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[193852_at] CUB domain, Lectin C-type domain short and long forms

Description Y70C5C.2 /REP_DB=WormBase Gene ID /WP=CE16674 /TR=O62498 /GB=CAB16536.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=CUB domain, Lectin C-type domain short and long forms
Cluster 6grp_total > 59      4grp_total > 46      6grp_cgc > 39      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 446
1 2 3 4 range
A 384.9
(3)
P 		102.8
(-1.8)
P 		33.4
(-3)
A 		34.9
(-3)
A 		352
B 448.9
(3)
P 		64.5
(-2.2)
A 		21
(-2.8)
A 		3.5
(-3)
A 		445
C 361.1
(3)
P 		56.8
(-2.1)
A 		23.9
(-2.7)
A 		3.4
(-3)
A 		358
avr 398.3
(3) 		74.7
(-2.1) 		26.1
(-2.8) 		13.9
(-3) 		384

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 68
1 2 3 4 5 6 range
A 69.5
(3)
A 		9.7
(-2.4)
A 		2.9
(-3)
A 		7.9
(-2.5)
A 		14.4
(-2)
A 		65.4
(2.6)
A 		67
B 22.6
(-0.9)
A 		3.7
(-2.9)
A 		2.9
(-3)
A 		34.7
(0.3)
A 		46.9
(1.6)
A 		60
(3)
A 		57
C 40
(0.3)
A 		33
(-0.3)
A 		2.7
(-3)
A 		41.8
(0.4)
A 		50
(1.2)
P 		70.8
(3)
P 		68
avr 44
(0.9) 		15.5
(-1.8) 		2.8
(-3) 		28.1
(-0.6) 		37.1
(0.3) 		65.4
(3) 		63
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 143
1 2 3 4 range
A 140.1
(3)
P 		22.3
(-2.2)
P 		8.7
(-2.8)
A 		5.1
(-3)
A 		135
B 143.2
(3)
P 		15.9
(-2.4)
A 		4.9
(-2.8)
A 		0.7
(-3)
A 		143
C 119.5
(3)
P 		16.3
(-2.2)
A 		8.3
(-2.6)
A 		0.6
(-3)
A 		119
avr 134.3
(3) 		18.2
(-2.3) 		7.3
(-2.8) 		2.1
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 23
1 2 3 4 5 6 range
A 12.8
(1.8)
A 		3.4
(-1.9)
A 		0.6
(-3)
A 		2
(-2.5)
A 		4.3
(-1.5)
A 		15.9
(3)
A 		15
B 7.9
(-1)
A 		1.2
(-2.9)
A 		0.7
(-3)
A 		9.2
(-0.6)
A 		19.1
(2.1)
A 		22.4
(3)
A 		22
C 14.8
(0.7)
A 		10.1
(-0.5)
A 		0.7
(-3)
A 		8.4
(-1)
A 		16.2
(1)
P 		23.7
(3)
P 		23
avr 11.8
(0.3) 		4.9
(-1.7) 		0.7
(-3) 		6.5
(-1.3) 		13.2
(0.8) 		20.7
(3) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193852_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12876
Sequence Type Exemplar sequence
Representative Public ID Y70C5C.2 NCBI
Target Description Y70C5C.2 /REP_DB=WormBase Gene ID /WP=CE16674 /TR=O62498 /GB=CAB16536.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=CUB domain, Lectin C-type domain short and long forms
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_074826(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074826 NCBI Caenorhabditis elegans C-type LECtin family member (clec-9) (clec-9) mRNA, complete cds. 11/11 None
SNAP00000034981 ENSEMBL cdna:SNAP chromosome:CEL140:V:16707663:16709228:-1 11/11 None
GENEFINDER00000034986 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:16707663:16709158:-1 11/11 None
Y70C5C.2 ENSEMBL cdna:known chromosome:CEL140:V:16707663:16709228:-1 gene:Y70C5C.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
chrV:16707662-16709158(-) 100.0 100.0
Public Domain and Genome References
Gene Title CUB domain, Lectin C-type domain short and long forms
Gene Symbol clec-9
Ensembl Y70C5C.2
Entrez Gene 190567 Entrez gene
SwissProt O62498 EMBL-EBI
WormBase CE35697 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 CAB16536 Hypothetical protein Y70C5C.2 [Caenorhabditis elegans] ref|NP_507227.2| C-type LECtin family member (clec-9) [Caenorhabditis elegans] 0.0
blast CAE65367 Hypothetical protein CBG10312 [Caenorhabditis briggsae] 1.0E-116
blast CAB54396 Hypothetical protein Y38E10A.5 [Caenorhabditis elegans] ref|NP_496688.1| C-type LECtin family member (clec-4) [Caenorhabditis elegans] 1.0E-111
Protein Domains
Database ID Description E-Value
Pfam IPR001304 EMBL-EBI C-type lectin 7.2E-8
Pfam IPR001304 EMBL-EBI C-type lectin 2.0E-7
Pfam IPR000859 EMBL-EBI CUB 3.8E-14
Pfam IPR001304 EMBL-EBI C-type lectin 2.0E-7
Pfam IPR000859 EMBL-EBI CUB 3.8E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000034986 1 50-72
Sequence
Target Sequence 
>C. ELEGANS:193852_AT
ttatcggtgccacctggaccactaaagacacctattcttggtttgacgggtccccgtgga
actttaaccaaatcaatccagcgtctccaaaaaagaactgtcttgccatggtaacttccc
tcaatgatgcaagtgcatcaggatcttggtacccaattgtttgttactctgcctatggat
acctttgcaagagacctgcaggcgttcaatgcccccagtacccaccggttacagtaaccc
cggctccctcgaatccatctggttgcaatagtacaattatgtccttcggaactatcacat
caccaaattttccgatgaattacaacaatataacatcgtgcaactatctactcactacac
tcggatcctacaatgtcatgttaaagttcaacaaattctatactgatatgaaaaacgact
ttgtaactttatacgacggagattcgactaaaagtccagtgattgcaaagtacagtggat
actacgaatggcctttcttcaacgtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTATCGGTGCCACCTGGACCACTAA 38 681 548 Antisense
TAACCAAATCAATCCAGCGTCTCCA 107 639 612 Antisense
AACTGTCTTGCCATGGTAACTTCCC 382 141 643 Antisense
GTGCATCAGGATCTTGGTACCCAAT 38 481 680 Antisense
CCCAATTGTTTGTTACTCTGCCTAT 367 257 699 Antisense
AAGAGACCTGCAGGCGTTCAATGCC 640 153 736 Antisense
TCCCTCGAATCCATCTGGTTGCAAT 105 597 792 Antisense
GTCCTTCGGAACTATCACATCACCA 473 475 828 Antisense
GTGCAACTATCTACTCACTACACTC 381 481 885 Antisense
CACTACACTCGGATCCTACAATGTC 566 195 900 Antisense
CTACGAATGGCCTTTCTTCAACGTG 489 225 1029 Antisense
Sequence Source Affymetrix Proprietary Database