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[188345_s_at] collagen

Description F12F6.9 /REP_DB=WormBase Gene ID /WP=CE05597 /TR=Q19368 /GB=CAA97787.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 70      6grp_total > 91      4grp_total > 49      6grp_cgc > 96      6grp_high1_sub > 04      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 997
1 2 3 4 range
A 6.4
(-3)
A 		1003.3
(3)
P 		599.9
(0.6)
P 		46.1
(-2.8)
A 		997
B 45.6
(-3)
A 		780.1
(3)
P 		618.4
(1.7)
P 		42.7
(-3)
A 		737
C 38.2
(-3)
A 		600
(2.8)
P 		619
(3)
P 		76.8
(-2.6)
A 		581
avr 30.1
(-3) 		794.5
(3) 		612.4
(1.6) 		55.2
(-2.8) 		764

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 789
1 2 3 4 5 6 range
A 416.1
(-0.5)
P 		447.4
(-0.3)
P 		295.1
(-1.6)
P 		834.1
(3)
P 		489.6
(0.1)
P 		125
(-3)
P 		709
B 335.7
(-0.9)
P 		447.1
(0.1)
P 		319.5
(-1)
P 		769.5
(3)
P 		490.4
(0.5)
P 		95.3
(-3)
P 		674
C 457.1
(0.5)
P 		389.2
(-0.1)
P 		270.3
(-1.1)
P 		746.8
(3)
P 		529.2
(1.1)
P 		44.8
(-3)
A 		702
avr 403
(-0.3) 		427.9
(-0.1) 		295
(-1.2) 		783.5
(3) 		503.1
(0.6) 		88.4
(-3) 		695
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 216
1 2 3 4 range
A 2.3
(-3)
A 		217.8
(3)
P 		156.8
(1.3)
P 		6.7
(-2.9)
A 		216
B 14.5
(-2.8)
A 		192.7
(3)
P 		143.3
(1.4)
P 		9.1
(-3)
A 		184
C 12.7
(-3)
A 		172.5
(1.7)
P 		215.7
(3)
P 		13
(-3)
A 		203
avr 9.8
(-3) 		194.3
(3) 		171.9
(2.3) 		9.6
(-3) 		185

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 197
1 2 3 4 5 6 range
A 76.7
(-1.5)
P 		159.1
(1.3)
P 		64.3
(-1.9)
P 		211.5
(3)
P 		147.7
(0.9)
P 		30.4
(-3)
P 		181
B 116.8
(-0.1)
P 		148.8
(1)
P 		77.6
(-1.5)
P 		203.8
(3)
P 		199.2
(2.8)
P 		35.5
(-3)
P 		168
C 169.4
(2.9)
P 		118.8
(1)
P 		68.8
(-0.9)
P 		150.2
(2.2)
P 		171.3
(3)
P 		15
(-3)
A 		156
avr 121
(0.5) 		142.2
(1.3) 		70.2
(-1.4) 		188.5
(3) 		172.7
(2.4) 		27
(-3) 		162
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188345_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9540
Sequence Type Exemplar sequence
Representative Public ID F12F6.9 NCBI
Target Description F12F6.9 /REP_DB=WormBase Gene ID /WP=CE05597 /TR=Q19368 /GB=CAA97787.1 /SUBMIT=HINXTON /CHR=4 /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_069774(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069774 NCBI Caenorhabditis elegans F12F6.9 (collagen) mRNA, complete cds. 11/11 None
SNAP00000024850 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11550018:11551908:-1 11/11 None
GENEFINDER00000024865 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11550018:11551908:-1 11/11 None
F12F6.9 ENSEMBL cdna:known chromosome:CEL140:IV:11549996:11551931:-1 gene:F12F6.9 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:11550023-11551914(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-128
Ensembl F12F6.9
Entrez Gene 178076 Entrez gene
SwissProt Q19368 EMBL-EBI
WormBase CE05597 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
Protein Similarities
Method ID Description E-Value
blast CAA97787 Hypothetical protein F12F6.9 [Caenorhabditis elegans] ref|NP_502175.1| F12F6.9 [Caenorhabditis elegans] 1.0E-167
blast CAE62101 Hypothetical protein CBG06131 [Caenorhabditis briggsae] 1.0E-120
blast NP_491106 COLlagen family member (col-49) [Caenorhabditis elegans] gb|AAB97570.1| Collagen protein 49 [Caenorhabditis elegans] 2.0E-14
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502175.1 1 7-29
F12F6.9 1 7-29
SNAP00000024850 1 7-29
GENEFINDER00000024865 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188345_S_AT
attaaattctgtccatgtcctctagaacttgagcttttgaagggaaaacactcgaaatca
gttcgtccgtcaccaccagcgtctccttcttcaacatctcagccgactacatctgcaaca
acaacttccgaaccattgtcaccttctaccactattgtaacagatgctccagaacttgtt
acaactgaaacttcaacagaagatcttgcggtaatggaagatatcactgccacaactaca
atggaaactataacctttgcttcacaagacttaggaaaagaagaaattcgagaaccagaa
aatgtgtttggaagagctcctggagccgaaacgggaccgcaaggagggaatgagattgaa
gtattgaattatgacgatgaggaaattcgcacgattgaacttccaaaagaatatgaacat
gaagagacacgtggcccaataattaccgaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTAAATTCTGTCCATGTCCTCTAG 275 13 766 Antisense
ACTCGAAATCAGTTCGTCCGTCACC 489 93 815 Antisense
TCAACATCTCAGCCGACTACATCTG 673 629 856 Antisense
AACAACTTCCGAACCATTGTCACCT 82 133 885 Antisense
TGTCACCTTCTACCACTATTGTAAC 360 559 902 Antisense
AGATGCTCCAGAACTTGTTACAACT 620 67 927 Antisense
GGAAGATATCACTGCCACAACTACA 5 533 981 Antisense
GGAAACTATAACCTTTGCTTCACAA 9 529 1008 Antisense
GTGTTTGGAAGAGCTCCTGGAGCCG 568 483 1069 Antisense
CCTGGAGCCGAAACGGGACCGCAAG 441 259 1084 Antisense
ACACGTGGCCCAATAATTACCGAAG 681 103 1192 Antisense
Sequence Source Affymetrix Proprietary Database