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[188401_s_at]

Description F39H11.4 /REP_DB=WormBase Gene ID /WP=CE17816 /CHR=1 /FEA=Sanger Annotation /DEF=collagen (HINXTON) TR:O17866 protein_id:CAB03084.1
Cluster 6grp_highest_10_10 > 90      6grp_high1_10_10 > 19      4grp_highest_8_8 > 41      4grp_high_8_8 > 50      6grp_highest_nonorm > 51      6grp_total > 02      4grp_total > 53      6grp_cgc > 42      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 543
1 2 3 4 range
A 716.8
(3)
P 		501.7
(0.6)
P 		427
(-0.2)
P 		174.3
(-3)
P 		543
B 649.3
(3)
P 		503.3
(1.1)
P 		364.3
(-0.8)
P 		199.3
(-3)
P 		450
C 583
(3)
P 		401.5
(0.2)
P 		532.3
(2.2)
P 		195.5
(-3)
P 		388
avr 649.7
(3) 		468.8
(0.6) 		441.2
(0.3) 		189.7
(-3) 		460

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 415
1 2 3 4 5 6 range
A 611.1
(1.4)
P 		696.6
(3)
P 		382.2
(-3)
P 		411
(-2.5)
P 		686.6
(2.8)
P 		428.7
(-2.1)
P 		314
B 775.5
(2.6)
P 		797.3
(3)
P 		565.4
(-1.3)
P 		494.6
(-2.7)
P 		728.4
(1.7)
P 		476.9
(-3)
P 		320
C 702.6
(1.7)
P 		782.8
(3)
P 		499.2
(-1.8)
P 		455.7
(-2.5)
P 		733.1
(2.2)
P 		425.1
(-3)
P 		358
avr 696.4
(1.8) 		758.9
(3) 		482.3
(-2.3) 		453.8
(-2.8) 		716
(2.2) 		443.6
(-3) 		315
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 236
1 2 3 4 range
A 261
(3)
P 		108.9
(-0.9)
P 		111.6
(-0.8)
P 		25.5
(-3)
P 		236
B 207
(3)
P 		124.3
(-0)
P 		84.4
(-1.5)
P 		42.5
(-3)
P 		165
C 193
(3)
P 		115.4
(0.1)
P 		185.5
(2.7)
P 		33
(-3)
P 		160
avr 220.3
(3) 		116.2
(-0.3) 		127.2
(0) 		33.7
(-3) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 213
1 2 3 4 5 6 range
A 112.7
(-1.9)
P 		247.7
(3)
P 		83.2
(-3)
P 		104.2
(-2.2)
P 		207.2
(1.5)
P 		104.4
(-2.2)
P 		165
B 269.8
(2)
P 		265.4
(1.9)
P 		137.3
(-2.8)
P 		131
(-3)
P 		296
(3)
P 		177.8
(-1.3)
P 		165
C 260.4
(3)
P 		238.9
(2.2)
P 		127
(-1.7)
P 		91.6
(-3)
P 		237.2
(2.2)
P 		142.3
(-1.2)
P 		169
avr 214.3
(1.5) 		250.7
(3) 		115.8
(-2.7) 		108.9
(-3) 		246.8
(2.8) 		141.5
(-1.6) 		142
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188401_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1296
Sequence Type Exemplar sequence
Representative Public ID F39H11.4 NCBI
Target Description F39H11.4 /REP_DB=WormBase Gene ID /WP=CE17816 /CHR=1 /FEA=Sanger Annotation /DEF=collagen (HINXTON) TR:O17866 protein_id:CAB03084.1
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_170906(11), NM_170904(11), NM_059957(11), NM_170905(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_170906 NCBI Caenorhabditis elegans CoLlagen with Endostatin domain family member (cle-1) (cle-1) mRNA, complete cds. 11/11 None
NM_170904 NCBI Caenorhabditis elegans CoLlagen with Endostatin domain family member (cle-1) (cle-1) mRNA, complete cds. 11/11 A 
NM_059957 NCBI Caenorhabditis elegans CoLlagen with Endostatin domain family member (cle-1) (cle-1) mRNA, complete cds. 11/11 A 
NM_170905 NCBI Caenorhabditis elegans CoLlagen with Endostatin domain family member (cle-1) (cle-1) mRNA, complete cds. 11/11 A 
SNAP00000035955 ENSEMBL cdna:SNAP chromosome:CEL140:I:8714111:8719080:-1 11/11 None
GENEFINDER00000035957 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8714111:8719080:-1 11/11 None
C36B1.1c ENSEMBL cdna:known chromosome:CEL140:I:8713812:8719080:-1 gene:C36B1.1 11/11 None
C36B1.1b ENSEMBL cdna:known chromosome:CEL140:I:8714111:8727491:-1 gene:C36B1.1 11/11 A 
C36B1.1a ENSEMBL cdna:known chromosome:CEL140:I:8714111:8732404:-1 gene:C36B1.1 11/11 A 
C36B1.1d ENSEMBL cdna:known chromosome:CEL140:I:8714111:8732404:-1 gene:C36B1.1 11/11 A 
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
chrI:8714041-8719011(-) 100.0 100.0
Public Domain and Genome References
Ensembl C36B1.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB03084 Hypothetical protein C36B1.1c [Caenorhabditis elegans] ref|NP_740898.1| CoLlagen with Endostatin domain family member (cle-1) [Caenorhabditis elegans] gb|AAD47825.1| CLE-1C protein [Caenorhabditis elegans] 0.0
blast CAD21701 Hypothetical protein C36B1.1a [Caenorhabditis elegans] emb|CAD21644.2| Hypothetical protein C36B1.1a [Caenorhabditis elegans] ref|NP_740896.2| CoLlagen with Endostatin domain family member (cle-1) [Caenorhabditis elegans] 0.0
blast CAD21700 Hypothetical protein C36B1.1b [Caenorhabditis elegans] emb|CAD21643.1| Hypothetical protein C36B1.1b [Caenorhabditis elegans] ref|NP_740897.1| CoLlagen with Endostatin domain family member (cle-1) [Caenorhabditis elegans] gb|AAD47824.1| CLE-1B protein [Caenorhabditis elegans] 0.0
blast CAD56563 Hypothetical protein C36B1.1d [Caenorhabditis elegans] emb|CAD56581.2| Hypothetical protein C36B1.1d [Caenorhabditis elegans] ref|NP_492358.3| CoLlagen with Endostatin domain family member (cle-1) [Caenorhabditis elegans] 0.0
blast AAD47823 CLE-1A protein [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Pfam IPR003961 EMBL-EBI Fibronectin, type III 9.2E-16
Pfam IPR003961 EMBL-EBI Fibronectin, type III 4.0E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.0E-7
Pfam IPR010515 EMBL-EBI Collagenase NC10 and endostatin 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:188401_S_AT
atatgattgccctgtcacaaccattctctggtaatcttcacgggctccgaggagcagatc
ttcaatgttatcgtgaagctcgtgcagctggatatactacaacattccgtgcaatgcttt
cgagtaatgtacaggatttggttagaattgtgcattccgttgattttgacacaactgttg
tgaatgttgctggacatcatttgttcccaagttggagatcatttgtcaatggagcacaaa
tgaatcctcatgccaaacttttctcattcgatagacatgatgtgctcaacgattctagat
ggccagataagcgagtttggcatggatccaaagatggtggaataagagctgaacaatact
gtgatggatggagaagagccgattcatctctgacttctttggcaggtcacatctcatcga
atacaagcattttccaatcaagtggatccgaaaaatgtgaaaataaattagtggtattgt
gtgttgagaacatgtccaagtatcacggtgaccgaattctccgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATATGATTGCCCTGTCACAACCATT 388 19 1409 Antisense
TAATCTTCACGGGCTCCGAGGAGCA 486 635 1440 Antisense
GCTCGTGCAGCTGGATATACTACAA 133 299 1486 Antisense
ACAACATTCCGTGCAATGCTTTCGA 214 113 1507 Antisense
GAATTGTGCATTCCGTTGATTTTGA 690 323 1553 Antisense
TGTTGCTGGACATCATTTGTTCCCA 329 563 1593 Antisense
GAATCCTCATGCCAAACTTTTCTCA 5 331 1650 Antisense
GTGCTCAACGATTCTAGATGGCCAG 553 479 1690 Antisense
ATCTCTGACTTCTTTGGCAGGTCAC 555 31 1794 Antisense
TTGGCAGGTCACATCTCATCGAATA 444 707 1807 Antisense
GTATCACGGTGACCGAATTCTCCGC 679 451 1908 Antisense
Sequence Source Affymetrix Proprietary Database