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[190025_at] cuticular collagen

Description F53G12.7 /REP_DB=WormBase Gene ID /WP=CE11018 /TR=O01799 /GB=AAB54156.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 91      4grp_total > 41      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_rule_based > S4      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 4.1
(-3)
A 		22.6
(3)
A 		12.2
(-0.4)
A 		10.1
(-1.1)
A 		19
B 4.4
(-3)
A 		10.9
(-0.7)
A 		21.2
(3)
A 		4.6
(-2.9)
A 		17
C 3.4
(-3)
A 		13.1
(3)
A 		10.3
(1.3)
A 		9.5
(0.8)
A 		10
avr 4
(-3) 		15.5
(3) 		14.6
(2.5) 		8.1
(-0.9) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4824
1 2 3 4 5 6 range
A 15.3
(-3)
A 		20.5
(-3)
A 		127.2
(-2.8)
A 		4161.3
(2.7)
P 		4369.1
(3)
P 		844.9
(-1.9)
P 		4354
B 5
(-3)
A 		4.2
(-3)
A 		116.1
(-2.9)
A 		4828.1
(3)
P 		4623.3
(2.7)
P 		1192.7
(-1.5)
P 		4824
C 10.7
(-3)
A 		17.4
(-3)
A 		101.4
(-2.9)
A 		4701.6
(3)
P 		3994.9
(2.1)
P 		1142.8
(-1.6)
P 		4691
avr 10.3
(-3) 		14
(-3) 		114.9
(-2.9) 		4563.7
(3) 		4329.1
(2.7) 		1060.1
(-1.6) 		4553
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4
1 2 3 4 range
A 1.5
(-3)
A 		4.9
(3)
A 		3.2
(0)
A 		1.5
(-3)
A 		3
B 1.4
(-2.4)
A 		2.7
(-0.4)
A 		4.9
(3)
A 		1
(-3)
A 		4
C 1.1
(-3)
A 		3.8
(3)
A 		3.6
(2.6)
A 		1.6
(-1.9)
A 		3
avr 1.3
(-3) 		3.8
(2.8) 		3.9
(3) 		1.4
(-2.8) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1877
1 2 3 4 5 6 range
A 2.8
(-3)
A 		7.3
(-3)
A 		27.7
(-2.9)
A 		1055.4
(1.8)
P 		1318.4
(3)
P 		205.7
(-2.1)
P 		1316
B 1.7
(-3)
A 		1.4
(-3)
A 		28.2
(-2.9)
A 		1278.8
(1.1)
P 		1878.4
(3)
P 		444.7
(-1.6)
P 		1877
C 4
(-3)
A 		5.3
(-3)
A 		25.8
(-2.9)
A 		945.5
(1.4)
P 		1292.7
(3)
P 		382.5
(-1.2)
P 		1289
avr 2.8
(-3) 		4.7
(-3) 		27.2
(-2.9) 		1093.2
(1.4) 		1496.5
(3) 		344.3
(-1.6) 		1494
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190025_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2549
Sequence Type Exemplar sequence
Representative Public ID F53G12.7 NCBI
Target Description F53G12.7 /REP_DB=WormBase Gene ID /WP=CE11018 /TR=O01799 /GB=AAB54156.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular 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_058278(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058278 NCBI Caenorhabditis elegans COLlagen family member (col-45) (col-45) mRNA, complete cds. 11/11 None
SNAP00000020922 ENSEMBL cdna:SNAP chromosome:CEL140:I:114106:117401:1 11/11 None
GENEFINDER00000020931 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:116317:117401:1 11/11 None
F53G12.7 ENSEMBL cdna:known chromosome:CEL140:I:115739:117438:1 gene:F53G12.7 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
chrI:115738-117401(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-45
Ensembl F53G12.7
Entrez Gene 171605 Entrez gene
SwissProt O01799 EMBL-EBI
WormBase CE11018 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 AAB54156 Collagen protein 45 [Caenorhabditis elegans] ref|NP_490679.1| COLlagen family member (col-45) [Caenorhabditis elegans] 1.0E-105
blast CAE60316 Hypothetical protein CBG03907 [Caenorhabditis briggsae] 1.0E-91
blast CAE60316 Hypothetical protein CBG03907 [Caenorhabditis briggsae] 2.0E-91
blast AAB54156 Collagen protein 45 [Caenorhabditis elegans] ref|NP_490679.1| COLlagen family member (col-45) [Caenorhabditis elegans] 1.0E-71
blast CAE60316 Hypothetical protein CBG03907 [Caenorhabditis briggsae] 6.0E-60
blast AAM15577 Hypothetical protein F53G12.8 [Caenorhabditis elegans] ref|NP_490678.3| F53G12.8 [Caenorhabditis elegans] 5.0E-20
blast AAA29370 collagen 3.0E-12
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_490679.1 1 20-42
F53G12.7 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:190025_AT
ggagcaccacatgccgagtgtagacggggtccaccgggaccaccgggtgatgacggggtc
gacggaacggacggaaaagacggtgcacctggaaccgatggaaaagacggtcaggtacca
caaggaccagccgacggaggttatcaagagggaccatctgatgcagttgaagcatgcaca
cgtgaatgcccaccaggaccgcctggaccaactggagcgcccggagacaaaggatctcga
ggctaccctggagaatctggagagccaggcaccccgggaagcgccggaccgaaaggaaat
gctggaccagctggaccaccaggaccacccggatatccaggacgtcctggagaaaccgga
gatcacggaaagacgatcgccggagaggcgccacctggaccaccaggacgacaaggagaa
atgggtccacaaggaccaccgggaccaccagggccacgtggaaaggacggagccggtgga
gagaagggtgctccgggagatcaaggtaatccgggaccatatggaaaacctgggcaaccg
ggagctccaggacccgatggctctgctggtgagaagg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCACCACATGCCGAGTGTAGAC 302 521 373 Antisense
TCCACCGGGACCACCGGGTGATGAC 448 227 402 Antisense
GATGACGGGGTCGACGGAACGGACG 499 101 421 Antisense
AAGGACCAGCCGACGGAGGTTATCA 100 159 494 Antisense
AAGCATGCACACGTGAATGCCCACC 491 151 542 Antisense
ACTGGAGCGCCCGGAGACAAAGGAT 368 97 583 Antisense
GATCTCGAGGCTACCCTGGAGAATC 161 419 605 Antisense
GAGAATCTGGAGAGCCAGGCACCCC 263 391 623 Antisense
GAGAGAAGGGTGCTCCGGGAGATCA 81 393 851 Antisense
AACCTGGGCAACCGGGAGCTCCAGG 488 139 899 Antisense
CCCGATGGCTCTGCTGGTGAGAAGG 258 261 925 Antisense
Sequence Source Affymetrix Proprietary Database