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[172862_x_at] cuticle collagen /// cuticle collagen

Description T28C6.6 /REP_DB=WormBase Gene ID /WP=CE03749 /GEN=col-3 /TR=Q27318 /GB=CAA90997.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 50      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 09      6grp_total > 41      4grp_total > 59      6grp_highest_sub > 03_04      6grp_cgc > 83      6grp_high1_sub > 03_04      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49139
1 2 3 4 range
A 34846
(0.6)
P 		54473.8
(3)
P 		51952.8
(2.7)
P 		6113.9
(-3)
P 		48360
B 36689.9
(1.2)
P 		44493.5
(2.2)
P 		50192.7
(3)
P 		5334.7
(-3)
P 		44858
C 32698.6
(1.5)
P 		41487.7
(3)
P 		38335.8
(2.5)
P 		5758.2
(-3)
P 		35730
avr 34744.8
(1.2) 		46818.3
(3) 		46827.1
(3) 		5735.6
(-3) 		41092

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28941
1 2 3 4 5 6 range
A 47550.5
(1.8)
P 		43271
(0.2)
P 		50671.3
(3)
P 		47401.1
(1.8)
P 		35361.2
(-2.8)
P 		34964.9
(-3)
P 		15706
B 36438.7
(0.1)
P 		39638.8
(0.9)
P 		47136.2
(3)
P 		42272
(1.7)
P 		29891.1
(-1.8)
P 		25354.9
(-3)
P 		21781
C 35197
(-0.6)
P 		42682.1
(1)
P 		52517.7
(3)
P 		47249.3
(1.9)
P 		37676.1
(-0.1)
P 		23576.9
(-3)
P 		28941
avr 39728.7
(0.2) 		41864
(0.8) 		50108.4
(3) 		45640.8
(1.8) 		34309.5
(-1.3) 		27965.6
(-3) 		22143
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12687
1 2 3 4 range
A 12687.4
(2.6)
P 		11824.8
(2.2)
P 		13581.5
(3)
P 		895
(-3)
P 		12687
B 11700.1
(3)
P 		10988.9
(2.6)
P 		11630.8
(3)
P 		1136.8
(-3)
P 		10563
C 10824.1
(1.8)
P 		11927.9
(2.3)
P 		13361.2
(3)
P 		970.9
(-3)
P 		12390
avr 11737.2
(2.4) 		11580.5
(2.4) 		12857.8
(3) 		1000.9
(-3) 		11857

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7497
1 2 3 4 5 6 range
A 8765.6
(-2.8)
P 		15389.3
(3)
P 		11035.1
(-0.8)
P 		12022
(0.1)
P 		10670.5
(-1.1)
P 		8512.9
(-3)
P 		6876
B 12678.9
(2.2)
P 		13194.1
(3)
P 		11446.1
(0.2)
P 		11196.4
(-0.2)
P 		12144.4
(1.3)
P 		9454.7
(-3)
P 		3739
C 13046
(2.6)
P 		13023.6
(2.6)
P 		13366.7
(3)
P 		9501.9
(-1.2)
P 		12191.4
(1.7)
P 		7892.6
(-3)
P 		5474
avr 11496.8
(0.3) 		13869
(3) 		11949.3
(0.8) 		10906.8
(-0.4) 		11668.8
(0.5) 		8620.1
(-3) 		5249
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172862_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9016
Sequence Type Exemplar sequence
Representative Public ID T28C6.6 NCBI
Target Description T28C6.6 /REP_DB=WormBase Gene ID /WP=CE03749 /GEN=col-3 /TR=Q27318 /GB=CAA90997.1 /SUBMIT=HINXTON /CHR=4 /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_069125(11), NM_069126(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069125 NCBI Caenorhabditis elegans COLlagen family member (col-117) (col-117) mRNA, complete cds. 11/11 None
NM_069126 NCBI Caenorhabditis elegans COLlagen family member (col-3) (col-3) mRNA, complete cds. 11/11 None
SNAP00000005654 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8822988:8824146:-1 11/11 None
SNAP00000005655 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8824796:8825954:1 11/11 None
GENEFINDER00000005663 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8824796:8825954:1 11/11 None
GENEFINDER00000005664 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8822988:8824146:-1 11/11 None
T28C6.4 ENSEMBL cdna:known chromosome:CEL140:IV:8822942:8824158:-1 gene:T28C6.4 11/11 None
T28C6.6 ENSEMBL cdna:known chromosome:CEL140:IV:8824784:8825998:1 gene:T28C6.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_073485 1/11 Cross Hyb Matching Probes A 
NM_073487 2/11 Cross Hyb Matching Probes A 
NM_073512 1/11 Cross Hyb Matching Probes A 
NM_059194 1/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes A 
NM_069706 4/11 Cross Hyb Matching Probes A 
NM_068118 1/11 Cross Hyb Matching Probes A 
NM_067732 2/11 Cross Hyb Matching Probes None
SNAP00000014505 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014522 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 1/11 Cross Hyb Matching Probes None
SNAP00000036391 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 1/11 Cross Hyb Matching Probes None
SNAP00000036392 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 1/11 Cross Hyb Matching Probes None
SNAP00000023158 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023159 1/11 Cross Hyb Matching Probes None
SNAP00000028258 2/11 Cross Hyb Matching Probes None
GENEFINDER00000028265 2/11 Cross Hyb Matching Probes None
SNAP00000037122 4/11 Cross Hyb Matching Probes None
GENEFINDER00000037126 4/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000017929 2/11 Cross Hyb Matching Probes None
SNAP00000017931 1/11 Cross Hyb Matching Probes None
GENEFINDER00000017933 2/11 Cross Hyb Matching Probes None
F27C1.8 1/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
Y41D4A.2 2/11 Cross Hyb Matching Probes None
F30B5.1 1/11 Cross Hyb Matching Probes A 
C29F4.1.2 4/11 Cross Hyb Matching Probes None
C29F4.1.1 4/11 Cross Hyb Matching Probes None
F55C10.2 1/11 Cross Hyb Matching Probes A 
F55C10.3 2/11 Cross Hyb Matching Probes A 
T11F9.9 1/11 Cross Hyb Matching Probes R A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:8824801-8825960(+) 86.0 100.0
chrIV:11225492-11226462(+) 93.56 96.33
chrIV:8822993-8824152(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
cuticle collagen
Gene Symbol col-117
col-3
Ensembl T28C6.4
T28C6.6
Entrez Gene 177694 Entrez gene
177695 Entrez gene
SwissProt Q27318 EMBL-EBI
WormBase CE03749 Wormbase
CE03749 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 CAA90997 Hypothetical protein T28C6.6 [Caenorhabditis elegans] emb|CAA90995.1| Hypothetical protein T28C6.4 [Caenorhabditis elegans] ref|NP_501527.1| COLlagen family member (col-3) [Caenorhabditis elegans] ref|NP_501526.1| COLlagen family member (col-117) [Caenorhabditis elegans] gb|AAP97870.1| COLlagen structural gene, probable cuticle component, from embryo to adult (28.7 kD) (col-3) [Caenorhabditis elegans] gb|AAP97868.1| COLlagen structural gene, probable cuticle component, from embryo to adult (28.7 kD) (col-117) [Caenorhabditis elegans] 1.0E-32
blast CAE56383 Hypothetical protein CBG24065 [Caenorhabditis briggsae] emb|CAE57041.1| Hypothetical protein CBG24927 [Caenorhabditis briggsae] 9.0E-32
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.9E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.9E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501526.1 1 12-34
NP_501527.1 1 12-34
T28C6.4 1 12-34
T28C6.6 1 12-34
SNAP00000005654 1 12-34
SNAP00000005655 1 12-34
GENEFINDER00000005663 1 12-34
GENEFINDER00000005664 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172862_X_AT
aggagccgctggaccagctggaaccccaggaaagccaggacgcccaggaaagccaggagc
accaggacttccaggaaacccaggacgcccaccacagcaaccatgtgagccaattacccc
accaccatgcaagccatgcccagccggaccagctggagccccaggaccagcaggaccagc
cggagatgccggagccaacggaaacccaggagccccaggaaacgacggacaaccaggagc
cccaggaaacaagggaccatctggaccaaacggaaacccaggagccccaggagccccagg
acagccaggacaagacgctccatccgagccaattacaccaggagcaccaggaccagctgg
accagccggaccacaaggaccaccaggagccccaggacagccaggacacgatggacaacc
aggagccccaggaccaaagggaccaaatggaaacccaggagccccaggagccgacggaaa
cccaggagccccaggacaagctggaacttccggaggtgccggagagaagggaatctgtcc
aaagtactgcgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGAGCCGCTGGACCAGCTGGAACC 25 57 318 Antisense
GAAAGCCAGGAGCACCAGGACTTCC 320 359 365 Antisense
CAACCATGTGAGCCAATTACCCCAC 224 187 415 Antisense
AGGACCAGCCGGAGATGCCGGAGCC 39 57 489 Antisense
TGCCGGAGCCAACGGAAACCCAGGA 544 575 504 Antisense
ACAACCAGGAGCCCCAGGAAACAAG 181 111 546 Antisense
CAGGACAGCCAGGACAAGACGCTCC 132 209 614 Antisense
CCGAGCCAATTACACCAGGAGCACC 704 257 641 Antisense
CAAATGGAAACCCAGGAGCCCCAGG 221 193 761 Antisense
CAAGCTGGAACTTCCGGAGGTGCCG 201 187 814 Antisense
GGGAATCTGTCCAAAGTACTGCGCC 622 493 846 Antisense
Sequence Source Affymetrix Proprietary Database