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[188352_at] collagen

Description T21B4.2 /REP_DB=WormBase Gene ID /WP=CE16427 /TR=O18097 /GB=CAB03369.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 48      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 234
1 2 3 4 range
A 44
(-3)
A 		198.4
(1.4)
A 		252.5
(3)
A 		110.1
(-1.1)
A 		209
B 18.2
(-3)
A 		202.9
(1.8)
A 		247.1
(3)
P 		96.6
(-0.9)
A 		229
C 55.9
(-3)
A 		108.2
(-1.4)
A 		248.5
(3)
A 		93
(-1.8)
A 		193
avr 39.4
(-3) 		169.8
(0.7) 		249.4
(3) 		99.9
(-1.3) 		210

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19499
1 2 3 4 5 6 range
A 145.7
(-3)
A 		77.6
(-3)
A 		120.3
(-3)
A 		8481.1
(0.2)
P 		16032
(3)
P 		2496.2
(-2.1)
P 		15954
B 10
(-3)
A 		78.1
(-3)
A 		98.2
(-3)
A 		7543.7
(-0.1)
P 		15740.8
(3)
P 		2292.2
(-2.1)
P 		15731
C 89.4
(-3)
A 		153.4
(-3)
A 		26.4
(-3)
A 		6455.5
(-1)
P 		19509.1
(3)
P 		2111.1
(-2.4)
P 		19483
avr 81.7
(-3) 		103
(-3) 		81.6
(-3) 		7493.4
(-0.4) 		17094
(3) 		2299.8
(-2.2) 		17012
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 16
(-3)
A 		43.1
(0.3)
A 		66
(3)
A 		16.1
(-3)
A 		50
B 5.8
(-3)
A 		50.1
(2.2)
A 		57.3
(3)
P 		20.6
(-1.3)
A 		52
C 18.5
(-2.8)
A 		31.1
(-1.7)
A 		86.6
(3)
A 		15.7
(-3)
A 		71
avr 13.4
(-3) 		41.4
(-0) 		70
(3) 		17.5
(-2.6) 		57

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6392
1 2 3 4 5 6 range
A 26.9
(-3)
A 		27.6
(-3)
A 		26.2
(-3)
A 		2151
(-0.4)
P 		4837.8
(3)
P 		607.8
(-2.3)
P 		4812
B 3.5
(-3)
A 		26
(-3)
A 		23.9
(-3)
A 		1998.1
(-1.1)
P 		6395.3
(3)
P 		854.7
(-2.2)
P 		6392
C 33.1
(-3)
A 		46.8
(-3)
A 		6.7
(-3)
A 		1298.2
(-1.8)
P 		6312.9
(3)
P 		706.7
(-2.3)
P 		6306
avr 21.2
(-3) 		33.5
(-3) 		18.9
(-3) 		1815.8
(-1.2) 		5848.7
(3) 		723.1
(-2.3) 		5830
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188352_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3637
Sequence Type Exemplar sequence
Representative Public ID T21B4.2 NCBI
Target Description T21B4.2 /REP_DB=WormBase Gene ID /WP=CE16427 /TR=O18097 /GB=CAB03369.1 /SUBMIT=HINXTON /CHR=2 /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_064264(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064264 NCBI Caenorhabditis elegans T21B4.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000006684 ENSEMBL cdna:SNAP chromosome:CEL140:II:12493703:12495060:-1 11/11 None
GENEFINDER00000006692 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12493703:12495060:-1 11/11 None
T21B4.2 ENSEMBL cdna:known chromosome:CEL140:II:12493703:12494997:-1 gene:T21B4.2 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
chrII:12493699-12494994(-) 92.23 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-85
Ensembl T21B4.2
Entrez Gene 188672 Entrez gene
SwissProt O18097 EMBL-EBI
WormBase CE16427 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 CAB03369 Hypothetical protein T21B4.2 [Caenorhabditis elegans] ref|NP_496665.1| T21B4.2 [Caenorhabditis elegans] 3.0E-34
blast CAE65336 Hypothetical protein CBG10272 [Caenorhabditis briggsae] 7.0E-32
blast CAE65336 Hypothetical protein CBG10272 [Caenorhabditis briggsae] 8.0E-32
blast CAE62989 Hypothetical protein CBG07217 [Caenorhabditis briggsae] 1.0E-24
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0017
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.5E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.3E-4
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0017
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.5E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.3E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496665.1 1 17-39
T21B4.2 1 17-39
SNAP00000006684 1 38-60
GENEFINDER00000006692 1 38-60
Sequence
Target Sequence 
>C. ELEGANS:188352_AT
ggatacgctaccggaggtggaggcggtggaggtggcggaggatgctgctcttgcggaatt
ggagccgccggaccagctggaccaccaggagccgatggaaatccaggaactgacggagct
gccggaaacccaggacaagctggagccgacgcttcacaagatgctccatctgcctcagat
ttctgcttcgactgcccaccaggaccagctggaccagccggaaacgccggaccaccagga
gctccaggaggaccaggagccccaggaaacactccatctggcggagccgccggaccacca
ggaccaccaggaccaccaggaggacccggaaatgacggacaaccaggaggaccaggaaac
ccgggagctccaggagcagtcaccgaggttccaggccaacaaggaccaccaggaccacca
ggaccagccggaccaccaggaccagccggaaacgccggacaagctggatatgctcagcca
ggaccggccggaccaccaggagacgctggaccggacggag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATACGCTACCGGAGGTGGAGGCG 524 507 325 Antisense
ATACGCTACCGGAGGTGGAGGCGGT 6 9 327 Antisense
CAGGAACTGACGGAGCTGCCGGAAA 380 207 428 Antisense
GGAACTGACGGAGCTGCCGGAAACC 131 529 430 Antisense
GGAGCCGACGCTTCACAAGATGCTC 381 521 466 Antisense
ACGCTTCACAAGATGCTCCATCTGC 40 93 473 Antisense
TTCACAAGATGCTCCATCTGCCTCA 271 687 477 Antisense
CCACCAGGAGGACCCGGAAATGACG 250 271 637 Antisense
GAGGTTCCAGGCCAACAAGGACCAC 88 401 709 Antisense
GAAACGCCGGACAAGCTGGATATGC 202 359 773 Antisense
CCAGGAGACGCTGGACCGGACGGAG 393 271 820 Antisense
Sequence Source Affymetrix Proprietary Database