 EMBL-EBI CUB 6.6E-5
Pfam IPR000859 EMBL-EBI CUB 1.4E-12
Pfam IPR000859 EMBL-EBI CUB 3.2E-10
Pfam IPR000859 EMBL-EBI CUB 2.5E-14
Sequence
Target Sequence 
>C. ELEGANS:189993_AT
aagcaacaccatgctggagtatccaacctgccatgtgcaagcaaatgcctgcaatttgtc
cggatccaaagaagatttatggaggccaatacactagatctggaaatatcacatctccag
gatatcccgtgcaatattacaataacttggactgcttgtacactattacttctccaaaca
aaacgtatatcactctcacattcaatccatatctagtggaaggttatgtggattatgttc
tgatttatgatggcccagacactacttatccaagccttggaagatcaaacacacctccag
ttatccaaagtggaaatggcggaaactttacatcacctaattatccaaatgactatgatt
cctatacagagcaaatgttctacttaacagttgctgatggattccaagtgaatgttacaa
ttgatgatttcctaacagagaacagatttgatgttctagaagtttatgataattatacaa
ttccaggagtcaatatgattgcaaacttaaccggtgattcaattgctccatggaattggc
tctctcaatccagccatgtcacaatgagattccgaaccgatggttccgtacag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGCAACACCATGCTGGAGTATCCA 610 151 416 Antisense
GTATCCAACCTGCCATGTGCAAGCA 507 455 434 Antisense
TGCCTGCAATTTGTCCGGATCCAAA 502 583 461 Antisense
TATGGAGGCCAATACACTAGATCTG 501 653 493 Antisense
GACTGCTTGTACACTATTACTTCTC 408 375 565 Antisense
AAAACGTATATCACTCTCACATTCA 286 131 595 Antisense
CACTCTCACATTCAATCCATATCTA 14 199 606 Antisense
TTATGTTCTGATTTATGATGGCCCA 315 679 648 Antisense
GGCCCAGACACTACTTATCCAAGCC 133 543 667 Antisense
AGATCAAACACACCTCCAGTTATCC 596 65 697 Antisense
ATTCCGAACCGATGGTTCCGTACAG 414 7 984 Antisense
Sequence Source Affymetrix Proprietary Database