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[192026_at] cuticular collagen

Description C46A5.3 /REP_DB=WormBase Gene ID /WP=CE08753 /GEN=col-14 /TR=Q18648 /GB=AAB03143.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      6grp_highest_nonorm > 59      6grp_total > 83      4grp_total > 57      6grp_highest_sub > 05      6grp_cgc > 87      6grp_high1_sub > 05      6grp_cgc_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2851
1 2 3 4 range
A 116.3
(-2.8)
A 		2391.6
(2)
P 		2870.3
(3)
P 		19.7
(-3)
A 		2851
B 135.6
(-2.8)
A 		1880.3
(1.5)
P 		2499.9
(3)
P 		74.9
(-3)
A 		2425
C 113.6
(-2.8)
A 		2004.7
(1.4)
P 		2754.1
(3)
P 		25.4
(-3)
A 		2729
avr 121.8
(-2.8) 		2092.2
(1.6) 		2708.1
(3) 		40
(-3) 		2668

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5985
1 2 3 4 5 6 range
A 990.6
(-3)
P 		2212.8
(-1.6)
P 		1673.3
(-2.2)
P 		3828.3
(0.1)
P 		6420.9
(3)
P 		2633.1
(-1.2)
P 		5430
B 779.3
(-3)
P 		2136.2
(-1.2)
P 		2035.5
(-1.4)
P 		4702.3
(2.1)
P 		5398.1
(3)
P 		2857.1
(-0.3)
P 		4619
C 928.5
(-3)
P 		2107.4
(-1.8)
P 		2006.4
(-1.9)
P 		4258.6
(0.4)
P 		6763.9
(3)
P 		1801.7
(-2.1)
P 		5835
avr 899.5
(-3) 		2152.1
(-1.6) 		1905.1
(-1.9) 		4263.1
(0.8) 		6194.3
(3) 		2430.6
(-1.3) 		5295
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 957
1 2 3 4 range
A 42.3
(-2.7)
A 		519.1
(1.1)
P 		750.4
(3)
P 		2.9
(-3)
A 		748
B 43.3
(-2.7)
A 		464.4
(1.8)
P 		579.3
(3)
P 		16
(-3)
A 		563
C 37.6
(-2.8)
A 		576.4
(0.6)
P 		959.9
(3)
P 		4.3
(-3)
A 		956
avr 41.1
(-2.7) 		520
(1.1) 		763.2
(3) 		7.7
(-3) 		756

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2011
1 2 3 4 5 6 range
A 182.6
(-3)
P 		787
(-0.9)
P 		364.4
(-2.4)
P 		971
(-0.3)
P 		1937.5
(3)
P 		641.1
(-1.4)
P 		1755
B 271.1
(-3)
P 		711.1
(-1.6)
P 		494.3
(-2.3)
P 		1245.5
(0)
P 		2193.2
(3)
P 		1065.4
(-0.5)
P 		1922
C 344.2
(-3)
P 		643
(-2)
P 		510.7
(-2.5)
P 		856.4
(-1.3)
P 		2188.7
(3)
P 		603.1
(-2.2)
P 		1845
avr 266
(-3) 		713.7
(-1.5) 		456.5
(-2.4) 		1024.3
(-0.5) 		2106.5
(3) 		769.9
(-1.4) 		1841
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192026_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10284
Sequence Type Exemplar sequence
Representative Public ID C46A5.3 NCBI
Target Description C46A5.3 /REP_DB=WormBase Gene ID /WP=CE08753 /GEN=col-14 /TR=Q18648 /GB=AAB03143.1 /SUBMIT=ST.LOUIS /CHR=4 /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_068872(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068872 NCBI Caenorhabditis elegans COLlagen family member (col-14) (col-14) mRNA, complete cds. 11/11 None
SNAP00000025529 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7753505:7754595:1 11/11 None
GENEFINDER00000025537 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7753505:7754595:1 11/11 None
C46A5.3 ENSEMBL cdna:known chromosome:CEL140:IV:7753391:7754629:1 gene:C46A5.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_061259 1/11 Cross Hyb Matching Probes A 
SNAP00000026473 1/11 Cross Hyb Matching Probes None
GENEFINDER00000026484 1/11 Cross Hyb Matching Probes None
C50D2.4 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:7753510-7754601(+) 95.62 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-14
Ensembl C46A5.3
Entrez Gene 177559 Entrez gene
SwissProt P18834 EMBL-EBI
WormBase CE29723 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 CAE70872 Hypothetical protein CBG17662 [Caenorhabditis briggsae] 9.0E-68
blast AAB03143 Collagen protein 14 [Caenorhabditis elegans] ref|NP_501273.2| COLlagen family member (col-14) [Caenorhabditis elegans] sp|P18834|COL14_CAEEL Cuticle collagen 9.0E-68
blast T29810 hypothetical protein C46A5.3 - Caenorhabditis elegans 9.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.7E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0010
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-14
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.7E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0010
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501273.2 1 32-54
C46A5.3 1 32-54
SNAP00000025529 1 13-35
GENEFINDER00000025537 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:192026_AT
tgaatcattcaactccgaaggtggagggtgctgcacttgtcatcgtggaccaccaggacc
agctggagatggtggacgtgatggagccgatggagtggatggaacaccgggagagattgg
acctccaggacccccagctccaccaggaccagatccacactcactcttcccaccacaatg
tccatgtgaggctccaccaggtgacggtggaccaccaggacaaccaggaccagatggacc
accaggagccccaggaaatgccggagaggacgggaaaccaggagatcaaggaccacgtgg
accaccaggaattccaggagctccaggacaaccaggacgtccaggaccaccaggagagcc
aggaacctacaagactgaagttggaccagctggaagagccggagctccaggaagaccagg
accaccaggacaaccaggaccagctggaccaccaggagaaaatggaaagggaggtggcca
aggaccatcagggctcccaggaccaccagggcaaccaggacaaaatggagcaccaggaga
agttggacaaccaggagacaacggagctccaggaagttgcgatcattg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAATCATTCAACTCCGAAGGTGGA 591 575 375 Antisense
GGTGGAGGGTGCTGCACTTGTCATC 34 499 394 Antisense
GATGGTGGACGTGATGGAGCCGATG 666 407 442 Antisense
GGAACACCGGGAGAGATTGGACCTC 707 527 475 Antisense
TCTTCCCACCACAATGTCCATGTGA 58 619 539 Antisense
CACAATGTCCATGTGAGGCTCCACC 173 195 548 Antisense
CACCAGGTGACGGTGGACCACCAGG 21 201 569 Antisense
GGAGAGCCAGGAACCTACAAGACTG 91 519 727 Antisense
ACAAGACTGAAGTTGGACCAGCTGG 219 113 743 Antisense
AGGTGGCCAAGGACCATCAGGGCTC 50 57 846 Antisense
GAGCTCCAGGAAGTTGCGATCATTG 462 387 938 Antisense
Sequence Source Affymetrix Proprietary Database