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[189911_s_at] cuticular collagen

Description F26F12.1 /REP_DB=WormBase Gene ID /WP=CE07146 /TR=Q19813 /GB=AAC25888.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 94      4grp_total > 57      6grp_cgc > 89      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 77.2
(-1.8)
P 		96.9
(0.3)
A 		122.3
(3)
P 		65.8
(-3)
A 		57
B 19.4
(-3)
A 		48.1
(1.7)
A 		55.7
(3)
A 		20.4
(-2.8)
A 		36
C 18
(-2.7)
A 		98.4
(2)
M 		115.9
(3)
P 		12.6
(-3)
A 		103
avr 38.2
(-2.5) 		81.1
(1.4) 		98
(3) 		32.9
(-3) 		65

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10353
1 2 3 4 5 6 range
A 175.5
(-2.9)
P 		98.9
(-3)
P 		41
(-3)
A 		328.9
(-2.8)
P 		7388.2
(3)
P 		2275.7
(-1.2)
P 		7347
B 40.2
(-3)
A 		119.6
(-2.9)
P 		81.5
(-3)
P 		255.7
(-2.8)
P 		7632.8
(3)
P 		2218.6
(-1.3)
P 		7593
C 71.3
(-3)
P 		48.1
(-3)
P 		118.5
(-3)
P 		273.1
(-2.9)
P 		10393
(3)
P 		1671.8
(-2.1)
P 		10345
avr 95.7
(-3) 		88.9
(-3) 		80.3
(-3) 		285.9
(-2.9) 		8471.3
(3) 		2055.4
(-1.6) 		8391
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38
1 2 3 4 range
A 28.1
(2)
P 		21
(0.1)
A 		32
(3)
P 		9.6
(-3)
A 		22
B 6.2
(-1.7)
A 		11.9
(2.3)
A 		12.9
(3)
A 		4.3
(-3)
A 		9
C 6
(-2.4)
A 		28.3
(1.1)
M 		40.4
(3)
P 		2.1
(-3)
A 		38
avr 13.4
(-0.9) 		20.4
(0.9) 		28.4
(3) 		5.3
(-3) 		23

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3354
1 2 3 4 5 6 range
A 32.4
(-2.9)
P 		35.2
(-2.9)
P 		8.9
(-3)
A 		83.4
(-2.8)
P 		2229.4
(3)
P 		554.1
(-1.5)
P 		2221
B 14
(-3)
A 		39.8
(-2.9)
P 		19.8
(-3)
P 		67.7
(-2.9)
P 		3101.1
(3)
P 		827.3
(-1.4)
P 		3087
C 26.4
(-3)
P 		14.7
(-3)
P 		30.2
(-3)
P 		54.9
(-2.9)
P 		3363
(3)
P 		559.6
(-2)
P 		3348
avr 24.3
(-3) 		29.9
(-3) 		19.6
(-3) 		68.7
(-2.9) 		2897.8
(3) 		647
(-1.7) 		2878
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189911_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11991
Sequence Type Exemplar sequence
Representative Public ID F26F12.1 NCBI
Target Description F26F12.1 /REP_DB=WormBase Gene ID /WP=CE07146 /TR=Q19813 /GB=AAC25888.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=cuticular 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_072124(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072124 NCBI Caenorhabditis elegans COLlagen family member (col-140) (col-140) mRNA, complete cds. 11/11 None
SNAP00000007006 ENSEMBL cdna:SNAP chromosome:CEL140:V:5838488:5839405:-1 11/11 None
GENEFINDER00000007015 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5838488:5839405:-1 11/11 None
F26F12.1 ENSEMBL cdna:known chromosome:CEL140:V:5838447:5839408:-1 gene:F26F12.1 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
chrV:5838487-5839405(-) 97.01 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-140
Ensembl F26F12.1
Entrez Gene 178971 Entrez gene
SwissProt Q19813 EMBL-EBI
WormBase CE07146 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 NP_504525 COLlagen family member (col-140) [Caenorhabditis elegans] gb|AAC25888.1| Collagen protein 140 [Caenorhabditis elegans] 3.0E-55
blast CAE64560 Hypothetical protein CBG09310 [Caenorhabditis briggsae] 5.0E-51
blast CAE63664 Hypothetical protein CBG08166 [Caenorhabditis briggsae] 3.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.5E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.4E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.6E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504525.1 1 5-27
F26F12.1 1 5-27
SNAP00000007006 1 5-27
GENEFINDER00000007015 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:189911_S_AT
gccaatccggattcccagaacaatgtaactgcggaccacgctccgaaggatgcccaccag
gaccaccaggaactccaggagagcaaggaccacagggagagtctggacctgacggagacg
atggaaagccaggacttgccggagaagtcgtcgctatcgttcacgatcttccaggaggat
gcattcaatgcccaccaggacgtccaggaccacgtggaccaccaggagaggtcggaccag
ctggaccatccggagacaacggacgcaagggaccaccaggaccaccaggaggaccaggag
gaccaggagagggaggagatggaggtcgcccagga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCAATCCGGATTCCCAGAACAATG 47 279 257 Antisense
ATCCGGATTCCCAGAACAATGTAAC 107 39 261 Antisense
AGGACCACAGGGAGAGTCTGGACCT 622 53 342 Antisense
GGGAGAGTCTGGACCTGACGGAGAC 282 495 351 Antisense
CTGGACCTGACGGAGACGATGGAAA 552 241 359 Antisense
AGGACTTGCCGGAGAAGTCGTCGCT 85 55 387 Antisense
GAGAAGTCGTCGCTATCGTTCACGA 586 391 398 Antisense
ATCGTTCACGATCTTCCAGGAGGAT 454 35 412 Antisense
GCTGGACCATCCGGAGACAACGGAC 381 295 496 Antisense
GGAGACAACGGACGCAAGGGACCAC 404 519 508 Antisense
GGGAGGAGATGGAGGTCGCCCAGGA 541 493 567 Antisense
Sequence Source Affymetrix Proprietary Database