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[189693_at] cuticular collagen

Description K01A2.7 /REP_DB=WormBase Gene ID /WP=CE19515 /TR=Q9TZ57 /GB=AAC69507.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 90      4grp_total > 56      6grp_cgc > 96      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 139
1 2 3 4 range
A 81.7
(1.5)
A 		23.2
(-3)
A 		101.6
(3)
A 		36.1
(-2)
A 		78
B 27.3
(-3)
A 		148.5
(2.4)
A 		161.8
(3)
A 		36.2
(-2.6)
A 		135
C 97
(3)
A 		94.3
(2.7)
A 		95.1
(2.8)
A 		41.3
(-3)
A 		56
avr 68.7
(-0.7) 		88.7
(0.7) 		119.5
(3) 		37.9
(-3) 		82

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 112
1 2 3 4 5 6 range
A 26.5
(-2.8)
A 		29.6
(-2.6)
A 		22.6
(-3)
A 		116.5
(2.6)
A 		124
(3)
A 		49.1
(-1.4)
A 		101
B 133.7
(3)
A 		89.8
(0)
A 		45.3
(-3)
A 		124.5
(2.4)
A 		61.9
(-1.9)
A 		67.2
(-1.5)
A 		88
C 105.8
(2.5)
A 		72.2
(0.3)
A 		21.5
(-3)
A 		114.2
(3)
A 		82.9
(1)
A 		112.1
(2.9)
A 		93
avr 88.7
(1) 		63.9
(-0.7) 		29.8
(-3) 		118.4
(3) 		89.6
(1) 		76.1
(0.1) 		89
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 29.7
(3)
A 		5
(-3)
A 		26.6
(2.2)
A 		5.3
(-2.9)
A 		25
B 8.7
(-2.8)
A 		36.7
(2.8)
A 		37.5
(3)
A 		7.7
(-3)
A 		30
C 32.1
(2.8)
A 		27.1
(1.6)
A 		33.1
(3)
A 		7
(-3)
A 		26
avr 23.5
(0.9) 		22.9
(0.8) 		32.4
(3) 		6.7
(-3) 		26

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 4.9
(-3)
A 		10.5
(-2)
A 		4.9
(-3)
A 		29.5
(1.5)
A 		37.4
(3)
A 		11.9
(-1.7)
A 		33
B 46.5
(3)
A 		29.9
(0.2)
A 		11
(-3)
A 		33
(0.7)
A 		25.1
(-0.6)
A 		25.1
(-0.6)
A 		36
C 39.2
(3)
A 		22
(-0.1)
A 		5.5
(-3)
A 		23
(0.1)
A 		26.8
(0.8)
A 		37.5
(2.7)
A 		34
avr 30.2
(3) 		20.8
(0.6) 		7.1
(-3) 		28.5
(2.6) 		29.8
(2.9) 		24.8
(1.6) 		23
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189693_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5886
Sequence Type Exemplar sequence
Representative Public ID K01A2.7 NCBI
Target Description K01A2.7 /REP_DB=WormBase Gene ID /WP=CE19515 /TR=Q9TZ57 /GB=AAC69507.1 /SUBMIT=ST.LOUIS /CHR=2 /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_061301(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061301 NCBI Caenorhabditis elegans COLlagen family member (col-69) (col-69) mRNA, complete cds. 11/11 None
SNAP00000016833 ENSEMBL cdna:SNAP chromosome:CEL140:II:303923:305421:-1 11/11 None
GENEFINDER00000016844 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:303923:305529:-1 11/11 None
K01A2.7 ENSEMBL cdna:known chromosome:CEL140:II:303923:305529:-1 gene:K01A2.7 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
chrII:303922-305529(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-69
Ensembl K01A2.7
Entrez Gene 186819 Entrez gene
SwissProt Q9TZ57 EMBL-EBI
WormBase CE19515 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 AAC69507 Collagen protein 69 [Caenorhabditis elegans] ref|NP_493702.1| COLlagen family member (col-69) [Caenorhabditis elegans] 1.0E-122
blast AAC69507 Collagen protein 69 [Caenorhabditis elegans] ref|NP_493702.1| COLlagen family member (col-69) [Caenorhabditis elegans] 1.0E-112
blast CAE62866 Hypothetical protein CBG07049 [Caenorhabditis briggsae] 2.0E-82
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-8
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.8E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493702.1 1 17-39
K01A2.7 1 17-39
GENEFINDER00000016844 1 17-39
Sequence
Target Sequence 
>C. ELEGANS:189693_AT
cttgtggaccttctggaattcccgggctcccagggaatcccggatacacctctcctccag
gacttcctgggccaccggggccttgtggtgaagctggacgggaaggtcccaatggtacac
caggccttaagggagagcctggaaataactcgatccgtcagatatccctaccaggccgta
aaggccctccaggacttcctggtcaatgcggaccaccagggccacctggatatacaccgc
ctccaggaccaccaggaacacctggagttcagggagaagctggacaggatggagaaccag
gggtacctggagttactggctatccaggagttcgtgggccaccggggcaggatgctgaat
attgtccgtgtccaccaaagaacgcaggagtcaatcggaatagttatgtgcagccggcac
cagtgtccacaagctacgccacagcatcccaaagccgttacgtgtcagagtacaataaag
aggatgagtacaggaaacgagtgctggctcgagtgctcaagaagcagagacgactacttt
tggcgaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTGTGGACCTTCTGGAATTCCCGG 696 209 602 Antisense
GGCTCCCAGGGAATCCCGGATACAC 200 539 626 Antisense
GGAAGGTCCCAATGGTACACCAGGC 183 533 702 Antisense
TAACTCGATCCGTCAGATATCCCTA 394 639 747 Antisense
CTACCAGGCCGTAAAGGCCCTCCAG 151 221 769 Antisense
GACTTCCTGGTCAATGCGGACCACC 513 371 794 Antisense
CCAGGGCCACCTGGATATACACCGC 288 271 817 Antisense
GGGGTACCTGGAGTTACTGGCTATC 79 493 901 Antisense
GATGCTGAATATTGTCCGTGTCCAC 113 415 952 Antisense
GTGCTGGCTCGAGTGCTCAAGAAGC 329 479 1102 Antisense
GCAGAGACGACTACTTTTGGCGACA 632 309 1125 Antisense
Sequence Source Affymetrix Proprietary Database