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[188400_s_at] collagen /// collagen

Description C34F6.2 /REP_DB=WormBase Gene ID /WP=CE15671 /TR=O17641 /GB=CAB03941.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 57      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 644
1 2 3 4 range
A 159.7
(-1.6)
A 		513.1
(2.2)
A 		589.3
(3)
A 		32.6
(-3)
A 		557
B 127.8
(-1.9)
A 		505.2
(1.6)
A 		655.5
(3)
A 		11.8
(-3)
A 		644
C 221.2
(-0.8)
A 		434.7
(2.2)
A 		489.4
(3)
A 		68
(-3)
A 		421
avr 169.6
(-1.5) 		484.3
(2) 		578.1
(3) 		37.5
(-3) 		541

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10059
1 2 3 4 5 6 range
A 156.6
(-3)
A 		414.7
(-2.8)
A 		497
(-2.8)
M 		814.8
(-2.5)
P 		8806.7
(3)
P 		2340.8
(-1.5)
P 		8650
B 238.1
(-3)
A 		355.9
(-2.9)
A 		309.9
(-3)
A 		659.8
(-2.7)
P 		9079.8
(3)
P 		2361.6
(-1.6)
P 		8842
C 335.6
(-3)
A 		318.7
(-3)
M 		443.7
(-2.9)
P 		603.8
(-2.8)
P 		10215.6
(3)
P 		1851.9
(-2.1)
P 		9897
avr 243.4
(-3) 		363.1
(-2.9) 		416.9
(-2.9) 		692.8
(-2.7) 		9367.4
(3) 		2184.8
(-1.7) 		9124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 168
1 2 3 4 range
A 58.2
(-0.9)
A 		111.4
(1.3)
A 		154.1
(3)
A 		4.8
(-3)
A 		149
B 40.8
(-1.5)
A 		124.8
(1.9)
A 		151.9
(3)
A 		2.5
(-3)
A 		149
C 73.2
(-0.7)
A 		125
(1.3)
A 		170.6
(3)
A 		11.5
(-3)
A 		159
avr 57.4
(-1) 		120.4
(1.5) 		158.9
(3) 		6.3
(-3) 		153

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3660
1 2 3 4 5 6 range
A 28.9
(-3)
A 		147.5
(-2.7)
A 		108.2
(-2.8)
M 		206.6
(-2.6)
P 		2657.5
(3)
P 		569.9
(-1.8)
P 		2629
B 82.8
(-3)
A 		118.5
(-2.9)
A 		75.3
(-3)
A 		174.8
(-2.8)
P 		3689
(3)
P 		880.6
(-1.7)
P 		3614
C 124.4
(-2.9)
A 		97.2
(-3)
M 		112.9
(-3)
P 		121.4
(-3)
P 		3305.6
(3)
P 		620
(-2)
P 		3208
avr 78.7
(-3) 		121.1
(-2.9) 		98.8
(-3) 		167.6
(-2.8) 		3217.4
(3) 		690.2
(-1.8) 		3139
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188400_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16737
Sequence Type Exemplar sequence
Representative Public ID C34F6.2 NCBI
Target Description C34F6.2 /REP_DB=WormBase Gene ID /WP=CE15671 /TR=O17641 /GB=CAB03941.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=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_077468(11), NM_077469(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077468 NCBI Caenorhabditis elegans C34F6.2 (collagen) mRNA, complete cds. 11/11 None
NM_077469 NCBI Caenorhabditis elegans C34F6.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000004400 ENSEMBL cdna:SNAP chromosome:CEL140:X:11199399:11200299:1 11/11 None
GENEFINDER00000004419 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11199399:11200299:1 11/11 None
SNAP00000004401 ENSEMBL cdna:SNAP chromosome:CEL140:X:11201462:11202365:1 11/11 None
GENEFINDER00000004417 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:11201462:11202365:1 11/11 None
C34F6.2 ENSEMBL cdna:known chromosome:CEL140:X:11199386:11200341:1 gene:C34F6.2 11/11 None
C34F6.3 ENSEMBL cdna:known chromosome:CEL140:X:11201462:11202409:1 gene:C34F6.3 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:11199398-11200299(+) 96.01 100.0
chrX:11201741-11202365(+) 68.08 72.07
Public Domain and Genome References
Gene Title collagen
collagen
Gene Symbol col-178
col-179
Ensembl C34F6.2
C34F6.3
Entrez Gene 181307 Entrez gene
181308 Entrez gene
SwissProt O17641 EMBL-EBI
O17642 EMBL-EBI
WormBase CE15671 Wormbase
CE15672 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03942 Hypothetical protein C34F6.3 [Caenorhabditis elegans] ref|NP_509870.1| C34F6.3 [Caenorhabditis elegans] 1.0E-65
blast CAB03941 Hypothetical protein C34F6.2 [Caenorhabditis elegans] ref|NP_509869.1| C34F6.2 [Caenorhabditis elegans] 2.0E-65
blast CAE70685 Hypothetical protein CBG17402 [Caenorhabditis briggsae] 4.0E-58
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509869.1 1 16-38
NP_509870.1 1 16-38
C34F6.2 1 16-38
C34F6.3 1 16-38
SNAP00000004400 1 16-38
GENEFINDER00000004419 1 16-38
SNAP00000004401 1 16-38
GENEFINDER00000004417 1 16-38
Sequence
Target Sequence 
>C. ELEGANS:188400_S_AT
gtcaaactccacaaacttgctgttcatgcggtattggagaaactggaccagctggagttc
caggacaagaaggagcccctggaaatgacggaaaagctggacaaccaggagcaccaggag
ctgacgctgacgagcaaggttttcattacaaggctccagaattctgcttcgactgcccag
ctggaccaccaggagccgttggaggaccaggaccaaagggaccaccaggaccaccaggag
gtccaggagagcttggaggaccaggacgtggaggaaaccgcggaccaccaggaccacgtg
gaccaccaggagaggctggaccagacggagagggaggacgtccaggacaagccggacaaa
ctcgctcagctccatctccaccaggacaaccaggacaaccaggagaaccaggatcgccag
gagagccaggaccagatggacgtgctggacatccaggacgtaacggaccaccaggaccac
caggagacaatggaggtcaaggagagccaggaaaggacggagaagatggagagaacggag
ctgctggagccgctggaccaaagggatctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCAAACTCCACAAACTTGCTGTTC 353 463 254 Antisense
ACTCCACAAACTTGCTGTTCATGCG 353 99 259 Antisense
ACTTGCTGTTCATGCGGTATTGGAG 431 101 268 Antisense
AGGACAAGAAGGAGCCCCTGGAAAT 234 55 315 Antisense
GAGCCCCTGGAAATGACGGAAAAGC 430 385 326 Antisense
GACCAGATGGACGTGCTGGACATCC 655 383 683 Antisense
GGACGTGCTGGACATCCAGGACGTA 311 523 691 Antisense
CATCCAGGACGTAACGGACCACCAG 373 209 703 Antisense
GACAATGGAGGTCAAGGAGAGCCAG 206 365 739 Antisense
AGAGAACGGAGCTGCTGGAGCCGCT 95 67 783 Antisense
GGAGCCGCTGGACCAAAGGGATCTT 52 523 799 Antisense
Sequence Source Affymetrix Proprietary Database