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[189387_at] cuticle collagen

Description T11B7.3 /REP_DB=WormBase Gene ID /WP=CE03649 /TR=Q22389 /GB=CAA90989.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 54      6grp_total > 93      4grp_total > 58      6grp_highest_sub > 05      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1110
1 2 3 4 range
A 675
(-1.4)
P 		1284
(3)
P 		1030.3
(1.1)
P 		462.2
(-3)
P 		822
B 560.9
(-1.4)
P 		1227.6
(3)
P 		1139.8
(2.4)
P 		323.6
(-3)
P 		904
C 696.8
(-1.2)
P 		1433.9
(3)
P 		1189.1
(1.6)
P 		379.2
(-3)
P 		1055
avr 644.2
(-1.3) 		1315.2
(3) 		1119.7
(1.7) 		388.3
(-3) 		927

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1361
1 2 3 4 5 6 range
A 784.8
(-2.4)
P 		954
(-1.4)
P 		857.4
(-2)
P 		1045
(-0.8)
P 		1667.6
(3)
P 		691.6
(-3)
P 		976
B 747
(-3)
P 		884.6
(-2.2)
P 		916.9
(-2)
P 		1183.3
(-0.5)
P 		1811
(3)
P 		789.9
(-2.8)
P 		1064
C 864.2
(-1.7)
P 		861.9
(-1.7)
P 		786.8
(-2.1)
P 		855.1
(-1.8)
P 		1932.6
(3)
P 		572.1
(-3)
P 		1361
avr 798.7
(-2.4) 		900.2
(-1.8) 		853.7
(-2.1) 		1027.8
(-1.2) 		1803.7
(3) 		684.5
(-3) 		1119
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 351
1 2 3 4 range
A 245.8
(2.1)
P 		278.7
(3)
P 		269.3
(2.7)
P 		67.7
(-3)
P 		211
B 178.9
(-0.2)
P 		303.2
(3)
P 		264.1
(2)
P 		69
(-3)
P 		234
C 230.6
(-0.1)
P 		412.3
(3)
P 		414.4
(3)
P 		63.9
(-3)
P 		351
avr 218.4
(0.4) 		331.4
(3) 		315.9
(2.6) 		66.9
(-3) 		265

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 591
1 2 3 4 5 6 range
A 144.7
(-3)
P 		339.3
(0.3)
P 		186.7
(-2.3)
P 		265
(-1)
P 		503.2
(3)
P 		168.4
(-2.6)
P 		359
B 259.9
(-2.6)
P 		294.4
(-2.2)
P 		222.7
(-3)
P 		313.4
(-1.9)
P 		735.8
(3)
P 		294.6
(-2.2)
P 		513
C 320.3
(-1)
P 		263
(-1.8)
P 		200.2
(-2.6)
P 		172
(-3)
P 		625.4
(3)
P 		191.5
(-2.7)
P 		453
avr 241.6
(-2.4) 		298.9
(-1.6) 		203.2
(-3) 		250.1
(-2.3) 		621.5
(3) 		218.2
(-2.8) 		418
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189387_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8369
Sequence Type Exemplar sequence
Representative Public ID T11B7.3 NCBI
Target Description T11B7.3 /REP_DB=WormBase Gene ID /WP=CE03649 /TR=Q22389 /GB=CAA90989.1 /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_069131(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069131 NCBI Caenorhabditis elegans COLlagen family member (col-118) (col-118) mRNA, complete cds. 11/11 None
SNAP00000029867 ENSEMBL cdna:SNAP chromosome:CEL140:IV:8848202:8849604:1 11/11 None
GENEFINDER00000029871 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:8848202:8851109:1 11/11 None
T11B7.3 ENSEMBL cdna:known chromosome:CEL140:IV:8848164:8849604:1 gene:T11B7.3 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:8848210-8849610(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-118
Ensembl T11B7.3
Entrez Gene 177699 Entrez gene
SwissProt Q22389 EMBL-EBI
WormBase CE03649 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 CAA90989 Hypothetical protein T11B7.3 [Caenorhabditis elegans] ref|NP_501532.1| COLlagen family member (col-118) [Caenorhabditis elegans] 8.0E-83
blast CAA90989 Hypothetical protein T11B7.3 [Caenorhabditis elegans] ref|NP_501532.1| COLlagen family member (col-118) [Caenorhabditis elegans] 3.0E-82
blast CAE67061 Hypothetical protein CBG12469 [Caenorhabditis briggsae] 2.0E-49
blast AAA92323 Collagen protein 144 [Caenorhabditis elegans] ref|NP_505374.2| COLlagen family member (col-144) [Caenorhabditis elegans] 4.0E-14
blast AAA92323 Collagen protein 144 [Caenorhabditis elegans] ref|NP_505374.2| COLlagen family member (col-144) [Caenorhabditis elegans] 6.0E-14
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.3E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.9E-10
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.3E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.8E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.9E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501532.1 1 5-27
T11B7.3 1 5-27
SNAP00000029867 1 7-29
GENEFINDER00000029871 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189387_AT
aatgtgattctgctccacagtgtccacctggaccaccaggaccacaaggagctccaggag
caccaggaactcctggagaaaatggaccacgtggaatggataatccacactccctcggca
gtacatcttgtgatcaacaatccattggatgtgtccaatgtccacgtggaccaccaggac
caccaggagatgtcggatcagttggacaaagaggaccagatggcgcatcaggtgctcctg
gagcagcatctcaaattcacggaaaaccgggactaccaggaccaccaggagatgcaggag
cacctggagcaccgggacaagacggagcgccaggacatccaggagccgatggtcaacgtc
aaagagggcagccagggccaccaggaccaccaggacgtccaggaaaagttggaatcaatg
gagagcctggacaaaaaggaattgatggggaaaatggaagtgaaggaattccaggtgttc
caggaccacgcggagctcccggacaaccaggaacaattggagttccaggaggcccaggaa
ttccaggtcgtgacggccaatactgtccatgtccaccacgttcattcatcttggca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGTGATTCTGCTCCACAGTGTCC 656 163 275 Antisense
GGAATGGATAATCCACACTCCCTCG 143 533 367 Antisense
CCCTCGGCAGTACATCTTGTGATCA 286 259 386 Antisense
TGTGTCCAATGTCCACGTGGACCAC 464 555 424 Antisense
GGACCAGATGGCGCATCAGGTGCTC 245 523 487 Antisense
GGACATCCAGGAGCCGATGGTCAAC 316 525 607 Antisense
TCAAAGAGGGCAGCCAGGGCCACCA 490 629 633 Antisense
GGAATTCCAGGTGTTCCAGGACCAC 634 531 739 Antisense
CCCAGGAATTCCAGGTCGTGACGGC 226 253 807 Antisense
TCGTGACGGCCAATACTGTCCATGT 668 603 822 Antisense
TCCACCACGTTCATTCATCTTGGCA 335 589 846 Antisense
Sequence Source Affymetrix Proprietary Database