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[189864_s_at] cuticular collagen

Description F19C7.7 /REP_DB=WormBase Gene ID /WP=CE04421 /TR=Q19592 /GB=AAA83511.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 84      4grp_total > 58      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 58.9
(-3)
A 		92.2
(2.1)
A 		98.3
(3)
A 		89.9
(1.7)
A 		39
B 57.9
(1.3)
A 		39.9
(-0.6)
A 		74.1
(3)
P 		17.2
(-3)
A 		57
C 54.7
(1)
A 		68.7
(3)
A 		48.3
(0.1)
A 		26
(-3)
A 		43
avr 57.2
(-0.4) 		66.9
(1.6) 		73.6
(3) 		44.4
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 210
1 2 3 4 5 6 range
A 15.4
(-3)
A 		14.8
(-3)
A 		67.2
(-1)
A 		145.3
(1.9)
P 		174.4
(3)
P 		111.8
(0.6)
A 		160
B 28.7
(-3)
A 		47.1
(-2.4)
A 		68.6
(-1.8)
A 		116.7
(-0.3)
P 		224.6
(3)
P 		91.2
(-1.1)
P 		196
C 25.8
(-3)
A 		57
(-1.7)
A 		82.2
(-0.6)
P 		127.9
(1.4)
A 		165.1
(3)
P 		78.8
(-0.7)
A 		139
avr 23.3
(-3) 		39.6
(-2.4) 		72.7
(-1.2) 		130
(0.9) 		188
(3) 		93.9
(-0.4) 		165
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22
1 2 3 4 range
A 21.4
(0.9)
A 		20
(0.3)
A 		25.7
(3)
A 		13.2
(-3)
A 		13
B 18.5
(3)
A 		9.9
(-0.5)
A 		17.2
(2.5)
P 		3.7
(-3)
A 		15
C 18.1
(2.3)
A 		19.8
(3)
A 		16.8
(1.8)
A 		4.4
(-3)
A 		15
avr 19.3
(2.7) 		16.6
(1.5) 		19.9
(3) 		7.1
(-3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 89
1 2 3 4 5 6 range
A 2.8
(-3)
A 		5.3
(-2.7)
A 		14.6
(-1.6)
A 		36.9
(1.1)
P 		52.6
(3)
P 		27.2
(-0.1)
A 		50
B 10
(-3)
A 		15.7
(-2.6)
A 		16.7
(-2.5)
A 		30.9
(-1.5)
P 		91.3
(3)
P 		34
(-1.2)
P 		81
C 9.6
(-3)
A 		17.4
(-1.9)
A 		20.9
(-1.5)
P 		25.7
(-0.8)
A 		53.4
(3)
P 		26.4
(-0.7)
A 		44
avr 7.5
(-3) 		12.8
(-2.5) 		17.4
(-2) 		31.2
(-0.6) 		65.8
(3) 		29.2
(-0.8) 		58
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189864_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10608
Sequence Type Exemplar sequence
Representative Public ID F19C7.7 NCBI
Target Description F19C7.7 /REP_DB=WormBase Gene ID /WP=CE04421 /TR=Q19592 /GB=AAA83511.1 /SUBMIT=ST.LOUIS /CHR=4 /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_068197(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068197 NCBI Caenorhabditis elegans COLlagen family member (col-110) (col-110) mRNA, complete cds. 11/11 None
SNAP00000030500 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4608285:4609649:-1 11/11 None
GENEFINDER00000030507 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4608285:4609649:-1 11/11 None
F19C7.7 ENSEMBL cdna:known chromosome:CEL140:IV:4608201:4609670:-1 gene:F19C7.7 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
chrIV:4608290-4609655(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-110
Ensembl F19C7.7
Entrez Gene 177225 Entrez gene
SwissProt Q19592 EMBL-EBI
WormBase CE04421 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 AAA83511 Collagen protein 110 [Caenorhabditis elegans] ref|NP_500598.1| COLlagen family member (col-110) [Caenorhabditis elegans] 1.0E-101
blast CAE58553 Hypothetical protein CBG01712 [Caenorhabditis briggsae] 1.0E-78
blast AAK68452 Collagen protein 108 [Caenorhabditis elegans] ref|NP_500133.2| COLlagen family member (col-108) [Caenorhabditis elegans] 2.0E-24
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.4E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500598.1 1 13-35
F19C7.7 1 13-35
SNAP00000030500 1 13-35
GENEFINDER00000030507 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:189864_S_AT
tggctgttgtattcctggagctccaggccccagcggaaccccaggaagacatggacgcca
cggagctcctggagcacctggaagaccaggaaatcctggagagccaccgagaggtccatg
tgatccaacacttgcaagcccatgtgactgtccagctggagagccgggagagccgggacc
ccgtgggtcaccaggtaacaatggattgcctggattgaaggggcgacgtggattcgatgg
gctggatggacgtccgggaaggcctggaaaaactggaatcgacggagttccagggacaaa
gggagaagacggagctgatggagaacctggggaggttgatacttccgatgttggaccacc
tggggat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGCTGTTGTATTCCTGGAGCTCCA 641 543 312 Antisense
ACCCCAGGAAGACATGGACGCCACG 174 87 349 Antisense
AATCCTGGAGAGCCACCGAGAGGTC 275 167 403 Antisense
GAGGTCCATGTGATCCAACACTTGC 245 403 422 Antisense
CACTTGCAAGCCCATGTGACTGTCC 161 197 440 Antisense
TGACTGTCCAGCTGGAGAGCCGGGA 594 569 456 Antisense
CCCCGTGGGTCACCAGGTAACAATG 409 257 490 Antisense
AGGGGCGACGTGGATTCGATGGGCT 504 57 530 Antisense
GGCTGGATGGACGTCCGGGAAGGCC 16 541 551 Antisense
ACCTGGGGAGGTTGATACTTCCGAT 233 87 636 Antisense
TTCCGATGTTGGACCACCTGGGGAT 548 697 654 Antisense
Sequence Source Affymetrix Proprietary Database