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[188366_s_at] collagen /// collagen

Description F54D1.2 /REP_DB=WormBase Gene ID /WP=CE05937 /TR=Q20761 /GB=CAB00858.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 90      6grp_total > 93      4grp_total > 50      6grp_cgc > 98      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 798
1 2 3 4 range
A 180.8
(-2.3)
A 		858.7
(3)
P 		617.3
(1.1)
P 		85.7
(-3)
A 		773
B 160
(-2.1)
A 		635.8
(2.2)
P 		719
(3)
P 		61
(-3)
A 		658
C 159.1
(-2.6)
A 		793.3
(3)
P 		550.4
(0.9)
P 		112.9
(-3)
A 		680
avr 166.6
(-2.3) 		762.6
(3) 		628.9
(1.8) 		86.5
(-3) 		676

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 868
1 2 3 4 5 6 range
A 95.9
(-3)
A 		627
(0.7)
P 		316.4
(-1.5)
A 		426.3
(-0.7)
P 		963.5
(3)
P 		347.1
(-1.3)
P 		868
B 174.4
(-3)
A 		708.5
(1.7)
P 		492.9
(-0.2)
P 		430.1
(-0.8)
P 		857.3
(3)
P 		293.1
(-2)
P 		683
C 212.8
(-3)
P 		622.7
(0.3)
P 		410.3
(-1.4)
P 		389.7
(-1.6)
P 		963.4
(3)
P 		271.6
(-2.5)
P 		751
avr 161
(-3) 		652.7
(0.8) 		406.5
(-1.1) 		415.4
(-1) 		928.1
(3) 		303.9
(-1.9) 		767
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 216
1 2 3 4 range
A 65.8
(-1.2)
A 		186.4
(3)
P 		161.4
(2.1)
P 		12.5
(-3)
A 		174
B 51
(-1.5)
A 		157
(2.6)
P 		166.6
(3)
P 		13
(-3)
A 		154
C 52.7
(-2)
A 		228.1
(3)
P 		191.8
(2)
P 		19
(-3)
A 		209
avr 56.5
(-1.6) 		190.5
(3) 		173.3
(2.4) 		14.8
(-3) 		176

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 331
1 2 3 4 5 6 range
A 17.7
(-3)
A 		223
(1.5)
P 		68.9
(-1.9)
A 		108.1
(-1)
P 		290.8
(3)
P 		84.5
(-1.5)
P 		273
B 60.7
(-3)
A 		235.8
(0.7)
P 		119.7
(-1.8)
P 		113.9
(-1.9)
P 		348.3
(3)
P 		109.3
(-2)
P 		288
C 78.9
(-3)
P 		190
(-0.1)
P 		104.4
(-2.3)
P 		78.4
(-3)
P 		311.7
(3)
P 		90.9
(-2.7)
P 		233
avr 52.4
(-3) 		216.3
(0.7) 		97.7
(-2) 		100.1
(-1.9) 		316.9
(3) 		94.9
(-2) 		265
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188366_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8713
Sequence Type Exemplar sequence
Representative Public ID F54D1.2 NCBI
Target Description F54D1.2 /REP_DB=WormBase Gene ID /WP=CE05937 /TR=Q20761 /GB=CAB00858.1 /SUBMIT=HINXTON /CHR=4 /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_069714(11), NM_069715(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069714 NCBI Caenorhabditis elegans F54D1.2 (collagen) mRNA, complete cds. 11/11 None
NM_069715 NCBI Caenorhabditis elegans F54D1.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000005950 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11263372:11264302:1 11/11 None
SNAP00000005951 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11264918:11265848:-1 11/11 None
GENEFINDER00000005959 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11263372:11264302:1 11/11 None
GENEFINDER00000005960 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11264918:11265848:-1 11/11 None
F54D1.2 ENSEMBL cdna:known chromosome:CEL140:IV:11263372:11264302:1 gene:F54D1.2 11/11 None
F54D1.3 ENSEMBL cdna:known chromosome:CEL140:IV:11264918:11265896:-1 gene:F54D1.3 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
chrIV:11263377-11264308(+) 88.47 100.0
chrIV:11264923-11265854(-) 86.55 100.0
Public Domain and Genome References
Gene Title collagen
collagen
Gene Symbol col-126
col-127
Ensembl F54D1.2
F54D1.3
Entrez Gene 178034 Entrez gene
186228 Entrez gene
SwissProt Q20761 EMBL-EBI
Q20764 EMBL-EBI
WormBase CE05937 Wormbase
CE05938 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 CAB00860 Hypothetical protein F54D1.3 [Caenorhabditis elegans] ref|NP_502116.1| F54D1.3 [Caenorhabditis elegans] 4.0E-72
blast CAB00860 Hypothetical protein F54D1.3 [Caenorhabditis elegans] ref|NP_502116.1| F54D1.3 [Caenorhabditis elegans] 2.0E-62
blast CAB00858 Hypothetical protein F54D1.2 [Caenorhabditis elegans] ref|NP_502115.1| F54D1.2 [Caenorhabditis elegans] 2.0E-62
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.8E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.8E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502115.1 1 5-27
NP_502116.1 1 20-42
F54D1.2 1 5-27
F54D1.3 1 20-42
SNAP00000005950 1 5-27
SNAP00000005951 1 5-27
GENEFINDER00000005959 1 5-27
GENEFINDER00000005960 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:188366_S_AT
gctccaggaccaagagggggcgacagcactgttacctatgctccaatcaactgcccacaa
gtttcattcgattgcattaagtgcccagcaggaccagccggaccagctggatcatccgga
ccagcaggaccagcaggaccatctggacaaccaggaactccaggacaacgtggaaacgat
ggattcccaggagctccaggagcaccaggagacaatggtcaaccaggattcccaggacaa
gatggagctccaggacaaccaggagccgatggacaacgtggagctggaactc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTCCAGGACCAAGAGGGGGCGACA 449 297 370 Antisense
GACCAAGAGGGGGCGACAGCACTGT 515 383 377 Antisense
GCGACAGCACTGTTACCTATGCTCC 554 289 389 Antisense
ACAGCACTGTTACCTATGCTCCAAT 429 109 392 Antisense
CACTGTTACCTATGCTCCAATCAAC 471 195 396 Antisense
GCCCACAAGTTTCATTCGATTGCAT 278 287 422 Antisense
CATTCGATTGCATTAAGTGCCCAGC 280 215 434 Antisense
ATTGCATTAAGTGCCCAGCAGGACC 148 5 440 Antisense
CCAGCTGGATCATCCGGACCAGCAG 207 273 472 Antisense
AGGAGCCGATGGACAACGTGGAGCT 24 57 630 Antisense
GATGGACAACGTGGAGCTGGAACTC 373 407 637 Antisense
Sequence Source Affymetrix Proprietary Database