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[189629_at] cuticular collagen

Description ZC373.7 /REP_DB=WormBase Gene ID /WP=CE02380 /TR=Q23263 /GB=CAA88979.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 26      6grp_high1_10_10 > 62      6grp_highest_nonorm > 25      6grp_total > 62      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 92      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 687
1 2 3 4 range
A 527.2
(0.5)
P 		580.4
(1)
P 		808.6
(3)
P 		121.9
(-3)
A 		687
B 483.9
(1.3)
P 		621.7
(3)
P 		583.1
(2.5)
P 		130.8
(-3)
A 		491
C 460
(-0.1)
P 		747.2
(3)
P 		589.5
(1.3)
P 		186.1
(-3)
A 		561
avr 490.4
(1) 		649.8
(2.9) 		660.4
(3) 		146.3
(-3) 		514

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9302
1 2 3 4 5 6 range
A 776.8
(-2.9)
P 		2262
(-1.5)
P 		6980.7
(3)
P 		6934.1
(3)
P 		2225.3
(-1.5)
P 		699.5
(-3)
P 		6281
B 871.9
(-2.7)
P 		1588.6
(-2.3)
P 		9340.4
(3)
P 		4877.6
(-0)
P 		1989.6
(-2)
P 		494.1
(-3)
P 		8846
C 1243.4
(-2.5)
P 		1501.3
(-2.3)
P 		9727
(3)
P 		4997.4
(-0.1)
P 		3783.5
(-0.8)
P 		424.7
(-3)
P 		9302
avr 964
(-2.7) 		1784
(-2.1) 		8682.7
(3) 		5603
(0.7) 		2666.1
(-1.4) 		539.4
(-3) 		8143
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 197
1 2 3 4 range
A 192
(2.4)
P 		126
(0.4)
P 		211.4
(3)
P 		17.8
(-3)
A 		194
B 154.3
(3)
P 		153.5
(3)
P 		135.1
(2.1)
P 		27.9
(-3)
A 		126
C 152.3
(1)
P 		214.8
(3)
P 		205.4
(2.7)
P 		31.4
(-3)
A 		183
avr 166.2
(2.3) 		164.8
(2.3) 		184
(3) 		25.7
(-3) 		158

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2334
1 2 3 4 5 6 range
A 143.2
(-3)
P 		804.5
(-0.5)
P 		1520.2
(2.1)
P 		1758.7
(3)
P 		671.5
(-1)
P 		170.3
(-2.9)
P 		1616
B 303.4
(-2.7)
P 		528.8
(-2)
P 		2268.1
(3)
P 		1291.9
(0.2)
P 		808.4
(-1.2)
P 		184.3
(-3)
P 		2084
C 460.9
(-2.2)
P 		458.1
(-2.2)
P 		2475.7
(3)
P 		1005
(-0.8)
P 		1224.3
(-0.2)
P 		142.2
(-3)
P 		2334
avr 302.5
(-2.6) 		597.1
(-1.7) 		2088
(3) 		1351.9
(0.7) 		901.4
(-0.7) 		165.6
(-3) 		1922
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189629_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16439
Sequence Type Exemplar sequence
Representative Public ID ZC373.7 NCBI
Target Description ZC373.7 /REP_DB=WormBase Gene ID /WP=CE02380 /TR=Q23263 /GB=CAA88979.1 /SUBMIT=HINXTON /CHR=X /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_077291(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077291 NCBI Caenorhabditis elegans COLlagen family member (col-176) (col-176) mRNA, complete cds. 11/11 None
SNAP00000017668 ENSEMBL cdna:SNAP chromosome:CEL140:X:10077556:10078499:1 11/11 None
GENEFINDER00000017670 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:10077556:10078499:1 11/11 None
ZC373.7 ENSEMBL cdna:known chromosome:CEL140:X:10077542:10078530:1 gene:ZC373.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_062479 1/11 Cross Hyb Matching Probes A 
SNAP00000005486 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005502 1/11 Cross Hyb Matching Probes None
F11G11.12 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10077555-10078499(+) 95.19 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-176
Ensembl ZC373.7
Entrez Gene 181219 Entrez gene
SwissProt Q23263 EMBL-EBI
WormBase CE02380 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 CAA88979 Hypothetical protein ZC373.7 [Caenorhabditis elegans] ref|NP_509692.1| COLlagen family member (col-176) [Caenorhabditis elegans] 3.0E-64
blast CAE58777 Hypothetical protein CBG01972 [Caenorhabditis briggsae] 4.0E-58
blast CAB00860 Hypothetical protein F54D1.3 [Caenorhabditis elegans] ref|NP_502116.1| F54D1.3 [Caenorhabditis elegans] 8.0E-44
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0011
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509692.1 1 7-29
ZC373.7 1 7-29
SNAP00000017668 1 7-29
GENEFINDER00000017670 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189629_AT
aagggacaagacagcaccacaacctttgctccaatcaactgcccaactgccccatccgac
tgcatcaagtgtgctccaggaccagccggacctgctggatcagctggaccagcaggacca
aagggaccagatggacgcccaggacagccaggatctgctggacacccaggagctccagga
caaccaggatccaagggaaacaatggagctccaggagccgccggagggccaggacagcca
ggacgtccaggaaaggacggacaacgcggaaagggatccgctggagctccaggagcccca
ggaaaggccggaccagccggaccagccggaggaccaggaaacaacggatccgctggaact
ccagga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGGGACAAGACAGCACCACAACCT 175 159 388 Antisense
CCCCATCCGACTGCATCAAGTGTGC 578 261 437 Antisense
ATCCGACTGCATCAAGTGTGCTCCA 136 39 441 Antisense
ACTGCATCAAGTGTGCTCCAGGACC 295 97 446 Antisense
CCAGCCGGACCTGCTGGATCAGCTG 617 273 469 Antisense
AAAGGGACCAGATGGACGCCCAGGA 615 121 507 Antisense
ACAACCAGGATCCAAGGGAAACAAT 180 111 567 Antisense
GCGGAAAGGGATCCGCTGGAGCTCC 56 293 653 Antisense
GAGGACCAGGAAACAACGGATCCGC 269 403 716 Antisense
GAAACAACGGATCCGCTGGAACTCC 85 355 725 Antisense
CAACGGATCCGCTGGAACTCCAGGA 663 183 729 Antisense
Sequence Source Affymetrix Proprietary Database