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[172803_x_at]

Description C34H4.4 /REP_DB=WormBase Gene ID /WP=CE27821 /TR=O45140 /GB=AAC04393.3 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 43      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 17      6grp_total > 21      4grp_total > 58      6grp_highest_sub > 02_03      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22222
1 2 3 4 range
A 7777.8
(-1.2)
P 		23415.2
(3)
P 		22386.1
(2.7)
P 		1285.3
(-3)
P 		22130
B 8057.7
(-1.1)
P 		21855
(2.9)
P 		22350.7
(3)
P 		1568.8
(-3)
P 		20782
C 8045.5
(-0.7)
P 		19355.3
(3)
P 		18719.3
(2.8)
P 		1193.1
(-3)
P 		18162
avr 7960.3
(-1) 		21541.8
(3) 		21152
(2.9) 		1349.1
(-3) 		20193

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12744
1 2 3 4 5 6 range
A 8356.9
(-2.8)
P 		18122.3
(3)
P 		13063.4
(0)
P 		11270.4
(-1.1)
P 		8088.7
(-2.9)
P 		7993.5
(-3)
P 		10129
B 6760
(-2.8)
P 		15103.6
(3)
P 		14964.8
(2.9)
P 		9418.4
(-0.9)
P 		7807.7
(-2.1)
P 		6440
(-3)
P 		8664
C 10117.2
(-0.1)
P 		15170.1
(3)
P 		13862.2
(2.2)
P 		7703.8
(-1.6)
P 		11161.4
(0.5)
P 		5378.8
(-3)
P 		9791
avr 8411.4
(-1.9) 		16132
(3) 		13963.5
(1.6) 		9464.2
(-1.2) 		9019.3
(-1.5) 		6604.1
(-3) 		9528
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6336
1 2 3 4 range
A 2831.9
(-0.2)
P 		5082.8
(2.2)
P 		5852.2
(3)
P 		188.1
(-3)
P 		5664
B 2569.5
(-0.4)
P 		5397.7
(3)
P 		5179.2
(2.7)
P 		334.3
(-3)
P 		5063
C 2663.3
(-0.7)
P 		5564.8
(2.1)
P 		6524.3
(3)
P 		201.2
(-3)
P 		6323
avr 2688.2
(-0.4) 		5348.4
(2.5) 		5851.9
(3) 		241.2
(-3) 		5611

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4905
1 2 3 4 5 6 range
A 1540.5
(-3)
P 		6445.2
(3)
P 		2844.9
(-1.4)
P 		2858.4
(-1.4)
P 		2440.8
(-1.9)
P 		1946.2
(-2.5)
P 		4905
B 2352.2
(-3)
P 		5027.4
(3)
P 		3633.9
(-0.1)
P 		2494.6
(-2.7)
P 		3172.2
(-1.2)
P 		2401.5
(-2.9)
P 		2675
C 3750
(1.3)
P 		4628.9
(3)
P 		3528.2
(0.9)
P 		1549.2
(-3)
P 		3611.7
(1)
P 		1800.6
(-2.5)
P 		3080
avr 2547.6
(-2.1) 		5367.2
(3) 		3335.7
(-0.7) 		2300.7
(-2.5) 		3074.9
(-1.1) 		2049.4
(-3) 		3318
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172803_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10778
Sequence Type Exemplar sequence
Representative Public ID C34H4.4 NCBI
Target Description C34H4.4 /REP_DB=WormBase Gene ID /WP=CE27821 /TR=O45140 /GB=AAC04393.3 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
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_182305(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_182305 NCBI Caenorhabditis elegans COLlagen family member (col-107) (col-107) mRNA, complete cds. 11/11 None
SNAP00000036194 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1548732:1549672:1 11/11 None
GENEFINDER00000036201 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1548732:1549672:1 11/11 None
C34H4.4b ENSEMBL cdna:known chromosome:CEL140:IV:1548722:1549716:1 gene:C34H4.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_060547 1/11 Cross Hyb Matching Probes A 
NM_072973 1/11 Cross Hyb Matching Probes A 
NM_072975 1/11 Cross Hyb Matching Probes A 
NM_061512 1/11 Cross Hyb Matching Probes A 
NM_067693 7/11 Cross Hyb Matching Probes None
SNAP00000014505 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014522 1/11 Cross Hyb Matching Probes None
SNAP00000000119 1/11 Cross Hyb Matching Probes None
SNAP00000003625 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003631 1/11 Cross Hyb Matching Probes None
SNAP00000023008 1/11 Cross Hyb Matching Probes None
SNAP00000023010 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023016 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023019 1/11 Cross Hyb Matching Probes None
F27C1.8 1/11 Cross Hyb Matching Probes A 
F15D3.3 1/11 Cross Hyb Matching Probes A 
T13B5.4 1/11 Cross Hyb Matching Probes A 
C34H4.4a 7/11 Cross Hyb Matching Probes None
B0222.6 1/11 Cross Hyb Matching Probes A 
B0222.8 1/11 Cross Hyb Matching Probes A 
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176961 2 1 NM_182305 172803_x_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:1548737-1549678(+) 90.4 100.0
Public Domain and Genome References
Ensembl C34H4.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAC04393 Collagen protein 107, isoform a [Caenorhabditis elegans] ref|NP_500094.1| COLlagen family member (col-107) [Caenorhabditis elegans] 4.0E-43
blast AAO44912 Collagen protein 107, isoform b [Caenorhabditis elegans] ref|NP_872105.1| COLlagen family member (col-107) [Caenorhabditis elegans] 4.0E-43
blast CAE67959 Hypothetical protein CBG13563 [Caenorhabditis briggsae] 6.0E-38
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_872105.1 1 7-29
C34H4.4b 1 7-29
SNAP00000036194 1 7-29
GENEFINDER00000036201 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:172803_X_AT
ggaatcggaatcgtcaactccgccgacgccggaggttgcatcaagtgcccagccggagag
ccaggaccagccggaccagacggaccagccggagccccaggagccgacggacagccagga
gccccaggaaacgccggacaagacggagccccaggagccgctggtgagcaaggagacgcc
ggagccgccggacaagacggagaagccggagcaccaggaggcccaggaaagaacggacaa
cgcggatccggagccccaggaccagccggaccagaaggaccagccggaccagccggacaa
gacggagcaccaggacaagacggagccccaggaaacgccggatcagaaggaccagccgga
gccccaggaaaggacggagaagccggagctccaggacaagacggagaggccggaggcgag
ggaattccaggccaagacgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAATCGGAATCGTCAACTCCGCCG 277 533 367 Antisense
ACGCCGGAGGTTGCATCAAGTGCCC 400 85 392 Antisense
TGGTGAGCAAGGAGACGCCGGAGCC 444 553 528 Antisense
GAGCACCAGGAGGCCCAGGAAAGAA 10 385 575 Antisense
GAACGGACAACGCGGATCCGGAGCC 41 345 597 Antisense
GGACCAGCCGGACAAGACGGAGCAC 396 523 652 Antisense
GGAGCACCAGGACAAGACGGAGCCC 301 519 670 Antisense
AAACGCCGGATCAGAAGGACCAGCC 146 127 699 Antisense
CAGCCGGAGCCCCAGGAAAGGACGG 246 203 719 Antisense
AGAAGCCGGAGCTCCAGGACAAGAC 11 75 744 Antisense
CGAGGGAATTCCAGGCCAAGACGCT 655 247 783 Antisense
Sequence Source Affymetrix Proprietary Database