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[173727_s_at] EGF-like repeats

Description CEC9824 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F40F4.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C11982 /WB_GENE_ID=F40F4.6 /WP=CE04536 /CHR=X /FEA=Genomic Cluster /DEF=EGF-like repeats; C.elegans cDNA clone yk144f9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 32      6grp_high1_10_10 > 03      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 13      6grp_total > 34      4grp_total > 60      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3429
1 2 3 4 range
A 4532.5
(2.1)
P 		5052.9
(3)
P 		4771.7
(2.5)
P 		1624
(-3)
P 		3429
B 4536.9
(3)
P 		4122.2
(2.1)
P 		4543.3
(3)
P 		1840.8
(-3)
P 		2703
C 4134.3
(3)
P 		3879.8
(2.3)
P 		4136.3
(3)
P 		1851.7
(-3)
P 		2285
avr 4401.2
(2.8) 		4351.6
(2.7) 		4483.8
(3) 		1772.2
(-3) 		2712

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2482
1 2 3 4 5 6 range
A 3918.2
(2.5)
P 		4095.7
(3)
P 		3092.6
(-0.1)
P 		2398.9
(-2.2)
P 		2154.6
(-3)
P 		2313.9
(-2.5)
P 		1941
B 3827.3
(3)
P 		3819
(3)
P 		3720
(2.7)
P 		2310.1
(-1.1)
P 		1613.3
(-3)
P 		2005.3
(-1.9)
P 		2214
C 3673.8
(2.5)
P 		3550.2
(2.1)
P 		3797.4
(3)
P 		2214.3
(-3)
P 		2496.4
(-1.9)
P 		2251.2
(-2.9)
P 		1583
avr 3806.4
(2.9) 		3821.6
(3) 		3536.7
(2) 		2307.8
(-2.2) 		2088.1
(-3) 		2190.1
(-2.6) 		1734
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1413
1 2 3 4 range
A 1650.3
(3)
P 		1096.9
(0.6)
P 		1247.4
(1.3)
P 		237.7
(-3)
P 		1413
B 1446.8
(3)
P 		1018.1
(0.6)
P 		1052.8
(0.8)
P 		392.3
(-3)
P 		1055
C 1368.6
(2.6)
P 		1115.5
(1.3)
P 		1441.6
(3)
P 		312.2
(-3)
P 		1129
avr 1488.6
(3) 		1076.8
(0.9) 		1247.3
(1.8) 		314.1
(-3) 		1175

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1011
1 2 3 4 5 6 range
A 722.3
(-1.9)
P 		1456.6
(3)
P 		673.5
(-2.3)
P 		608.4
(-2.7)
P 		650.2
(-2.4)
P 		563.4
(-3)
P 		893
B 1331.7
(3)
P 		1271.2
(2.5)
P 		903.3
(-0.6)
P 		611.9
(-3)
P 		655.4
(-2.6)
P 		747.8
(-1.9)
P 		720
C 1361.7
(3)
P 		1083.3
(1.2)
P 		966.5
(0.4)
P 		445.3
(-3)
P 		807.8
(-0.6)
P 		753.6
(-1)
P 		916
avr 1138.6
(1.9) 		1270.4
(3) 		847.8
(-0.5) 		555.2
(-3) 		704.5
(-1.7) 		688.3
(-1.9) 		715
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173727_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26238
Sequence Type Exemplar sequence
Representative Public ID CEC9824 NCBI
Target Description CEC9824 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F40F4.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C11982 /WB_GENE_ID=F40F4.6 /WP=CE04536 /CHR=X /FEA=Genomic Cluster /DEF=EGF-like repeats; C.elegans cDNA clone yk144f9 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_076151(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076151 NCBI Caenorhabditis elegans F40F4.6 (F40F4.6) mRNA, complete cds. 11/11 None
SNAP00000025260 ENSEMBL cdna:SNAP chromosome:CEL140:X:3235900:3243613:-1 11/11 None
GENEFINDER00000025276 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3235900:3243613:-1 11/11 None
F40F4.6 ENSEMBL cdna:known chromosome:CEL140:X:3235757:3243613:-1 gene:F40F4.6 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
chrX:3235901-3243615(-) 100.0 100.0
Public Domain and Genome References
Gene Title EGF-like repeats
Ensembl F40F4.6
Entrez Gene 180613 Entrez gene
SwissProt Q20219 EMBL-EBI
WormBase CE04536 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 AAA81430 Hypothetical protein F40F4.6 [Caenorhabditis elegans] ref|NP_508552.1| F40F4.6 [Caenorhabditis elegans] 0.0
blast AAA83584 Hypothetical protein F28B4.3 [Caenorhabditis elegans] ref|NP_508551.1| F28B4.3 [Caenorhabditis elegans] 0.0
blast CAE68394 Hypothetical protein CBG14163 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001304 EMBL-EBI C-type lectin 7.1E-7
Pfam IPR002035 EMBL-EBI von Willebrand factor, type A 4.2E-29
Sequence
Target Sequence 
>C. ELEGANS:173727_S_AT
tccatacacatccgctcagtttgatgttgtatttatgatcgatggatcacaaagtgcaca
atccagctttgactcgctcaccaaatttgttcaaacattcatggtttcgttcaatgttgg
ccagagtggagctcgtgttggattaattgtcgtcggaggtgatatcacaaacccaattcc
tcctgctgccaatctgaactccctctcctctcaagcaatgttgaactctaacttggccca
actcagcggtggctacactgactttgaagacgccgggcaaattcttaactacactcttca
aattgtgtcttctcccgatttcatggcggcgaacaatggttaccgtagtggcattagcaa
ccatgtgttgatctaccttactacaactactggcttcgacaccgatccaactccggcagc
tcagacaattctcgcgcagaagcaatacggaatcatcactattggttatggtggcgcgac
tgataacaacaagttgcaaactatttccggaggaagtgcttgctcgtttacagct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCATACACATCCGCTCAGTTTGAT 237 591 6028 Antisense
AAGTGCACAATCCAGCTTTGACTCG 378 159 6079 Antisense
TTGACTCGCTCACCAAATTTGTTCA 48 701 6096 Antisense
CCCTCTCCTCTCAAGCAATGTTGAA 89 261 6228 Antisense
GTTGAACTCTAACTTGGCCCAACTC 451 437 6247 Antisense
AACTCAGCGGTGGCTACACTGACTT 573 139 6267 Antisense
GACGCCGGGCAAATTCTTAACTACA 97 379 6296 Antisense
CACTCTTCAAATTGTGTCTTCTCCC 202 197 6319 Antisense
CTTCTCCCGATTTCATGGCGGCGAA 19 221 6336 Antisense
ACCATGTGTTGATCTACCTTACTAC 148 87 6387 Antisense
AGGAAGTGCTTGCTCGTTTACAGCT 337 17 6538 Antisense
Sequence Source Affymetrix Proprietary Database