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[189099_at] cuticle collagen

Description M195.1 /REP_DB=WormBase Gene ID /WP=CE03514 /TR=Q21562 /GB=CAA91290.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 90      4grp_high_8_8 > 54      6grp_highest_nonorm > 79      6grp_total > 83      4grp_total > 49      6grp_cgc > 65      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3324
1 2 3 4 range
A 226.9
(-2.8)
P 		2544.6
(2.3)
P 		2859.9
(3)
P 		131.1
(-3)
P 		2729
B 208.3
(-2.9)
P 		2777.4
(1.8)
P 		3455.2
(3)
P 		174.3
(-3)
A 		3281
C 227.7
(-2.9)
P 		2617
(2.7)
P 		2747.8
(3)
P 		171.2
(-3)
P 		2577
avr 221
(-2.9) 		2646.3
(2.2) 		3021
(3) 		158.9
(-3) 		2862

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2731
1 2 3 4 5 6 range
A 364.8
(-3)
P 		2681
(3)
P 		1779
(0.7)
P 		1630
(0.3)
P 		2331.6
(2.1)
P 		1953.6
(1.1)
P 		2316
B 346.6
(-3)
P 		2313.9
(2.5)
P 		2029.5
(1.7)
P 		1712.5
(0.8)
P 		2502.9
(3)
P 		2426.9
(2.8)
P 		2156
C 360.8
(-3)
P 		2225.9
(1.1)
P 		1688.2
(-0.1)
P 		1388.4
(-0.7)
P 		3077.2
(3)
P 		1888.3
(0.4)
P 		2716
avr 357.4
(-3) 		2406.9
(2.4) 		1832.2
(0.9) 		1577
(0.2) 		2637.2
(3) 		2089.6
(1.6) 		2280
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 939
1 2 3 4 range
A 82.6
(-2.5)
P 		552.4
(1.4)
P 		747.6
(3)
P 		19.2
(-3)
P 		728
B 66.4
(-2.8)
P 		686
(2.1)
P 		800.7
(3)
P 		37.1
(-3)
A 		764
C 75.4
(-2.7)
P 		752.4
(1.7)
P 		957.7
(3)
P 		28.9
(-3)
P 		929
avr 74.8
(-2.7) 		663.6
(1.7) 		835.3
(3) 		28.4
(-3) 		807

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 950
1 2 3 4 5 6 range
A 67.2
(-3)
P 		953.5
(3)
P 		387.4
(-0.8)
P 		413.4
(-0.7)
P 		703.6
(1.3)
P 		475.6
(-0.2)
P 		886
B 120.6
(-3)
P 		770.2
(1.3)
P 		492.8
(-0.5)
P 		453.6
(-0.8)
P 		1016.9
(3)
P 		905
(2.3)
P 		896
C 133.7
(-3)
P 		679.2
(0.8)
P 		429.7
(-0.9)
P 		279.2
(-2)
P 		995.7
(3)
P 		632.1
(0.5)
P 		862
avr 107.2
(-3) 		801
(2.2) 		436.6
(-0.5) 		382.1
(-0.9) 		905.4
(3) 		670.9
(1.2) 		798
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189099_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4030
Sequence Type Exemplar sequence
Representative Public ID M195.1 NCBI
Target Description M195.1 /REP_DB=WormBase Gene ID /WP=CE03514 /TR=Q21562 /GB=CAA91290.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle 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_063358(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063358 NCBI Caenorhabditis elegans COLlagen family member (col-77) (col-77) mRNA, complete cds. 11/11 None
SNAP00000004358 ENSEMBL cdna:SNAP chromosome:CEL140:II:8358224:8359268:-1 11/11 None
GENEFINDER00000004367 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8358224:8359313:-1 11/11 None
M195.1 ENSEMBL cdna:known chromosome:CEL140:II:8358188:8359301:-1 gene:M195.1 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:8358220-8359265(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-77
Ensembl M195.1
Entrez Gene 174336 Entrez gene
SwissProt Q21562 EMBL-EBI
WormBase CE03514 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 CAA91290 Hypothetical protein M195.1 [Caenorhabditis elegans] ref|NP_495759.1| COLlagen family member (col-77) [Caenorhabditis elegans] 1.0E-51
blast CAE57699 Hypothetical protein CBG00703 [Caenorhabditis briggsae] 2.0E-49
blast CAA90188 Hypothetical protein F38A3.2 [Caenorhabditis elegans] ref|NP_496362.1| F38A3.2 [Caenorhabditis elegans] 3.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.7E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.2E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.7E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.2E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495759.1 1 20-42
M195.1 1 20-42
SNAP00000004358 1 20-42
GENEFINDER00000004367 1 34-56
Sequence
Target Sequence 
>C. ELEGANS:189099_AT
ccgtttctgctggaggttctgaagctggaggtcaatgctgctcatgcgggtctggaccag
ctggaccaccaggaaccccaggagaggacggacgtgacggaaacgacggacaaccaggac
cagacggacaaccaggatctgatgctccagctgaggctattccaactgctgatgacttct
gcttcgactgcccagccggaccaccaggaccagcaggaaacgccggaccaaagggagcac
caggaaacgccggagccccaggaaatgatggacaagccggagctccaggagcaccaggaa
acgatggaccacaaggaccaccaggacaagatggagccgctggacaaccaggaccagacg
gacagccaggagtcgttgaggaggtagctgttccagctgggccaccaggaccaccaggac
cacaaggagccccaggaacagatggacaaccaggatctgctggacaaccaggacaagatg
gaccacaaggaccagctggagacgccggaactgatggagctccaggacaagcaggagctg
ctggagaacaaggagaggctggacaaccaggagagggaggtggctgcgatcact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCGTTTCTGCTGGAGGTTCTGAAGC 354 265 302 Antisense
GCTGGAGGTCAATGCTGCTCATGCG 439 295 325 Antisense
GAGAGGACGGACGTGACGGAAACGA 666 395 383 Antisense
GAGGCTATTCCAACTGCTGATGACT 639 405 454 Antisense
CAACTGCTGATGACTTCTGCTTCGA 175 187 464 Antisense
ACGGACAGCCAGGAGTCGTTGAGGA 122 95 659 Antisense
GGAGTCGTTGAGGAGGTAGCTGTTC 443 515 670 Antisense
AGGAGGTAGCTGTTCCAGCTGGGCC 324 57 680 Antisense
ACCAGCTGGAGACGCCGGAACTGAT 118 87 792 Antisense
AGCAGGAGCTGCTGGAGAACAAGGA 427 77 831 Antisense
GGAGAGGGAGGTGGCTGCGATCACT 60 519 871 Antisense
Sequence Source Affymetrix Proprietary Database