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[194230_x_at] collagen

Description AU115274_rc /REP_DB=TREMBL Accession /GB=AU115274 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk730b12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 43      6grp_highest_nonorm > 25      6grp_total > 21      4grp_total > 57      6grp_highest_sub > 02_03      6grp_cgc > 54      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9061
1 2 3 4 range
A 1523.1
(-2.1)
P 		8111.3
(2.3)
P 		9142.8
(3)
P 		113.1
(-3)
A 		9030
B 1390.9
(-2.1)
P 		7870.7
(2.4)
P 		8686.1
(3)
P 		128.1
(-3)
A 		8558
C 3316.2
(-0.8)
P 		8195.2
(2.6)
P 		8738.5
(3)
P 		81.9
(-3)
A 		8657
avr 2076.7
(-1.6) 		8059.1
(2.5) 		8855.8
(3) 		107.7
(-3) 		8748

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6633
1 2 3 4 5 6 range
A 2304.5
(-2.5)
P 		6831.9
(2.1)
P 		7688.7
(3)
P 		3131.2
(-1.7)
P 		3237.4
(-1.5)
P 		1813.3
(-3)
P 		5875
B 2684.5
(-2.9)
P 		8446.7
(3)
P 		7801.9
(2.3)
P 		3217.9
(-2.3)
P 		4163.5
(-1.4)
P 		2564.1
(-3)
P 		5883
C 3602.9
(-1.5)
P 		7968.1
(3)
P 		4724.5
(-0.3)
P 		2540.2
(-2.6)
P 		5239.8
(0.2)
P 		2107.9
(-3)
P 		5860
avr 2864
(-2.2) 		7748.9
(3) 		6738.4
(1.9) 		2963.1
(-2.1) 		4213.6
(-0.8) 		2161.8
(-3) 		5587
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3032
1 2 3 4 range
A 554.5
(-1.6)
P 		1760.7
(1.4)
P 		2390.1
(3)
P 		16.6
(-3)
A 		2374
B 443.5
(-1.7)
P 		1943.9
(2.8)
P 		2012.8
(3)
P 		27.3
(-3)
A 		1986
C 1097.8
(-0.9)
P 		2356.2
(1.6)
P 		3045.6
(3)
P 		13.8
(-3)
A 		3032
avr 698.6
(-1.3) 		2020.3
(1.9) 		2482.8
(3) 		19.2
(-3) 		2464

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2387
1 2 3 4 5 6 range
A 424.8
(-3)
P 		2429.7
(3)
P 		1674.4
(0.7)
P 		794.1
(-1.9)
P 		976.9
(-1.3)
P 		441.5
(-3)
P 		2005
B 934.1
(-2.7)
P 		2811.6
(3)
P 		1894.5
(0.2)
P 		852.3
(-3)
P 		1691.6
(-0.4)
P 		956.1
(-2.7)
P 		1959
C 1335.4
(-0.4)
P 		2431.3
(3)
P 		1202.5
(-0.8)
P 		510.8
(-3)
P 		1695.5
(0.7)
P 		705.6
(-2.4)
P 		1921
avr 898.1
(-2.4) 		2557.5
(3) 		1590.5
(-0.1) 		719.1
(-2.9) 		1454.7
(-0.6) 		701.1
(-3) 		1856
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194230_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21053
Sequence Type Exemplar sequence
Representative Public ID AU115274 NCBI
Target Description AU115274_rc /REP_DB=TREMBL Accession /GB=AU115274 /CHR=3 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk730b12 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_181973(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_181973 NCBI Caenorhabditis elegans Y41C4A.16 (collagen) mRNA, complete cds. 11/11 None
SNAP00000034888 ENSEMBL cdna:SNAP chromosome:CEL140:III:11703886:11708153:1 11/11 None
GENEFINDER00000034914 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11703886:11704861:1 11/11 None
Y41C4A.16 ENSEMBL cdna:known chromosome:CEL140:III:11703855:11704861:1 gene:Y41C4A.16 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_181982 3/11 Cross Hyb Matching Probes None
NM_067302 1/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes None
NM_067732 1/11 Cross Hyb Matching Probes None
NM_063908 1/11 Cross Hyb Matching Probes A 
SNAP00000014220 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014231 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
SNAP00000034887 3/11 Cross Hyb Matching Probes None
GENEFINDER00000034916 3/11 Cross Hyb Matching Probes None
SNAP00000000290 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000294 1/11 Cross Hyb Matching Probes None
SNAP00000028258 1/11 Cross Hyb Matching Probes None
GENEFINDER00000028265 1/11 Cross Hyb Matching Probes None
C09G5.4 1/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
Y41C4A.19 3/11 Cross Hyb Matching Probes None
F14F7.1.2 1/11 Cross Hyb Matching Probes A 
F14F7.1.1 1/11 Cross Hyb Matching Probes A 
F14F7.1.3 1/11 Cross Hyb Matching Probes A 
Y41D4A.2 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:11704537-11704820(+) 100.0 100.0
chrIII:11705624-11705907(-) 90.46 90.46
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-95
Ensembl Y41C4A.16
Entrez Gene 176602 Entrez gene
SwissProt Q86MP1 EMBL-EBI
WormBase CE33480 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 CAD66222 Hypothetical protein Y41C4A.16 [Caenorhabditis elegans] ref|NP_871702.1| Y41C4A.16 [Caenorhabditis elegans] 8.0E-39
blast CAD66222 Hypothetical protein Y41C4A.16 [Caenorhabditis elegans] ref|NP_871702.1| Y41C4A.16 [Caenorhabditis elegans] 1.0E-38
blast CAE67677 Hypothetical protein CBG13240 [Caenorhabditis briggsae] 7.0E-35
blast CAE67677 Hypothetical protein CBG13240 [Caenorhabditis briggsae] 9.0E-35
blast CAE71355 Hypothetical protein CBG18258 [Caenorhabditis briggsae] 3.0E-21
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.5E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_871702.1 1 12-34
Y41C4A.16 1 12-34
SNAP00000034888 1 12-34
GENEFINDER00000034914 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:194230_X_AT
ccagggcaggctggatctccaggtcgcccaggagtcgatgctcaatctcaatccaaccca
ggagcgccaggacaagctgggccacaaggaccaccaggaccatccggagctccaggagcc
ccaggaggaccaggatatccaggaccaccagggcaaaagggaccatccggagctccagga
cagccaggatccgacggaaacccaggagcaccaggacagccaggacaatccggtggatcc
gg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGGGCAGGCTGGATCTCCAGGTC 66 273 15 Antisense
GCCCAGGAGTCGATGCTCAATCTCA 535 287 40 Antisense
CTCAATCTCAATCCAACCCAGGAGC 212 225 55 Antisense
AGGAGCGCCAGGACAAGCTGGGCCA 23 57 74 Antisense
AGGACAAGCTGGGCCACAAGGACCA 30 55 83 Antisense
GAGGACCAGGATATCCAGGACCACC 530 403 139 Antisense
GGACCACCAGGGCAAAAGGGACCAT 295 517 156 Antisense
AGGGCAAAAGGGACCATCCGGAGCT 436 57 164 Antisense
GGATCCGACGGAAACCCAGGAGCAC 651 509 201 Antisense
GAGCACCAGGACAGCCAGGACAATC 655 389 220 Antisense
AGCCAGGACAATCCGGTGGATCCGG 659 83 232 Antisense
Sequence Source Affymetrix Proprietary Database