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[188294_at] collagen

Description F32G8.5 /REP_DB=WormBase Gene ID /WP=CE05794 /TR=Q19979 /GB=CAA96649.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 99      4grp_total > 24      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 75
1 2 3 4 range
A 15.2
(-3)
A 		24.5
(-1.9)
A 		39.6
(0)
A 		64
(3)
A 		49
B 36.2
(-2.2)
A 		29.6
(-3)
A 		79.1
(3)
A 		49.1
(-0.6)
A 		50
C 64.8
(-3)
A 		87.4
(2.3)
A 		71.8
(-1.4)
A 		90.4
(3)
P 		26
avr 38.7
(-3) 		47.2
(-1.2) 		63.5
(2.1) 		67.8
(3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 347
1 2 3 4 5 6 range
A 78.9
(-2)
A 		20.7
(-3)
A 		78.6
(-2)
A 		91
(-1.8)
A 		123.1
(-1.2)
A 		360.8
(3)
P 		340
B 13.9
(-3)
A 		65.6
(-1.7)
A 		16.6
(-2.9)
A 		50.5
(-2.1)
A 		247.1
(2.7)
P 		259.8
(3)
P 		246
C 16.4
(-3)
A 		51.6
(-2.3)
A 		60.2
(-2.1)
A 		13.8
(-3)
A 		327.9
(3)
P 		221.9
(1)
P 		314
avr 36.4
(-3) 		46
(-2.8) 		51.8
(-2.6) 		51.8
(-2.6) 		232.7
(1.8) 		280.8
(3) 		244
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 5.5
(-2.8)
A 		5.3
(-3)
A 		10.3
(3)
A 		9.4
(1.9)
A 		5
B 11.5
(-0.7)
A 		7.3
(-3)
A 		18.3
(3)
A 		10.5
(-1.3)
A 		11
C 21.4
(0.8)
A 		25.1
(3)
A 		25
(2.9)
A 		15.2
(-3)
P 		10
avr 12.8
(-1.9) 		12.6
(-2.1) 		17.9
(3) 		11.7
(-3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 103
1 2 3 4 5 6 range
A 14.5
(-2.5)
A 		7.4
(-3)
A 		17.1
(-2.3)
A 		23.1
(-1.8)
A 		37.1
(-0.8)
A 		87.8
(3)
P 		80
B 4.8
(-3)
A 		21.8
(-1.9)
A 		4
(-3)
A 		13.4
(-2.4)
A 		100.4
(3)
P 		96.9
(2.8)
P 		96
C 6.1
(-2.8)
A 		15.8
(-2.2)
A 		15.3
(-2.3)
A 		2.8
(-3)
A 		106.1
(3)
P 		74.3
(1.2)
P 		103
avr 8.5
(-3) 		15
(-2.5) 		12.1
(-2.7) 		13.1
(-2.6) 		81.2
(2.6) 		86.3
(3) 		78
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188294_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11954
Sequence Type Exemplar sequence
Representative Public ID F32G8.5 NCBI
Target Description F32G8.5 /REP_DB=WormBase Gene ID /WP=CE05794 /TR=Q19979 /GB=CAA96649.1 /SUBMIT=HINXTON /CHR=5 /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_073308(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073308 NCBI Caenorhabditis elegans F32G8.5 (collagen) mRNA, complete cds. 11/11 None
SNAP00000017273 ENSEMBL cdna:SNAP chromosome:CEL140:V:10564013:10564732:1 11/11 None
GENEFINDER00000017278 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10563503:10568772:1 11/11 None
F32G8.5 ENSEMBL cdna:known chromosome:CEL140:V:10563503:10564732:1 gene:F32G8.5 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
chrV:10563502-10564732(+) 99.21 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-152
Ensembl F32G8.5
Entrez Gene 185212 Entrez gene
SwissProt Q19979 EMBL-EBI
WormBase CE05794 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 CAA96649 Hypothetical protein F32G8.5 [Caenorhabditis elegans] ref|NP_505709.1| F32G8.5 [Caenorhabditis elegans] 1.0E-123
blast CAA96649 Hypothetical protein F32G8.5 [Caenorhabditis elegans] ref|NP_505709.1| F32G8.5 [Caenorhabditis elegans] 1.0E-122
blast CAA96650 Hypothetical protein F32G8.6 [Caenorhabditis elegans] ref|NP_505710.1| abnormal CATecholamine distribution family member (cat-4) [Caenorhabditis elegans] sp|Q19980|GCH1_CAEEL GTP cyclohydrolase I (GTP-CH-I) 1.0E-109
blast CAE64846 Hypothetical protein CBG09642 [Caenorhabditis briggsae] 1.0E-101
blast CAA96649 Hypothetical protein F32G8.5 [Caenorhabditis elegans] ref|NP_505709.1| F32G8.5 [Caenorhabditis elegans] 1.0E-100
blast CAE64844 Hypothetical protein CBG09640 [Caenorhabditis briggsae] 2.0E-65
blast CAE64844 Hypothetical protein CBG09640 [Caenorhabditis briggsae] 6.0E-51
blast CAB04587 Hypothetical protein K08C9.4 [Caenorhabditis elegans] ref|NP_492936.1| COLlagen family member (col-65) [Caenorhabditis elegans] 1.0E-39
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.2E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.9E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.9E-11
Pfam IPR001474 EMBL-EBI GTP cyclohydrolase I 1.8E-65
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505709.1 1 7-29
F32G8.5 1 7-29
GENEFINDER00000017278 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188294_AT
aacaattgtccggtgggacctcctggtccaccaggagctgctggaacaaatggggaggac
gggagcccaggagttgcaggacaaaatggaaatgaaggaaagtcaataaatgcacaaatt
gatacatatgctaccccatcgtgtactcaatgcacaccaggacccccaggagcgccaggg
cccgatggagtttctgggccagttggaattaatggtcgaccaggagagaatggcgccgat
ggaaatccaggtgctcctggagaggttggtgcaccaggagatcaaggaggtgcaggaaac
caaggggctgctggaaaacccggcttgccaggaaagaatggacagagaggatctggtcac
cctggacctactggaccagtcggtgaaacgggaaacgctggtaacaatggacacccagga
gttgatggagaaaatggaaaacctggaactcgcggagaagccggattgcagggaaaagaa
ggtcaaacaggtccaattggaccagcgggacaaaaaggagaaaatggaatgccaggccta
gatgctggatattgtccatgcccggagagaactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACAATTGTCCGGTGGGACCTCCTG 495 133 277 Antisense
GGAGGACGGGAGCCCAGGAGTTGCA 359 515 330 Antisense
ATTGATACATATGCTACCCCATCGT 503 3 394 Antisense
TACCCCATCGTGTACTCAATGCACA 197 649 408 Antisense
CCCGATGGAGTTTCTGGGCCAGTTG 529 257 457 Antisense
TGCTCCTGGAGAGGTTGGTGCACCA 569 581 528 Antisense
CTGCTGGAAAACCCGGCTTGCCAGG 68 235 584 Antisense
GACAGAGAGGATCTGGTCACCCTGG 72 367 617 Antisense
CCCTGGACCTACTGGACCAGTCGGT 266 231 636 Antisense
GGAAAACCTGGAACTCGCGGAGAAG 702 527 712 Antisense
TATTGTCCATGCCCGGAGAGAACTT 29 661 826 Antisense
Sequence Source Affymetrix Proprietary Database