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[190134_s_at] collagen

Description T10B10.1 /REP_DB=WormBase Gene ID /WP=CE06399 /GEN=col-41 /TR=Q22369 /GB=CAA96674.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 20      4grp_total > 49      6grp_cgc > 63      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17808
1 2 3 4 range
A 23.1
(-3)
A 		17831.2
(3)
P 		15950.8
(2.4)
P 		113.8
(-3)
A 		17808
B 36.2
(-3)
A 		14262.8
(2.2)
P 		16430.6
(3)
P 		27.7
(-3)
A 		16403
C 24.8
(-3)
A 		13658.9
(3)
P 		13742.5
(3)
P 		109.5
(-3)
A 		13718
avr 28
(-3) 		15251
(3) 		15374.6
(3) 		83.7
(-3) 		15347

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10119
1 2 3 4 5 6 range
A 292.2
(-3)
A 		10323.9
(3)
P 		5594.3
(0.2)
P 		4207.4
(-0.7)
P 		1651.7
(-2.2)
P 		915.9
(-2.6)
P 		10032
B 204.5
(-3)
A 		9007.3
(3)
P 		6631.7
(1.4)
P 		4263.2
(-0.2)
P 		1239.5
(-2.3)
P 		708
(-2.7)
P 		8803
C 337.7
(-3)
A 		8621.3
(3)
P 		7686.2
(2.3)
P 		4326
(-0.1)
P 		1554
(-2.1)
P 		549.1
(-2.8)
P 		8284
avr 278.1
(-3) 		9317.5
(3) 		6637.4
(1.2) 		4265.5
(-0.4) 		1481.7
(-2.2) 		724.3
(-2.7) 		9039
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4784
1 2 3 4 range
A 8.4
(-3)
A 		3870.7
(2.6)
P 		4169.8
(3)
P 		16.7
(-3)
A 		4161
B 11.5
(-3)
A 		3522.6
(2.6)
P 		3807.3
(3)
P 		5.9
(-3)
A 		3801
C 8.2
(-3)
A 		3927
(1.9)
P 		4789.7
(3)
P 		18.5
(-3)
A 		4782
avr 9.4
(-3) 		3773.4
(2.3) 		4255.6
(3) 		13.7
(-3) 		4246

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3618
1 2 3 4 5 6 range
A 53.9
(-3)
A 		3671.7
(3)
P 		1218.3
(-1.1)
P 		1067.1
(-1.3)
P 		498.4
(-2.3)
P 		223
(-2.7)
P 		3618
B 71.1
(-3)
A 		2998.2
(3)
P 		1610.4
(0.2)
P 		1129.2
(-0.8)
P 		503.6
(-2.1)
P 		264
(-2.6)
P 		2927
C 125.2
(-3)
A 		2630.6
(3)
P 		1956.3
(1.4)
P 		870
(-1.2)
P 		502.8
(-2.1)
P 		183.8
(-2.9)
P 		2505
avr 83.4
(-3) 		3100.2
(3) 		1595
(0) 		1022.1
(-1.1) 		501.6
(-2.2) 		223.6
(-2.7) 		3017
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190134_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17662
Sequence Type Exemplar sequence
Representative Public ID T10B10.1 NCBI
Target Description T10B10.1 /REP_DB=WormBase Gene ID /WP=CE06399 /GEN=col-41 /TR=Q22369 /GB=CAA96674.1 /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_078121(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078121 NCBI Caenorhabditis elegans T10B10.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000009612 ENSEMBL cdna:SNAP chromosome:CEL140:X:15175023:15176379:-1 11/11 None
GENEFINDER00000009623 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:15175023:15176379:-1 11/11 None
T10B10.1 ENSEMBL cdna:known chromosome:CEL140:X:15174965:15176397:-1 gene:T10B10.1 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:15175022-15176379(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-41
Ensembl T10B10.1
Entrez Gene 181610 Entrez gene
SwissProt Q22369 EMBL-EBI
WormBase CE06399 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
16042 lipid catabolism 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
4623 phospholipase A2 activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA96674 Hypothetical protein T10B10.1 [Caenorhabditis elegans] ref|NP_510522.1| T10B10.1 [Caenorhabditis elegans] 1.0E-140
blast CAE63250 Hypothetical protein CBG07618 [Caenorhabditis briggsae] 1.0E-120
blast CAE66911 Hypothetical protein CBG12296 [Caenorhabditis briggsae] 5.0E-78
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.3E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.9E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510522.1 1 5-27
T10B10.1 1 5-27
SNAP00000009612 1 5-27
GENEFINDER00000009623 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:190134_S_AT
ccaggaaacgctggtcacgacgccttcccaggaaccccgggacaagctggaaagccagga
gctccaggaaaagatgccaactactgcccatgcccacaaagacaagacgacagaacccca
ccatcatctggaacatccgctccacagccaccaccacgtggatccactgctgctccagga
actcgtgctccaccagcaactcgcgctccaccagcaactcgtgctccaccagcaaccacc
cgcgctccaccagcaacaactcgtccagcaccagcttcacagccaccagtcagagagcca
gagactccagattctggatacccatccccagctccacaagagccagctcatccatcacca
agctacccgtctccaagctatccatctccaagctatccatccccaagctacccatctccg
agctacccatccccaagctatccagctgagccagcttattccgtcccaccaccagccaag
ccagagcagccatcaggaggatacgatgctccatctcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGGAAACGCTGGTCACGACGCCT 452 269 748 Antisense
TCCCAGGAACCCCGGGACAAGCTGG 535 595 773 Antisense
GGAAAAGATGCCAACTACTGCCCAT 435 527 814 Antisense
GCCCATGCCCACAAAGACAAGACGA 159 287 833 Antisense
TTCACAGCCACCAGTCAGAGAGCCA 704 681 1023 Antisense
CAGAGAGCCAGAGACTCCAGATTCT 646 205 1038 Antisense
CCACAAGAGCCAGCTCATCCATCAC 537 275 1081 Antisense
CAAGCTATCCATCTCCAAGCTATCC 153 185 1121 Antisense
CCAAGCTATCCAGCTGAGCCAGCTT 88 277 1180 Antisense
CCAAGCCAGAGCAGCCATCAGGAGG 350 277 1223 Antisense
AGGAGGATACGATGCTCCATCTCCA 303 57 1242 Antisense
Sequence Source Affymetrix Proprietary Database