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[174960_at] collagen

Description CEK120B8R_rc /REP_DB=TREMBL Accession /GB=D66653 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk120b8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      6grp_highest_nonorm > 59      6grp_total > 83      4grp_total > 49      6grp_highest_sub > 05      6grp_cgc > 88      6grp_high1_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5128
1 2 3 4 range
A 6
(-3)
A 		3272.1
(0.9)
P 		5018
(3)
P 		130.3
(-2.9)
P 		5012
B 42.6
(-3)
A 		5090.5
(2.9)
P 		5133.7
(3)
P 		121.8
(-2.9)
P 		5091
C 50.1
(-3)
A 		4841.4
(3)
P 		4742.5
(2.9)
P 		174.7
(-2.8)
P 		4791
avr 32.9
(-3) 		4401.3
(2.3) 		4964.7
(3) 		142.3
(-2.9) 		4932

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5934
1 2 3 4 5 6 range
A 872.6
(-3)
P 		2395.7
(-1)
P 		2150.3
(-1.3)
P 		3054.9
(-0.2)
P 		5502.9
(3)
P 		2989.6
(-0.3)
P 		4630
B 975.7
(-3)
P 		3016.9
(-0.7)
P 		2846.4
(-0.9)
P 		3962.3
(0.4)
P 		6225.8
(3)
P 		3474
(-0.1)
P 		5250
C 1113.7
(-3)
P 		2726.5
(-1.3)
P 		1949.1
(-2.1)
P 		3626.7
(-0.4)
P 		6806.6
(3)
P 		2662.9
(-1.4)
P 		5693
avr 987.3
(-3) 		2713
(-1) 		2315.3
(-1.5) 		3548
(-0) 		6178.4
(3) 		3042.2
(-0.6) 		5191
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1651
1 2 3 4 range
A 2.2
(-3)
A 		710.3
(0.2)
P 		1311.8
(3)
P 		19.1
(-2.9)
P 		1310
B 13.6
(-3)
A 		1257.2
(3)
P 		1189.6
(2.7)
P 		25.9
(-2.9)
P 		1244
C 16.6
(-3)
A 		1391.9
(2)
P 		1652.9
(3)
P 		29.5
(-3)
P 		1636
avr 10.8
(-3) 		1119.8
(1.8) 		1384.8
(3) 		24.8
(-2.9) 		1374

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2369
1 2 3 4 5 6 range
A 160.8
(-3)
P 		852
(-0.2)
P 		468.3
(-1.8)
P 		774.8
(-0.5)
P 		1660.5
(3)
P 		727.9
(-0.7)
P 		1500
B 339.5
(-3)
P 		1004.2
(-1.2)
P 		691.2
(-2)
P 		1049.5
(-1.1)
P 		2529.5
(3)
P 		1295.5
(-0.4)
P 		2190
C 412.8
(-3)
P 		831.9
(-1.6)
P 		496.1
(-2.7)
P 		729.3
(-1.9)
P 		2202.5
(3)
P 		891.4
(-1.4)
P 		1790
avr 304.4
(-3) 		896
(-1.1) 		551.9
(-2.2) 		851.2
(-1.2) 		2130.8
(3) 		971.6
(-0.8) 		1826
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174960_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20957
Sequence Type Exemplar sequence
Representative Public ID CEK120B8R NCBI
Target Description CEK120B8R_rc /REP_DB=TREMBL Accession /GB=D66653 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk120b8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_067299(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067299 NCBI Caenorhabditis elegans ZK1010.7 (collagen) mRNA, complete cds. 11/11 None
ZK1010.7 ENSEMBL cdna:known chromosome:CEL140:III:12991921:12993225:-1 gene:ZK1010.7 11/11 A 
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:12992016-12992398(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-97
Ensembl ZK1010.7
Entrez Gene 176721 Entrez gene
SwissProt O18286 EMBL-EBI
WormBase CE15507 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 CAB04973 Hypothetical protein ZK1010.7 [Caenorhabditis elegans] ref|NP_499700.1| ZK1010.7 [Caenorhabditis elegans] 7.0E-64
blast CAE69571 Hypothetical protein CBG15783 [Caenorhabditis briggsae] 3.0E-63
blast CAD66221 Hypothetical protein Y41C4A.19 [Caenorhabditis elegans] ref|NP_871711.1| Y41C4A.19 [Caenorhabditis elegans] 5.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.6E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499700.1 1 13-35
ZK1010.7 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:174960_AT
ggaacacgtcgttaagatcgttaagatccgatcactcattaacttatctcttcgtggttt
cccacccacgcctcttctttgccttcagagttcgggtaaatccgtgctgtcttttctcgt
ttcttttcaactgtatttgtaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAACACGTCGTTAAGATCGTTAAG 369 527 205 Antisense
AGATCGTTAAGATCCGATCACTCAT 113 67 219 Antisense
AGATCCGATCACTCATTAACTTATC 233 67 228 Antisense
ATCACTCATTAACTTATCTCTTCGT 108 29 235 Antisense
CATTAACTTATCTCTTCGTGGTTTC 248 215 241 Antisense
CCTCTTCTTTGCCTTCAGAGTTCGG 641 267 275 Antisense
TCTTTGCCTTCAGAGTTCGGGTAAA 439 1 280 Antisense
GAGTTCGGGTAAATCCGTGCTGTCT 72 395 292 Antisense
TTCGGGTAAATCCGTGCTGTCTTTT 555 693 295 Antisense
TTTTCTCGTTTCTTTTCAACTGTAT 430 677 316 Antisense
GTTTCTTTTCAACTGTATTTGTACA 55 451 323 Antisense
Sequence Source Affymetrix Proprietary Database