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[189803_at]

Description F38B6.5 /REP_DB=WormBase Gene ID /WP=CE04518 /TR=Q20142 /GB=AAA81141.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 81      4grp_total > 57      6grp_cgc > 86      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 333
1 2 3 4 range
A 30.2
(-2.6)
A 		178.7
(0.9)
A 		268.9
(3)
A 		13.9
(-3)
A 		255
B 14.2
(-2.8)
A 		228.1
(1)
A 		337.4
(3)
A 		4
(-3)
A 		333
C 30.5
(-2.3)
A 		204.2
(2.6)
A 		218.4
(3)
A 		5.2
(-3)
A 		213
avr 25
(-2.6) 		203.7
(1.4) 		274.9
(3) 		7.7
(-3) 		267

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 707
1 2 3 4 5 6 range
A 12.5
(-3)
A 		166.6
(-1.7)
A 		180.1
(-1.6)
A 		719.8
(3)
P 		307.2
(-0.5)
A 		110.3
(-2.2)
A 		707
B 95.2
(-2.3)
A 		200.4
(-1)
A 		128.8
(-1.9)
A 		525.4
(3)
A 		452.6
(2.1)
A 		35.1
(-3)
A 		490
C 70.9
(-2.3)
A 		157.6
(-1.3)
A 		176.4
(-1.1)
A 		533
(3)
A 		523.5
(2.9)
M 		14.1
(-3)
A 		519
avr 59.5
(-2.9) 		174.9
(-1.6) 		161.8
(-1.8) 		592.7
(3) 		427.8
(1.2) 		53.2
(-3) 		540
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 77
1 2 3 4 range
A 11
(-2.2)
A 		38.8
(0.2)
A 		70.3
(3)
A 		2
(-3)
A 		68
B 4.5
(-2.7)
A 		56.3
(1.3)
A 		78.2
(3)
A 		0.9
(-3)
A 		77
C 10.1
(-2.3)
A 		58.7
(1.6)
A 		76.1
(3)
A 		0.9
(-3)
A 		75
avr 8.5
(-2.4) 		51.3
(1.1) 		74.9
(3) 		1.3
(-3) 		74

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 182
1 2 3 4 5 6 range
A 2.3
(-3)
A 		59.2
(-1.1)
A 		39.2
(-1.8)
A 		182.6
(3)
P 		92.7
(0)
A 		26.9
(-2.2)
A 		180
B 33.1
(-2.3)
A 		66.7
(-1.1)
A 		31.3
(-2.4)
A 		139.2
(1.4)
A 		183.9
(3)
A 		13.1
(-3)
A 		171
C 26.3
(-2.2)
A 		48.1
(-1.4)
A 		44.9
(-1.5)
A 		107.2
(0.7)
A 		169.4
(3)
M 		4.7
(-3)
A 		165
avr 20.6
(-2.7) 		58
(-1.1) 		38.5
(-1.9) 		143
(2.7) 		148.7
(3) 		14.9
(-3) 		134
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189803_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16766
Sequence Type Exemplar sequence
Representative Public ID F38B6.5 NCBI
Target Description F38B6.5 /REP_DB=WormBase Gene ID /WP=CE04518 /TR=Q20142 /GB=AAA81141.1 /SUBMIT=ST.LOUIS /CHR=X /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_001029464(11), NM_001029465(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029464 NCBI Caenorhabditis elegans COLlagen family member (col-172) (col-172) mRNA, complete cds. 11/11 None
NM_001029465 NCBI Caenorhabditis elegans COLlagen family member (col-172) (col-172) mRNA, complete cds. 11/11 None
GENEFINDER00000034010 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6672937:6674253:1 11/11 None
SNAP00000034001 ENSEMBL cdna:SNAP chromosome:CEL140:X:6673098:6674253:1 11/11 None
F38B6.5a ENSEMBL cdna:known chromosome:CEL140:X:6672784:6674361:1 gene:F38B6.5 11/11 None
F38B6.5b.2 ENSEMBL cdna:known chromosome:CEL140:X:6673377:6674253:1 gene:F38B6.5 11/11 None
F38B6.5b.1 ENSEMBL cdna:known chromosome:CEL140:X:6673560:6674253:1 gene:F38B6.5 10/11 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
chrX:6672936-6674253(+) 100.0 100.0
Public Domain and Genome References
Ensembl F38B6.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA81141 Collagen protein 172, isoform a [Caenorhabditis elegans] ref|NP_001024635.1| COLlagen family member (col-172) [Caenorhabditis elegans] 1.0E-108
blast CAE65770 Hypothetical protein CBG10862 [Caenorhabditis briggsae] 1.0E-99
blast AAA81141 Collagen protein 172, isoform a [Caenorhabditis elegans] ref|NP_001024635.1| COLlagen family member (col-172) [Caenorhabditis elegans] 2.0E-88
blast CAE65770 Hypothetical protein CBG10862 [Caenorhabditis briggsae] 3.0E-80
blast AAM80556 cuticular collagen [Trichinella spiralis] 1.0E-34
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.0E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.3E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.3E-13
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.3E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001024635.1 1 20-42
F38B6.5a 1 20-42
GENEFINDER00000034010 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:189803_AT
gaatttcagccggcttcatgttgcacatgccaacaaggacctgttgggccagcaggacca
ccaggagacgatgggcttgatggtattgatggaaagtcgggagtcgatggaccacccgga
agagatggaattctcctgccaccccttggccaagctccggaaccatgtattatttgtcca
ccaggtcaaactggtcccccagggttcccaggacaaaaaggtccaaatgggccacgagga
agccctggactacaaggccaagacggaaagaagggagaacaaggaatgccaggtccacaa
ggtccgactggaagaccaggtagaccgggacccaagggaccaaaaggagaggatggaaga
gttattatggttgctggacccgcgggacccgcaggcccaccaggacttcctggaacccct
ggaaaacgaggagcgcgtggtatggacggcttgccgggaccacaaggtgcaccaggacaa
caaggagattccggactatcgggcccagacggaaaagaaggtgcaagaggggaacgtgga
ccacaaggacctcaagggctcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATTTCAGCCGGCTTCATGTTGCA 650 325 427 Antisense
AAGGACCTGTTGGGCCAGCAGGACC 327 161 461 Antisense
GAAGAGATGGAATTCTCCTGCCACC 541 337 545 Antisense
GCCAAGCTCCGGAACCATGTATTAT 611 277 575 Antisense
CATGTATTATTTGTCCACCAGGTCA 193 209 590 Antisense
GAAGCCCTGGACTACAAGGCCAAGA 366 343 665 Antisense
CCAGGTCCACAAGGTCCGACTGGAA 503 271 715 Antisense
TATGGACGGCTTGCCGGGACCACAA 319 651 867 Antisense
GGACCACAAGGTGCACCAGGACAAC 353 523 883 Antisense
GACTATCGGGCCCAGACGGAAAAGA 623 367 920 Antisense
GACCACAAGGACCTCAAGGGCTCAA 627 383 965 Antisense
Sequence Source Affymetrix Proprietary Database