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[188250_at] collagen

Description D2023.7 /REP_DB=WormBase Gene ID /WP=CE09077 /TR=O17734 /GB=CAB02874.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 83      4grp_total > 56      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 4
(-3)
A 		14.8
(-0.9)
A 		35.4
(3)
A 		14.4
(-1)
A 		31
B 7.1
(-2.2)
A 		7.8
(-2)
A 		21.7
(3)
A 		4.9
(-3)
A 		17
C 5.4
(-3)
A 		30
(-0)
A 		55.3
(3)
A 		6
(-2.9)
A 		50
avr 5.5
(-3) 		17.5
(-0.8) 		37.5
(3) 		8.4
(-2.5) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 19018
1 2 3 4 5 6 range
A 11.2
(-3)
A 		32.4
(-3)
A 		991.1
(-2.6)
P 		16256.3
(3)
P 		13520.2
(2)
P 		2490
(-2.1)
P 		16245
B 11.3
(-3)
A 		15.4
(-3)
A 		1078.5
(-2.5)
P 		13601.2
(3)
P 		13384.4
(2.9)
P 		2256.7
(-2)
P 		13590
C 70.5
(-3)
A 		47.9
(-3)
A 		1079.9
(-2.7)
P 		13613.1
(1.3)
P 		19028.9
(3)
P 		1956
(-2.4)
P 		18981
avr 31
(-3) 		31.9
(-3) 		1049.8
(-2.6) 		14490.2
(2.7) 		15311.2
(3) 		2234.2
(-2.1) 		15280
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 1.5
(-3)
A 		3.2
(-1.7)
A 		9.3
(3)
A 		2.1
(-2.5)
A 		8
B 2.3
(-1.1)
A 		1.9
(-1.7)
A 		5
(3)
A 		1
(-3)
A 		4
C 1.8
(-2.7)
A 		8.6
(-0.5)
A 		19.3
(3)
A 		1
(-3)
A 		18
avr 1.9
(-2.7) 		4.6
(-1) 		11.2
(3) 		1.4
(-3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6155
1 2 3 4 5 6 range
A 2.1
(-3)
A 		11.5
(-3)
A 		215.9
(-2.7)
P 		4123
(3)
P 		4079.8
(2.9)
P 		606.2
(-2.1)
P 		4121
B 3.9
(-3)
A 		5.1
(-3)
A 		261.9
(-2.7)
P 		3602.5
(1)
P 		5437.9
(3)
P 		841.5
(-2.1)
P 		5434
C 26.1
(-3)
A 		14.6
(-3)
A 		274.8
(-2.7)
P 		2737.6
(-0.3)
P 		6157.5
(3)
P 		654.8
(-2.4)
P 		6143
avr 10.7
(-3) 		10.4
(-3) 		250.9
(-2.7) 		3487.7
(1) 		5225.1
(3) 		700.8
(-2.2) 		5215
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188250_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14427
Sequence Type Exemplar sequence
Representative Public ID D2023.7 NCBI
Target Description D2023.7 /REP_DB=WormBase Gene ID /WP=CE09077 /TR=O17734 /GB=CAB02874.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=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_073580(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073580 NCBI Caenorhabditis elegans D2023.7 (collagen) mRNA, complete cds. 11/11 None
SNAP00000024930 ENSEMBL cdna:SNAP chromosome:CEL140:V:11832183:11833616:1 11/11 None
GENEFINDER00000024933 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11832183:11833616:1 11/11 None
D2023.7 ENSEMBL cdna:known chromosome:CEL140:V:11832183:11833791:1 gene:D2023.7 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:11832182-11833616(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-158
Ensembl D2023.7
Entrez Gene 179619 Entrez gene
SwissProt O17734 EMBL-EBI
WormBase CE09077 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
18346 protein amino acid prenylation 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
8318 protein prenyltransferase activity 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 CAB02874 Hypothetical protein D2023.7 [Caenorhabditis elegans] ref|NP_505981.1| D2023.7 [Caenorhabditis elegans] 6.0E-69
blast CAE75287 Hypothetical protein CBG23255 [Caenorhabditis briggsae] 1.0E-66
blast CAB01588 Hypothetical protein ZK836.1 [Caenorhabditis elegans] ref|NP_506061.1| ZK836.1 [Caenorhabditis elegans] gb|AAL08218.1| cuticle collagen protein LON-3 [Caenorhabditis elegans] gb|AAL76993.1| cuticle collagen LON-3 [Caenorhabditis elegans] sp|Q23628|LON3_CAEEL Cuticle collagen lon-3 precursor 4.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.7E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.9E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505981.1 1 7-29
D2023.7 1 7-29
SNAP00000024930 1 7-29
GENEFINDER00000024933 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188250_AT
gatgtattacttgtgctccaggaaagccaggatctccaggagagcgtggaaagccaggtc
tccgtggaatgcgtggaccacgtggaactggaggatctccaggaaccgatggatatccag
gacgtccaggagagatgggaccaccaggaccaccaggagacgatggaaagccaggatcga
atggagaaaaaggacaagatgtcgagcaaccaacaccaagaaagggaccacgtggaccac
caggagattctggaccaccaggaccagaaggagacgctggaaacgatggaccagttggag
ctgcaggagcaccaggaccagacggaatcaacggattccaaggaccaggtggaccaccag
gagaggaaggaaagccaggagaagatggaaaggtcggagacgatgctgcctattgtccat
gcccagacagaaacgctccaaaggagaactacgcttctgctccatcccacaacccatcaa
atgctccaggagccagttattctgctggaaccggtggatactctggtggcactgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTATTACTTGTGCTCCAGGAAA 217 409 458 Antisense
AGAGCGTGGAAAGCCAGGTCTCCGT 149 69 498 Antisense
TGGAAAGCCAGGTCTCCGTGGAATG 652 545 504 Antisense
GGAGGATCTCCAGGAACCGATGGAT 688 515 547 Antisense
AGATGTCGAGCAACCAACACCAAGA 665 67 654 Antisense
AAGGTCGGAGACGATGCTGCCTATT 565 159 847 Antisense
ATTGTCCATGCCCAGACAGAAACGC 595 3 869 Antisense
GCCCAGACAGAAACGCTCCAAAGGA 150 287 878 Antisense
GCTCCAGGAGCCAGTTATTCTGCTG 443 297 940 Antisense
ATTCTGCTGGAACCGGTGGATACTC 518 9 956 Antisense
CGGTGGATACTCTGGTGGCACTGGA 146 245 969 Antisense
Sequence Source Affymetrix Proprietary Database