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[173611_s_at]

Description CEK058A2R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y11D7A.11 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65490 /WB_GENE_ID=Y11D7A.11 /WP=CE20194 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk58a2 : 3prime end, single read.
Cluster 6grp_total > 99      4grp_total > 26      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 16.4
(-3)
A 		104.3
(3)
A 		61.6
(0.1)
A 		97.4
(2.5)
P 		88
B 38.2
(0.2)
A 		45.6
(1.2)
A 		15.8
(-3)
A 		57.9
(3)
A 		42
C 26.3
(-3)
A 		40.2
(-1.3)
A 		34.7
(-2)
A 		75.7
(3)
P 		49
avr 27
(-3) 		63.4
(1.4) 		37.4
(-1.8) 		77
(3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 989
1 2 3 4 5 6 range
A 32.1
(-2.9)
A 		15.5
(-3)
A 		21.4
(-3)
A 		134.6
(-2.1)
P 		769.1
(3)
P 		765.7
(3)
P 		754
B 7.5
(-3)
A 		13
(-3)
A 		54
(-2.7)
A 		134.2
(-2.2)
P 		829.9
(2)
P 		996.9
(3)
P 		989
C 56.8
(-2.9)
A 		45.9
(-3)
A 		53.5
(-2.9)
A 		219.5
(-1.7)
P 		827.3
(3)
P 		824.2
(3)
P 		781
avr 32.1
(-2.9) 		24.8
(-3) 		43
(-2.9) 		162.8
(-2) 		808.8
(2.6) 		862.3
(3) 		838
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 6
(-3)
A 		22.6
(3)
A 		16.1
(0.7)
A 		14.3
(0)
P 		17
B 12.2
(2.9)
A 		11.3
(2.3)
A 		3.7
(-3)
A 		12.3
(3)
A 		9
C 8.7
(-3)
A 		11.6
(1.2)
A 		12.1
(2)
A 		12.8
(3)
P 		4
avr 9
(-3) 		15.2
(3) 		10.6
(-1.5) 		13.1
(1) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 369
1 2 3 4 5 6 range
A 5.9
(-3)
A 		5.5
(-3)
A 		4.7
(-3)
A 		34.1
(-2.2)
P 		232.1
(3)
P 		186.4
(1.8)
P 		227
B 2.6
(-3)
A 		4.3
(-3)
A 		13.1
(-2.8)
A 		35.5
(-2.5)
P 		337.2
(2.4)
P 		371.8
(3)
P 		369
C 21.1
(-2.8)
A 		14
(-3)
A 		13.6
(-3)
A 		44.1
(-2.3)
P 		267.7
(2.8)
P 		275.9
(3)
P 		262
avr 9.9
(-3) 		7.9
(-3) 		10.5
(-2.9) 		37.9
(-2.3) 		279
(3) 		278
(3) 		271
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173611_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24739
Sequence Type Exemplar sequence
Representative Public ID CEK058A2R NCBI
Target Description CEK058A2R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y11D7A.11 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65490 /WB_GENE_ID=Y11D7A.11 /WP=CE20194 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk58a2 : 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_069216(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069216 NCBI Caenorhabditis elegans COLlagen family member (col-120) (col-120) mRNA, complete cds. 11/11 None
SNAP00000011209 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9260646:9261433:-1 11/11 None
GENEFINDER00000011231 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9260646:9261730:-1 11/11 None
Y11D7A.11 ENSEMBL cdna:known chromosome:CEL140:IV:9260598:9261730:-1 gene:Y11D7A.11 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
chrIV:9260614-9261737(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol col-120
Ensembl Y11D7A.11
Entrez Gene 177748 Entrez gene
SwissProt Q9XWR2 EMBL-EBI
WormBase CE20194 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 CAA21586 Hypothetical protein Y11D7A.11 [Caenorhabditis elegans] ref|NP_501617.1| COLlagen family member (col-120) [Caenorhabditis elegans] 1.0E-78
blast CAA21586 Hypothetical protein Y11D7A.11 [Caenorhabditis elegans] ref|NP_501617.1| COLlagen family member (col-120) [Caenorhabditis elegans] 2.0E-46
blast CAE69054 Hypothetical protein CBG15063 [Caenorhabditis briggsae] 3.0E-18
blast CAE69054 Hypothetical protein CBG15063 [Caenorhabditis briggsae] 7.0E-12
blast CAE69052 Hypothetical protein CBG15061 [Caenorhabditis briggsae] 4.0E-11
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.9E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.9E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501617.1 1 20-42
Y11D7A.11 1 20-42
GENEFINDER00000011231 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:173611_S_AT
tgttgcagctgtggaattggtcttgctgggccagcaggtttcccaggtcgaccaggacga
gatggaatagatggaccagccggaaaacctggacgagatgggcaagatttggatggagaa
tcgtcttctgatggatcacaaattgagcttgattgcccagcaggaccaccagggccacca
ggaaatccaggtcctcagggtaattctgggcgacctggaatggatggtatgcctggtaga
aatggaagatgcgggagaccaggagagcagggagaacgtggaccaaatggagaagatgga
cgacctggaagacgtggagacgatggaatgcccggaacagttaacgaaattccaggccaa
gcaggtccaccaggtcttcgtggtgctcctggagctactggatcgcaaggaccacgtgga
aatgatggtagaccaggaaacaagggaccagcaggaccacctggagaccaaggatttgat
ggagcaccaggaggacctggagctgatggagaacctggagcacaaggacctttgggagca
aagggagaatgttcacactgcccacctccacgaactgctcctggatactaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTTGCAGCTGTGGAATTGGTCTTG 551 563 365 Antisense
TTGCTGGGCCAGCAGGTTTCCCAGG 7 663 387 Antisense
AAATTGAGCTTGATTGCCCAGCAGG 489 115 504 Antisense
GGTCCTCAGGGTAATTCTGGGCGAC 498 501 554 Antisense
GAGACGATGGAATGCCCGGAACAGT 666 391 681 Antisense
CGAAATTCCAGGCCAAGCAGGTCCA 235 251 709 Antisense
TGCTCCTGGAGCTACTGGATCGCAA 568 581 748 Antisense
GCTACTGGATCGCAAGGACCACGTG 47 303 758 Antisense
GAACCTGGAGCACAAGGACCTTTGG 275 345 875 Antisense
AGGGAGAATGTTCACACTGCCCACC 427 57 906 Antisense
TCCACGAACTGCTCCTGGATACTAA 58 589 931 Antisense
Sequence Source Affymetrix Proprietary Database