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[173790_at]

Description CEK095B4F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K04H4.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D70046 /WB_GENE_ID=K04H4.1 /WP=CE00246 /CHR=3 /FEA=Genomic Cluster /GEN=emb-9 /DEF=Collagen; C.elegans cDNA clone yk95b4 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 30      6grp_high1_10_10 > 04      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 03      6grp_total > 24      4grp_total > 59      6grp_highest_sub > De      6grp_cgc > 32      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5401
1 2 3 4 range
A 5014.4
(2.4)
P 		5557.6
(3)
P 		4616.3
(2)
P 		156.6
(-3)
P 		5401
B 3836
(1)
P 		5555.2
(3)
P 		5527
(3)
P 		365.6
(-3)
P 		5190
C 3681.2
(0.9)
P 		5522.4
(3)
P 		4554.9
(1.9)
P 		199.7
(-3)
P 		5323
avr 4177.2
(1.5) 		5545.1
(3) 		4899.4
(2.3) 		240.6
(-3) 		5305

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3616
1 2 3 4 5 6 range
A 2665.6
(-0.9)
P 		4684.6
(3)
P 		3103.8
(-0)
P 		1538.6
(-3)
P 		2620
(-0.9)
P 		1989.5
(-2.1)
P 		3146
B 4023.7
(3)
P 		4003.6
(2.9)
P 		3550.1
(1.7)
P 		2839.2
(-0.2)
P 		2173.4
(-2.1)
P 		1827.5
(-3)
P 		2196
C 5085.7
(3)
P 		2570.6
(-1.2)
P 		3399.8
(0.2)
P 		2187.9
(-1.8)
P 		3292.5
(0)
P 		1469.5
(-3)
P 		3616
avr 3925
(3) 		3752.9
(2.5) 		3351.2
(1.4) 		2188.6
(-1.8) 		2695.3
(-0.4) 		1762.2
(-3) 		2163
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1803
1 2 3 4 range
A 1825.7
(3)
P 		1206.4
(0.9)
P 		1206.8
(0.9)
P 		22.9
(-3)
P 		1803
B 1223.3
(2.3)
P 		1372
(3)
P 		1280.7
(2.6)
P 		77.9
(-3)
P 		1294
C 1218.6
(1.6)
P 		1587.7
(3)
P 		1587.5
(3)
P 		33.7
(-3)
P 		1554
avr 1422.5
(3) 		1388.7
(2.9) 		1358.3
(2.7) 		44.8
(-3) 		1378

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1495
1 2 3 4 5 6 range
A 491.4
(-2.5)
P 		1666.1
(3)
P 		676
(-1.7)
P 		390.2
(-3)
P 		790.6
(-1.1)
P 		484.4
(-2.6)
P 		1276
B 1400
(3)
P 		1332.6
(2.4)
P 		862.1
(-1.5)
P 		752
(-2.4)
P 		883
(-1.3)
P 		681.5
(-3)
P 		719
C 1885.1
(3)
P 		784.4
(-1.6)
P 		865.3
(-1.2)
P 		440
(-3)
P 		1065.4
(-0.4)
P 		491.9
(-2.8)
P 		1445
avr 1258.8
(3) 		1261
(3) 		801.1
(-0.8) 		527.4
(-3) 		913
(0.2) 		552.6
(-2.8) 		734
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173790_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24080
Sequence Type Exemplar sequence
Representative Public ID CEK095B4F NCBI
Target Description CEK095B4F /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K04H4.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D70046 /WB_GENE_ID=K04H4.1 /WP=CE00246 /CHR=3 /FEA=Genomic Cluster /GEN=emb-9 /DEF=Collagen; C.elegans cDNA clone yk95b4 : 5prime 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_001027492(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027492 NCBI Caenorhabditis elegans K04H4.1b (collagen) mRNA, complete cds. 11/11 None
K04H4.1b ENSEMBL cdna:known chromosome:CEL140:III:9336786:9344344:-1 gene:K04H4.1 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176314 2 1 NM_001027492 173790_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:9336809-9344292(-) 99.23 99.84
Public Domain and Genome References
Ensembl K04H4.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAE52901 Hypothetical protein K04H4.1b [Caenorhabditis elegans] ref|NP_001022663.1| K04H4.1b [Caenorhabditis elegans] 0.0
blast CAA81584 Hypothetical protein K04H4.1a [Caenorhabditis elegans] ref|NP_001022662.1| K04H4.1a [Caenorhabditis elegans] 0.0
blast P17139 Collagen alpha 1(IV) chain precursor 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001442 EMBL-EBI Type 4 procollagen, C-terminal repeat 3.1E-70
Pfam IPR001442 EMBL-EBI Type 4 procollagen, C-terminal repeat 2.0E-75
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.8E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.7E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.7E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.4E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.0E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.0E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.4E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.2E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-12
Sequence
Target Sequence 
>C. ELEGANS:173790_AT
gaaccgataatcatcccaatcatcactcgctttttactatttatcaagttctacttaaat
ctttctttatattttctctctattaaatatcaaccattttctatgctttttacaatgttt
cttcaacaaaaaatcttccatactaacaaaactgccaaaagagagcaagttctgtgtgat
acgaattactcctgccccctttgaaaacaagat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAACCGATAATCATCCCAATCATCA 212 347 5239 Antisense
CAATCATCACTCGCTTTTTACTATT 189 181 5255 Antisense
ATCACTCGCTTTTTACTATTTATCA 106 29 5260 Antisense
TCAAGTTCTACTTAAATCTTTCTTT 302 633 5282 Antisense
AATCTTTCTTTATATTTTCTCTCTA 165 171 5296 Antisense
ATATCAACCATTTTCTATGCTTTTT 156 19 5325 Antisense
ATGCTTTTTACAATGTTTCTTCAAC 428 43 5341 Antisense
AATCTTCCATACTAACAAAACTGCC 345 169 5370 Antisense
AAGAGAGCAAGTTCTGTGTGATACG 346 153 5397 Antisense
TGTGTGATACGAATTACTCCTGCCC 329 555 5411 Antisense
CTCCTGCCCCCTTTGAAAACAAGAT 584 233 5427 Antisense
Sequence Source Affymetrix Proprietary Database