[Home] | [Total List]

[189482_s_at] Cuticle collagen

Description C35B8.1 /REP_DB=WormBase Gene ID /WP=CE02534 /TR=Q18480 /GB=AAC46553.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Cuticle collagen
Cluster 6grp_total > 94      4grp_total > 51      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 23.4
(-1.9)
A 		81.5
(3)
A 		61.7
(1.3)
A 		10
(-3)
A 		72
B 12.9
(-3)
A 		16.1
(-1.6)
A 		24.2
(2.1)
A 		26.2
(3)
A 		13
C 61
(3)
A 		38.3
(-1.1)
A 		36.1
(-1.5)
A 		28
(-3)
A 		33
avr 32.4
(-0.2) 		45.3
(3) 		40.7
(1.8) 		21.4
(-3) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3568
1 2 3 4 5 6 range
A 11.6
(-3)
A 		52.7
(-2.9)
A 		86.5
(-2.8)
A 		789.3
(-1.1)
P 		2425.8
(3)
P 		1880.7
(1.6)
P 		2414
B 18.4
(-3)
A 		74.3
(-2.9)
A 		35.8
(-3)
A 		582.5
(-1.9)
P 		3066.4
(3)
P 		2408.3
(1.7)
P 		3048
C 64.9
(-3)
A 		47.4
(-3)
A 		59.9
(-3)
A 		679
(-1.9)
P 		3580
(3)
P 		1803.2
(-0)
P 		3533
avr 31.6
(-3) 		58.1
(-2.9) 		60.7
(-2.9) 		683.6
(-1.7) 		3024.1
(3) 		2030.7
(1) 		2993
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 8.5
(-0.4)
A 		17.7
(3)
A 		16.1
(2.4)
A 		1.5
(-3)
A 		16
B 4.1
(-2.6)
A 		4
(-3)
A 		5.6
(3)
A 		5.6
(3)
A 		2
C 20.2
(3)
A 		11
(-0.6)
A 		12.6
(0.1)
A 		4.7
(-3)
A 		16
avr 10.9
(2.6) 		10.9
(2.6) 		11.4
(3) 		3.9
(-3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1244
1 2 3 4 5 6 range
A 2.1
(-3)
A 		18.7
(-2.9)
A 		18.8
(-2.9)
A 		200.2
(-1.4)
P 		732
(3)
P 		457.9
(0.7)
P 		730
B 6.4
(-3)
A 		24.7
(-2.9)
A 		8.7
(-3)
A 		154.3
(-2.3)
P 		1245.8
(3)
P 		898
(1.3)
P 		1239
C 24.1
(-2.9)
A 		14.5
(-3)
A 		15.2
(-3)
A 		136.5
(-2.4)
P 		1158.4
(3)
P 		603.6
(0.1)
P 		1144
avr 10.9
(-3) 		19.3
(-3) 		14.2
(-3) 		163.7
(-2.1) 		1045.4
(3) 		653.2
(0.7) 		1035
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189482_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17159
Sequence Type Exemplar sequence
Representative Public ID C35B8.1 NCBI
Target Description C35B8.1 /REP_DB=WormBase Gene ID /WP=CE02534 /TR=Q18480 /GB=AAC46553.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Cuticle 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_077154(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077154 NCBI Caenorhabditis elegans COLlagen family member (col-175) (col-175) mRNA, complete cds. 11/11 None
SNAP00000036132 ENSEMBL cdna:SNAP chromosome:CEL140:X:9233610:9234531:-1 11/11 None
GENEFINDER00000036148 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9233610:9234531:-1 11/11 None
C35B8.1 ENSEMBL cdna:known chromosome:CEL140:X:9233604:9234547:-1 gene:C35B8.1 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:9233609-9234531(-) 100.0 100.0
Public Domain and Genome References
Gene Title Cuticle collagen
Gene Symbol col-175
Ensembl C35B8.1
Entrez Gene 181154 Entrez gene
SwissProt Q18480 EMBL-EBI
WormBase CE02534 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_509555 COLlagen family member (col-175) [Caenorhabditis elegans] gb|AAC46553.1| Collagen protein 175 [Caenorhabditis elegans] 4.0E-79
blast CAE69856 Hypothetical protein CBG16184 [Caenorhabditis briggsae] 7.0E-71
blast AAA81159 Collagen protein 8 [Caenorhabditis elegans] ref|NP_498533.1| COLlagen family member (col-8) [Caenorhabditis elegans] 8.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.0E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.5E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509555.1 1 5-27
C35B8.1 1 5-27
SNAP00000036132 1 5-27
GENEFINDER00000036148 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:189482_S_AT
gaaattctgatagctgccaatgtgaatctcgtgctgctgcttgcccagctggatcaccag
gagaaaaaggagagccaggacttgccggacttccaggacctgatggagaggatggaaaag
acggagctccaggagttgctcttcttgtcactcatgacattccaggtggatgcatcaagt
gtccagctggaccacgtgggccacgaggagatgccggaccaccaggaccaccaggaaacg
gtggacgtccaggtcaacgcggtactccaggagaggccggaacaccagggccagtcggag
agccaggagagactggaggtccaggaccacaaggaagaccaggacaacgcggagagccag
gacaaccaggaaccgttcacacaccaggaaacccaggtcgtccaggaccacaaggaccac
gtggacaacaaggagagccaggaaaggatggatccaagggaaatccaggagacgaaggac
gtcaaggacacccaggaaaaaatggaagaactggagctcacggaaaggatggagcccctg
gaaagtgcggaaaggaaggaccaattgggccagacgctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAATTCTGATAGCTGCCAATGTGA 203 363 266 Antisense
TGCCAATGTGAATCTCGTGCTGCTG 234 587 280 Antisense
GTCACTCATGACATTCCAGGTGGAT 30 465 412 Antisense
GAAACGGTGGACGTCCAGGTCAACG 588 355 500 Antisense
GTCAACGCGGTACTCCAGGAGAGGC 605 463 518 Antisense
GAACACCAGGGCCAGTCGGAGAGCC 121 353 545 Antisense
GGACAACCAGGAACCGTTCACACAC 453 525 625 Antisense
GACGAAGGACGTCAAGGACACCCAG 274 379 736 Antisense
ATGGAAGAACTGGAGCTCACGGAAA 93 53 767 Antisense
ATGGAGCCCCTGGAAAGTGCGGAAA 139 51 794 Antisense
GAAGGACCAATTGGGCCAGACGCTG 78 333 820 Antisense
Sequence Source Affymetrix Proprietary Database