[Home] | [Total List]

[189452_at] cuticle collagen

Description F46C8.2 /REP_DB=WormBase Gene ID /WP=CE04577 /TR=Q9GYP3 /GB=AAF99941.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 92      4grp_total > 50      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 589
1 2 3 4 range
A 75.2
(-2.3)
A 		596.9
(3)
P 		445.8
(1.5)
P 		8.4
(-3)
A 		589
B 82
(-2.2)
A 		586.2
(3)
P 		482.6
(1.9)
P 		8.9
(-3)
A 		577
C 89.1
(-2.1)
A 		508.8
(3)
P 		390.9
(1.6)
P 		10.3
(-3)
A 		499
avr 82.1
(-2.2) 		564
(3) 		439.8
(1.7) 		9.2
(-3) 		555

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2629
1 2 3 4 5 6 range
A 83.9
(-3)
A 		333.3
(-2.3)
P 		260.1
(-2.5)
A 		2049.4
(2.4)
P 		2282.7
(3)
P 		365
(-2.2)
P 		2199
B 86.2
(-3)
A 		373.1
(-2.2)
P 		256.5
(-2.5)
P 		1825
(1.7)
P 		2286.5
(3)
P 		366.8
(-2.2)
P 		2200
C 110.4
(-3)
A 		280.5
(-2.6)
P 		285.5
(-2.6)
P 		1963.7
(1.3)
P 		2713.2
(3)
P 		307.9
(-2.5)
P 		2603
avr 93.5
(-3) 		329
(-2.4) 		267.4
(-2.6) 		1946
(1.8) 		2427.5
(3) 		346.6
(-2.3) 		2334
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 145
1 2 3 4 range
A 27.4
(-1.8)
A 		129.6
(3)
P 		116.5
(2.4)
P 		1.2
(-3)
A 		128
B 26.1
(-2)
A 		144.8
(3)
P 		111.8
(1.6)
P 		1.9
(-3)
A 		143
C 29.5
(-1.8)
A 		146.3
(3)
P 		136.2
(2.6)
P 		1.7
(-3)
A 		145
avr 27.7
(-1.9) 		140.2
(3) 		121.5
(2.2) 		1.6
(-3) 		139

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 914
1 2 3 4 5 6 range
A 15.5
(-3)
A 		118.5
(-2.1)
P 		56.7
(-2.6)
A 		519.8
(1.5)
P 		688.8
(3)
P 		88.9
(-2.3)
P 		673
B 30
(-3)
A 		124.2
(-2.4)
P 		62.3
(-2.8)
P 		483.4
(0)
P 		929
(3)
P 		136.8
(-2.3)
P 		899
C 40.9
(-3)
A 		85.6
(-2.7)
P 		72.7
(-2.8)
P 		394.9
(-0.5)
P 		878
(3)
P 		103.1
(-2.6)
P 		837
avr 28.8
(-3) 		109.4
(-2.4) 		63.9
(-2.7) 		466
(0.3) 		831.9
(3) 		109.6
(-2.4) 		803
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189452_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17231
Sequence Type Exemplar sequence
Representative Public ID F46C8.2 NCBI
Target Description F46C8.2 /REP_DB=WormBase Gene ID /WP=CE04577 /TR=Q9GYP3 /GB=AAF99941.1 /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_076875(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076875 NCBI Caenorhabditis elegans COLlagen family member (col-174) (col-174) mRNA, complete cds. 11/11 None
GENEFINDER00000044534 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:7546912:7548085:1 11/11 None
SNAP00000044529 ENSEMBL cdna:SNAP chromosome:CEL140:X:7547124:7548085:1 11/11 None
F46C8.2 ENSEMBL cdna:known chromosome:CEL140:X:7546831:7548256:1 gene:F46C8.2 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
chrX:7546910-7548084(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-174
Ensembl F46C8.2
Entrez Gene 181014 Entrez gene
SwissProt Q9GYP3 EMBL-EBI
WormBase CE04577 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 AAF99941 Collagen protein 174 [Caenorhabditis elegans] ref|NP_509276.1| COLlagen family member (col-174) [Caenorhabditis elegans] 7.0E-64
blast CAE70235 Hypothetical protein CBG16724 [Caenorhabditis briggsae] 4.0E-59
blast AAF99941 Collagen protein 174 [Caenorhabditis elegans] ref|NP_509276.1| COLlagen family member (col-174) [Caenorhabditis elegans] 1.0E-44
blast CAE70235 Hypothetical protein CBG16724 [Caenorhabditis briggsae] 3.0E-42
blast CAE61240 Hypothetical protein CBG05040 [Caenorhabditis briggsae] 7.0E-21
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.9E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.1E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.1E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509276.1 1 23-45
F46C8.2 1 23-45
GENEFINDER00000044534 1 23-45
Sequence
Target Sequence 
>C. ELEGANS:189452_AT
ctgacggagaagctggtgcacctggaaaagatggaccagacggaccagctgcgactcctg
ctccaaactatgactggtgcttcgattgcccaccaggcccaccaggaccagccggaagcg
ctggggttaagggaccatctggtaaccctggagccccaggaactgatggtccagctggaa
ataaaggaggccaaggaccacctggaaacgccggagctccaggtgcaaacggaaatcctg
gaaatgcaggaacgcccggaattcctggtaaaactattgaggttcctgcaccagcagggc
cagctggagctccaggaccagcaggaccacctggaaccgcaggaacaccgggttcacaag
gtcagccaggaaaggatggatctccaggagacgctggagacaatggtactgctggatctc
caggtcaccctggaggagaaggtccagtgggaccagacggtgccaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGACGGAGAAGCTGGTGCACCTGG 79 239 434 Antisense
GACTCCTGCTCCAAACTATGACTGG 677 373 486 Antisense
AACTATGACTGGTGCTTCGATTGCC 143 139 499 Antisense
AGGGACCATCTGGTAACCCTGGAGC 438 57 563 Antisense
AGCCCCAGGAACTGATGGTCCAGCT 441 81 585 Antisense
GCCGGAGCTCCAGGTGCAAACGGAA 156 283 643 Antisense
GGAAATGCAGGAACGCCCGGAATTC 236 527 673 Antisense
ACTATTGAGGTTCCTGCACCAGCAG 657 101 706 Antisense
GAACACCGGGTTCACAAGGTCAGCC 448 347 776 Antisense
GACAATGGTACTGCTGGATCTCCAG 276 363 832 Antisense
TCCAGTGGGACCAGACGGTGCCAGA 250 277 876 Antisense
Sequence Source Affymetrix Proprietary Database