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[190353_s_at]

Description K04H4.1 /REP_DB=WormBase Gene ID /WP=CE00246 /GEN=emb-9 /TR=SW:P17139 /GB=CAA81584.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Collagen
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 32      4grp_high_8_8 > 43      6grp_highest_nonorm > 04      6grp_total > 05      4grp_total > 52      6grp_highest_sub > De      6grp_cgc > 22      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7117
1 2 3 4 range
A 7434.8
(3)
P 		6148.3
(1.9)
P 		5424.1
(1.3)
P 		434.6
(-3)
P 		7000
B 6983.8
(3)
P 		6322.4
(2.4)
P 		4253
(0.5)
P 		365.9
(-3)
P 		6618
C 6282.7
(3)
P 		6047.5
(2.8)
P 		4947.4
(1.7)
P 		318.2
(-3)
P 		5965
avr 6900.4
(3) 		6172.7
(2.3) 		4874.8
(1.1) 		372.9
(-3) 		6528

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6594
1 2 3 4 5 6 range
A 7660
(3)
P 		5632.5
(0.8)
P 		3511.9
(-1.5)
P 		3378.8
(-1.7)
P 		3110.7
(-2)
P 		2178.3
(-3)
P 		5482
B 7039.5
(3)
P 		5846.3
(1.6)
P 		3114.6
(-1.5)
P 		3423
(-1.2)
P 		2509.7
(-2.2)
P 		1845.4
(-3)
P 		5194
C 6840.8
(3)
P 		5231
(1.3)
P 		5244.9
(1.3)
P 		2598.9
(-1.4)
P 		4023
(0.1)
P 		1066.3
(-3)
P 		5775
avr 7180.1
(3) 		5569.9
(1.2) 		3957.1
(-0.5) 		3133.6
(-1.4) 		3214.5
(-1.3) 		1696.7
(-3) 		5483
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2653
1 2 3 4 range
A 2707
(3)
P 		1334.6
(-0.1)
P 		1418
(0.1)
P 		63.6
(-3)
P 		2643
B 2227.1
(3)
P 		1561.5
(1.1)
P 		985.5
(-0.5)
P 		78
(-3)
P 		2149
C 2079.8
(3)
P 		1738.7
(2)
P 		1724.3
(1.9)
P 		53.7
(-3)
P 		2026
avr 2338
(3) 		1544.9
(0.9) 		1375.9
(0.5) 		65.1
(-3) 		2273

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2179
1 2 3 4 5 6 range
A 1412.1
(0.6)
P 		2003.2
(3)
P 		764.8
(-2)
P 		856.9
(-1.7)
P 		938.7
(-1.3)
P 		530.3
(-3)
P 		1473
B 2449.4
(3)
P 		1946
(1.3)
P 		756.3
(-2.8)
P 		906.6
(-2.3)
P 		1019.6
(-1.9)
P 		688.2
(-3)
P 		1761
C 2535.6
(3)
P 		1596.1
(0.4)
P 		1334.9
(-0.3)
P 		522.6
(-2.5)
P 		1301.8
(-0.4)
P 		357
(-3)
P 		2179
avr 2132.4
(3) 		1848.4
(1.9) 		952
(-1.4) 		762
(-2.1) 		1086.7
(-0.9) 		525.2
(-3) 		1607
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190353_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7359
Sequence Type Exemplar sequence
Representative Public ID K04H4.1 NCBI
Target Description K04H4.1 /REP_DB=WormBase Gene ID /WP=CE00246 /GEN=emb-9 /TR=SW:P17139 /GB=CAA81584.1 /SUBMIT=HINXTON /CHR=3 /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_001027492(11), NM_001027491(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
NM_001027491 NCBI Caenorhabditis elegans K04H4.1a (collagen) mRNA, complete cds. 11/11 None
SNAP00000032557 ENSEMBL cdna:SNAP chromosome:CEL140:III:9337061:9344295:-1 11/11 None
GENEFINDER00000032568 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9337061:9344295:-1 11/11 None
K04H4.1b ENSEMBL cdna:known chromosome:CEL140:III:9336786:9344344:-1 gene:K04H4.1 11/11 A 
K04H4.1a ENSEMBL cdna:known chromosome:CEL140:III:9337061:9344295:-1 gene:K04H4.1 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:9337056-9344291(-) 99.37 99.9
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
blast CAA40299 alpha1(IV) collagen [Caenorhabditis elegans] 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 7.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.8E-12
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
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 2.3E-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:190353_S_AT
cttggtcaaccaggatcttgcctctccaaattcaacacaatgccattcatgttctgtaat
atgaacagcgtctgccacgtttccagccgtaacgattactcgttctggttgtcaactgac
gagccaatgacaccaatgatgaatccagtcaccggaacagcaattcgtccatacatttct
cgttgtgccgtctgtgaagttccaactcaaatcatcgcagttcactctcaagacacatca
gttccacaatgtccacaaggatggtcgggtatgtggaccggatattcctttgtcatgcac
actgccgctggagccgaaggaactggacaaagtcttcaatcgcctggttcctgtctcgaa
gagttccgtgccgttccattcattgagtgccacggaagaggaacatgcaattattatgcc
accaatcacggattctggctttccatcgttgatca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTGGTCAACCAGGATCTTGCCTCT 652 217 4696 Antisense
ATATGAACAGCGTCTGCCACGTTTC 200 21 4754 Antisense
GATTACTCGTTCTGGTTGTCAACTG 531 429 4789 Antisense
TTCGTCCATACATTTCTCGTTGTGC 117 695 4859 Antisense
TTGTGCCGTCTGTGAAGTTCCAACT 585 689 4878 Antisense
AAATCATCGCAGTTCACTCTCAAGA 539 117 4904 Antisense
GACACATCAGTTCCACAATGTCCAC 4 367 4927 Antisense
GATATTCCTTTGTCATGCACACTGC 257 427 4976 Antisense
GTTCCTGTCTCGAAGAGTTCCGTGC 590 441 5042 Antisense
TGCCGTTCCATTCATTGAGTGCCAC 610 583 5064 Antisense
GATTCTGGCTTTCCATCGTTGATCA 53 433 5126 Antisense
Sequence Source Affymetrix Proprietary Database