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[189904_at] C-type lectin domain

Description F08H9.7 /REP_DB=WormBase Gene ID /WP=CE17642 /TR=Q19230 /GB=CAB01151.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=C-type lectin domain
Cluster 6grp_highest_10_10 > 30      6grp_high1_10_10 > 04      6grp_highest_nonorm > 20      6grp_total > 05      4grp_total > 60      6grp_highest_sub > De      6grp_cgc > 42      6grp_high1_sub > De      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1243
1 2 3 4 range
A 1044.7
(1.6)
P 		1321.7
(3)
P 		1219.1
(2.5)
P 		139.1
(-3)
A 		1183
B 1074.1
(3)
P 		904.5
(1.9)
P 		934.8
(2.1)
P 		126.7
(-3)
A 		947
C 1072.8
(3)
P 		1013.7
(2.6)
P 		948.8
(2.3)
P 		78.7
(-3)
A 		994
avr 1063.9
(2.9) 		1080
(3) 		1034.2
(2.7) 		114.8
(-3) 		965

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 995
1 2 3 4 5 6 range
A 1323.9
(3)
P 		1228.3
(2.1)
P 		898.4
(-1)
P 		815.8
(-1.8)
P 		984.7
(-0.2)
P 		688.3
(-3)
P 		636
B 1323.5
(3)
P 		1136.2
(1.5)
P 		954.8
(0)
P 		749.8
(-1.6)
P 		1051.2
(0.8)
P 		582.5
(-3)
P 		741
C 1344.9
(2.1)
P 		1494.2
(3)
P 		1188.2
(1.2)
P 		858.8
(-0.8)
P 		790.4
(-1.2)
P 		499.6
(-3)
P 		995
avr 1330.8
(3) 		1286.2
(2.6) 		1013.8
(0.4) 		808.1
(-1.2) 		942.1
(-0.1) 		590.1
(-3) 		741
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 367
1 2 3 4 range
A 380.4
(3)
P 		286.9
(1.4)
P 		318.7
(2)
P 		20.4
(-3)
A 		360
B 342.5
(3)
P 		223.4
(0.7)
P 		216.6
(0.6)
P 		27
(-3)
A 		316
C 355.1
(3)
P 		291.5
(1.9)
P 		330.7
(2.6)
P 		13.3
(-3)
A 		342
avr 359.3
(3) 		267.3
(1.4) 		288.7
(1.8) 		20.2
(-3) 		339

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 331
1 2 3 4 5 6 range
A 244
(-1.3)
P 		436.8
(3)
P 		195.6
(-2.4)
P 		206.9
(-2.1)
P 		297.1
(-0.1)
P 		167.6
(-3)
P 		269
B 460.5
(3)
P 		378.2
(1.1)
P 		231.9
(-2.2)
P 		198.6
(-3)
P 		427.1
(2.2)
P 		217.2
(-2.6)
P 		262
C 498.5
(3)
P 		455.9
(2.2)
P 		302.4
(-0.6)
P 		172.7
(-2.9)
P 		255.8
(-1.4)
P 		167.2
(-3)
P 		331
avr 401
(2.4) 		423.6
(3) 		243.3
(-1.5) 		192.7
(-2.8) 		326.7
(0.6) 		184
(-3) 		240
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189904_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14003
Sequence Type Exemplar sequence
Representative Public ID F08H9.7 NCBI
Target Description F08H9.7 /REP_DB=WormBase Gene ID /WP=CE17642 /TR=Q19230 /GB=CAB01151.1 /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_074188(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074188 NCBI Caenorhabditis elegans C-type LECtin family member (clec-56) (clec-56) mRNA, complete cds. 11/11 None
SNAP00000029733 ENSEMBL cdna:SNAP chromosome:CEL140:V:14475138:14479369:1 11/11 None
GENEFINDER00000029743 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:14477108:14481500:1 11/11 None
F08H9.7 ENSEMBL cdna:known chromosome:CEL140:V:14477061:14479369:1 gene:F08H9.7 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
chrV:14477107-14478803(+) 100.0 100.0
Public Domain and Genome References
Gene Title C-type lectin domain
Gene Symbol clec-56
Ensembl F08H9.7
Entrez Gene 179953 Entrez gene
SwissProt Q19230 EMBL-EBI
WormBase CE37968 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 CAB01151 Hypothetical protein F08H9.7 [Caenorhabditis elegans] ref|NP_506589.2| C-type LECtin family member (clec-56) [Caenorhabditis elegans] 0.0
blast CAB01145 Hypothetical protein F08H9.8 [Caenorhabditis elegans] ref|NP_506590.2| C-type LECtin family member (clec-54) [Caenorhabditis elegans] 0.0
blast CAB01149 Hypothetical protein F08H9.5 [Caenorhabditis elegans] ref|NP_506588.1| F08H9.5 [Caenorhabditis elegans] 1.0E-158
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-155
Protein Domains
Database ID Description E-Value
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 9.4E-14
Pfam IPR001304 EMBL-EBI C-type lectin 5.3E-6
Pfam IPR000859 EMBL-EBI CUB 2.4E-10
Pfam IPR000859 EMBL-EBI CUB 3.1E-19
Pfam IPR000859 EMBL-EBI CUB 1.1E-7
Pfam IPR000859 EMBL-EBI CUB 6.6E-5
Pfam IPR000859 EMBL-EBI CUB 9.4E-14
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:189904_AT
atccaaccggccgtgtgtaagcagatgccagctttgtgcccaactcagacatcctatgga
ggactctatacacgatcaggaactatcacttcgccaggatatccaactcagtattataac
aatttgaactgtttgtactcaattaaatcacctaacaatacttacattacaatggagttt
tctccatacttggttcaaagctattttgactacattaatgtttatgatggtccgaactca
acttctacatacctcggaacaactgatgacggttgggacgactactggtgggacagtcgt
cgtgactttgaaagttcaaacaactcaatcagttttgtattccgcactgatagcagtgtc
actaataaaggatggcaactaacttggagtgccaaaccaaacacgccaccaatcaagcaa
tctggacaaagtggaaacttcacatcacccaattatccgttgaactatgatccgtactca
gagcaattgtattacattaccgcgccaactggattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATCCAACCGGCCGTGTGTAAGCAGA 687 19 433 Antisense
TAAGCAGATGCCAGCTTTGTGCCCA 10 639 450 Antisense
TGCCCAACTCAGACATCCTATGGAG 467 583 469 Antisense
GGAGGACTCTATACACGATCAGGAA 621 515 490 Antisense
ATCACTTCGCCAGGATATCCAACTC 646 27 517 Antisense
GGAGTTTTCTCCATACTTGGTTCAA 252 357 606 Antisense
TGATGGTCCGAACTCAACTTCTACA 545 565 657 Antisense
GTTTTGTATTCCGCACTGATAGCAG 88 449 764 Antisense
AAACACGCCACCAATCAAGCAATCT 477 129 831 Antisense
TTCACATCACCCAATTATCCGTTGA 211 687 871 Antisense
TTACATTACCGCGCCAACTGGATTC 41 671 924 Antisense
Sequence Source Affymetrix Proprietary Database