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[177024_at] Cuticle collagen

Description C29E4.1 /REP_DB=WormBase Gene ID /WP=CE00083 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Cuticle collagen
Cluster 6grp_highest_10_10 > 35      6grp_high1_10_10 > 52      4grp_high_8_8 > 55      6grp_highest_nonorm > 25      6grp_total > 20      4grp_total > 57      6grp_highest_sub > 03      6grp_cgc > 73      6grp_high1_sub > 03      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16117
1 2 3 4 range
A 46.1
(-3)
M 		10840.8
(1.1)
P 		15828
(3)
P 		124.5
(-3)
P 		15782
B 49.2
(-3)
P 		12070
(1.5)
P 		16163.2
(3)
P 		57.8
(-3)
P 		16114
C 47.6
(-3)
A 		11116
(1.4)
P 		15003.2
(3)
P 		158.3
(-3)
P 		14956
avr 47.6
(-3) 		11342.3
(1.3) 		15664.8
(3) 		113.5
(-3) 		15617

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7091
1 2 3 4 5 6 range
A 278
(-3)
P 		5389.4
(1.6)
P 		6980.3
(3)
P 		4592.1
(0.9)
P 		1327.5
(-2.1)
P 		987
(-2.4)
P 		6702
B 352.9
(-3)
P 		5520.6
(1.4)
P 		7369.2
(3)
P 		4669.7
(0.7)
P 		1480.3
(-2)
P 		1034.4
(-2.4)
P 		7016
C 388.6
(-3)
P 		5687.7
(2.7)
P 		5955.8
(3)
P 		4479.1
(1.4)
P 		1391.7
(-1.9)
P 		937.7
(-2.4)
P 		5567
avr 339.8
(-3) 		5532.6
(1.8) 		6768.4
(3) 		4580.3
(1) 		1399.8
(-2) 		986.4
(-2.4) 		6429
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5217
1 2 3 4 range
A 16.8
(-3)
M 		2353.2
(0.4)
P 		4137.7
(3)
P 		18.2
(-3)
P 		4121
B 15.7
(-3)
P 		2981
(1.8)
P 		3745.4
(3)
P 		12.3
(-3)
P 		3733
C 15.8
(-3)
A 		3195.9
(0.7)
P 		5229.1
(3)
P 		26.7
(-3)
P 		5213
avr 16.1
(-3) 		2843.4
(0.9) 		4370.7
(3) 		19.1
(-3) 		4355

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1865
1 2 3 4 5 6 range
A 51.3
(-3)
P 		1916.7
(3)
P 		1520.2
(1.7)
P 		1164.7
(0.6)
P 		400.6
(-1.9)
P 		240.3
(-2.4)
P 		1865
B 122.8
(-3)
P 		1837.6
(3)
P 		1789.5
(2.8)
P 		1236.8
(0.9)
P 		601.4
(-1.3)
P 		385.7
(-2.1)
P 		1715
C 144
(-3)
P 		1735.5
(3)
P 		1515.8
(2.2)
P 		900.7
(-0.1)
P 		450.3
(-1.8)
P 		313.9
(-2.4)
P 		1592
avr 106
(-3) 		1829.9
(3) 		1608.5
(2.2) 		1100.7
(0.5) 		484.1
(-1.7) 		313.3
(-2.3) 		1724
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177024_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6291
Sequence Type Exemplar sequence
Representative Public ID C29E4.1 NCBI
Target Description C29E4.1 /REP_DB=WormBase Gene ID /WP=CE00083 /SUBMIT=ST.LOUIS /CHR=3 /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_066328(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066328 NCBI Caenorhabditis elegans COLlagen family member (col-90) (col-90) mRNA, complete cds. 11/11 None
SNAP00000010839 ENSEMBL cdna:SNAP chromosome:CEL140:III:7948814:7949831:1 11/11 None
GENEFINDER00000010850 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7948814:7949831:1 11/11 None
C29E4.1 ENSEMBL cdna:known chromosome:CEL140:III:7948766:7949926:1 gene:C29E4.1 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
chrIII:7948811-7949829(+) 100.0 100.0
Public Domain and Genome References
Gene Title Cuticle collagen
Gene Symbol col-90
Ensembl C29E4.1
Entrez Gene 176117 Entrez gene
SwissProt P34340 EMBL-EBI
WormBase CE00083 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 AAA27958 Collagen protein 90 [Caenorhabditis elegans] ref|NP_498729.1| COLlagen family member (col-90) [Caenorhabditis elegans] sp|P34340|YK61_CAEEL Putative cuticle collagen C29E4.1 1.0E-153
blast CAE66911 Hypothetical protein CBG12296 [Caenorhabditis briggsae] 1.0E-143
blast CAE66909 Hypothetical protein CBG12293 [Caenorhabditis briggsae] 1.0E-143
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.2E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498729.1 1 5-27
C29E4.1 1 5-27
SNAP00000010839 1 5-27
GENEFINDER00000010850 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:177024_AT
tcttggacgttctggagcatctggaatctcacttgcagctgttcatcacattccaggagg
atgcatcaactgcccagccggaccagctggaccaccaggacaacaaggaccagttggacc
acaaggattcccaggagttgttggaacatgtggaccatcgggagatgatggacaaccagg
accagctggaccacttggagataagggagcccaaggaccaaaaggattcgatggagccga
tggaccagatggcatgccaggaactgcatacttcccaggagctgttggacaaccaggaga
gccaggatggttgggacaaccaggacttccaggaaaacacggagaaccaggacaagatgg
agaagaaggaccaaagggagcaccaggaacaccaggatcaaatggaagagatgcttatcc
aggacaaccaggaaaggctggagagccaggagctgttggaaaagacgccaactattgccc
atgcccggctcgtcgcgactcaaagaccgaaagtgttcacgagccacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTTGGACGTTCTGGAGCATCTGGA 408 619 357 Antisense
GCATCTGGAATCTCACTTGCAGCTG 519 309 373 Antisense
CTTGCAGCTGTTCATCACATTCCAG 710 215 388 Antisense
GGAACATGTGGACCATCGGGAGATG 220 529 499 Antisense
GACCAGCTGGACCACTTGGAGATAA 392 383 536 Antisense
GAGCCGATGGACCAGATGGCATGCC 473 385 590 Antisense
GCATGCCAGGAACTGCATACTTCCC 19 311 608 Antisense
GCATACTTCCCAGGAGCTGTTGGAC 289 309 622 Antisense
GGAAAAGACGCCAACTATTGCCCAT 582 527 814 Antisense
CTCGTCGCGACTCAAAGACCGAAAG 98 223 845 Antisense
GACCGAAAGTGTTCACGAGCCACCA 589 381 861 Antisense
Sequence Source Affymetrix Proprietary Database