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[188312_at] collagen

Description F57B7.3 /REP_DB=WormBase Gene ID /WP=CE05991 /TR=Q20927 /GB=CAA98490.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 43      4grp_high_8_8 > 55      6grp_total > 10      4grp_total > 48      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2874
1 2 3 4 range
A 110.9
(-2.9)
P 		1851.2
(1.2)
P 		2618.8
(3)
P 		87.2
(-3)
A 		2532
B 113
(-2.8)
A 		1709.2
(0.5)
P 		2911.1
(3)
P 		36.8
(-3)
A 		2874
C 60.3
(-3)
A 		2076.3
(1.9)
P 		2529.1
(3)
P 		106.7
(-2.9)
P 		2469
avr 94.7
(-3) 		1878.9
(1.1) 		2686.3
(3) 		76.9
(-3) 		2609

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1614
1 2 3 4 5 6 range
A 40.5
(-3)
A 		1579.7
(3)
P 		811.4
(0)
P 		1403.3
(2.3)
P 		667.3
(-0.6)
P 		624.5
(-0.7)
P 		1539
B 107
(-3)
P 		1654
(3)
P 		841.2
(-0.2)
P 		1405.5
(2)
P 		765.2
(-0.4)
P 		647.1
(-0.9)
P 		1547
C 147.7
(-3)
P 		1537.2
(3)
P 		903.8
(0.3)
P 		1187.6
(1.5)
P 		940.7
(0.4)
P 		443.4
(-1.7)
P 		1390
avr 98.4
(-3) 		1590.3
(3) 		852.1
(0) 		1332.1
(2) 		791.1
(-0.2) 		571.7
(-1.1) 		1492
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 874
1 2 3 4 range
A 40.4
(-2.8)
P 		401.8
(0.5)
P 		684.6
(3)
P 		12.8
(-3)
A 		672
B 36
(-2.7)
A 		422.1
(0.7)
P 		674.6
(3)
P 		7.8
(-3)
A 		667
C 20
(-3)
A 		597
(1)
P 		881.5
(3)
P 		18
(-3)
P 		864
avr 32.1
(-2.8) 		473.6
(0.8) 		746.9
(3) 		12.9
(-3) 		734

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 554
1 2 3 4 5 6 range
A 7.5
(-3)
A 		561.8
(3)
P 		176.7
(-1.2)
P 		355.9
(0.8)
P 		201.4
(-0.9)
P 		152
(-1.4)
P 		554
B 37.2
(-3)
P 		550.5
(3)
P 		204.3
(-1)
P 		372.3
(0.9)
P 		310.9
(0.2)
P 		241.3
(-0.6)
P 		513
C 54.7
(-3)
P 		469.1
(3)
P 		230
(-0.5)
P 		238.8
(-0.3)
P 		304.4
(0.6)
P 		148.4
(-1.6)
P 		414
avr 33.1
(-3) 		527.1
(3) 		203.7
(-0.9) 		322.3
(0.5) 		272.2
(-0.1) 		180.6
(-1.2) 		494
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188312_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12694
Sequence Type Exemplar sequence
Representative Public ID F57B7.3 NCBI
Target Description F57B7.3 /REP_DB=WormBase Gene ID /WP=CE05991 /TR=Q20927 /GB=CAA98490.1 /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_073501(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073501 NCBI Caenorhabditis elegans F57B7.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000018332 ENSEMBL cdna:SNAP chromosome:CEL140:V:11451889:11452929:-1 11/11 None
GENEFINDER00000018334 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:11451889:11452929:-1 11/11 None
F57B7.3 ENSEMBL cdna:known chromosome:CEL140:V:11451889:11452929:-1 gene:F57B7.3 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:11451888-11452929(-) 95.27 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-156
Ensembl F57B7.3
Entrez Gene 186439 Entrez gene
SwissProt Q20927 EMBL-EBI
WormBase CE05991 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 CAA98490 Hypothetical protein F57B7.3 [Caenorhabditis elegans] ref|NP_505902.1| F57B7.3 [Caenorhabditis elegans] 6.0E-56
blast CAE75248 Hypothetical protein CBG23205 [Caenorhabditis briggsae] 2.0E-49
blast CAE59859 Hypothetical protein CBG03334 [Caenorhabditis briggsae] 9.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.0E-29
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505902.1 1 5-27
F57B7.3 1 5-27
SNAP00000018332 1 5-27
GENEFINDER00000018334 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:188312_AT
gagatcaaggccttgacggagcaccaggacagccaggaaatgttggacaaaacgctgttg
ttgccagtatcgctgcttccacatcggaatgcatcccatgcccagccggagccccaggac
cacaaggaccagatggagcaccaggtgcaccaggaccaagtggacagccaggtcaagacg
gagcatcaggacagccaggagccccaggagttgctggaccacaaggagatgcaggaacac
caggacagccaggacagcaaggacaagatggtcgcccaggacaaaatggacgtcgtggac
gtggaactccaggagccccaggagccccaggagctgccggagccccaggaaacaatggac
agccaggacaagacggagcaccaggacaagctggagcaccaggagcttccggaccagacg
gacaaccagggcaaccaggagaagatggacaaccaggagagaatggacttgacggagttc
caggaactgatgccgcttattgcccatgcccagctagaagtggacctgttgaggttgctc
cag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGATCAAGGCCTTGACGGAGCACC 210 397 317 Antisense
AAACGCTGTTGTTGCCAGTATCGCT 282 127 366 Antisense
TCGCTGCTTCCACATCGGAATGCAT 477 599 386 Antisense
TTCCACATCGGAATGCATCCCATGC 565 701 393 Antisense
AGACGGAGCATCAGGACAGCCAGGA 69 71 492 Antisense
CAAGGAGATGCAGGAACACCAGGAC 13 185 538 Antisense
GCAAGGACAAGATGGTCGCCCAGGA 281 321 573 Antisense
GACGTCGTGGACGTGGAACTCCAGG 513 373 605 Antisense
GAATGGACTTGACGGAGTTCCAGGA 84 333 777 Antisense
CCATGCCCAGCTAGAAGTGGACCTG 678 271 820 Antisense
AGTGGACCTGTTGAGGTTGCTCCAG 593 57 835 Antisense
Sequence Source Affymetrix Proprietary Database