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[172809_x_at] CUTICLE COLLAGEN 1

Description Y41E3.2 /REP_DB=WormBase Gene ID /WP=CE18370 /TR=O62432 /GB=CAB08999.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=CUTICLE COLLAGEN 1
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 80      4grp_highest_8_8 > 02      4grp_high_8_8 > 54      6grp_highest_nonorm > 08      6grp_total > 72      4grp_total > 57      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38852
1 2 3 4 range
A 4987.8
(-2.3)
P 		38773.1
(2.9)
P 		39211
(3)
P 		434.3
(-3)
P 		38777
B 5989.2
(-2)
P 		30330.1
(2.2)
P 		34845.4
(3)
P 		359.2
(-3)
P 		34486
C 4893.6
(-2)
P 		28070.6
(3)
P 		27581.5
(2.9)
P 		441.6
(-3)
P 		27629
avr 5290.2
(-2.1) 		32391.3
(2.7) 		33879.3
(3) 		411.7
(-3) 		33468

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18101
1 2 3 4 5 6 range
A 10072.3
(-3)
P 		25577.7
(3)
P 		23758.8
(2.3)
P 		25001.7
(2.8)
P 		22164.3
(1.7)
P 		13706.7
(-1.6)
P 		15505
B 8575.4
(-3)
P 		25459.5
(3)
P 		24901
(2.8)
P 		23660.7
(2.4)
P 		19313.9
(0.8)
P 		11712.9
(-1.9)
P 		16884
C 8735.6
(-3)
P 		26676.5
(3)
P 		23811.5
(2)
P 		22224.3
(1.5)
P 		23068.3
(1.8)
P 		10614.4
(-2.4)
P 		17941
avr 9127.8
(-3) 		25904.6
(3) 		24157.1
(2.4) 		23628.9
(2.2) 		21515.5
(1.4) 		12011.3
(-2) 		16777
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10187
1 2 3 4 range
A 1816
(-2)
P 		8416.6
(1.9)
P 		10250.5
(3)
P 		63.6
(-3)
P 		10187
B 1909.9
(-1.6)
P 		7490.8
(2.6)
P 		8074.5
(3)
P 		76.5
(-3)
P 		7998
C 1619.9
(-2)
P 		8070.5
(2)
P 		9613
(3)
P 		74.5
(-3)
P 		9539
avr 1781.9
(-1.9) 		7992.6
(2.1) 		9312.7
(3) 		71.5
(-3) 		9241

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7240
1 2 3 4 5 6 range
A 1856.8
(-3)
P 		9096.7
(3)
P 		5174.2
(-0.3)
P 		6341
(0.7)
P 		6688.2
(1)
P 		3337.2
(-1.8)
P 		7240
B 2983.8
(-3)
P 		8474.4
(3)
P 		6046.7
(0.3)
P 		6266.9
(0.6)
P 		7847
(2.3)
P 		4367.7
(-1.5)
P 		5491
C 3237.9
(-3)
P 		8139.8
(3)
P 		6060.4
(0.5)
P 		4469.3
(-1.5)
P 		7464.6
(2.2)
P 		3553.3
(-2.6)
P 		4902
avr 2692.8
(-3) 		8570.3
(3) 		5760.4
(0.1) 		5692.4
(0.1) 		7333.3
(1.7) 		3752.7
(-1.9) 		5878
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172809_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8862
Sequence Type Exemplar sequence
Representative Public ID Y41E3.2 NCBI
Target Description Y41E3.2 /REP_DB=WormBase Gene ID /WP=CE18370 /TR=O62432 /GB=CAB08999.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=CUTICLE COLLAGEN 1
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_070407(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070407 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-4) (dpy-4) mRNA, complete cds. 11/11 None
SNAP00000001434 ENSEMBL cdna:SNAP chromosome:CEL140:IV:14985607:14986759:-1 11/11 None
GENEFINDER00000001476 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:14985607:14986714:-1 11/11 None
Y41E3.2 ENSEMBL cdna:known chromosome:CEL140:IV:14985505:14986744:-1 gene:Y41E3.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_069428 1/11 Cross Hyb Matching Probes A 
NM_073485 2/11 Cross Hyb Matching Probes A 
NM_073487 1/11 Cross Hyb Matching Probes A 
NM_069160 1/11 Cross Hyb Matching Probes A 
NM_073512 1/11 Cross Hyb Matching Probes A 
NM_069299 1/11 Cross Hyb Matching Probes A 
NM_077154 1/11 Cross Hyb Matching Probes None
NM_072673 1/11 Cross Hyb Matching Probes A 
NM_078121 1/11 Cross Hyb Matching Probes A 
NM_070113 1/11 Cross Hyb Matching Probes A 
SNAP00000003708 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003712 1/11 Cross Hyb Matching Probes None
SNAP00000026309 1/11 Cross Hyb Matching Probes None
GENEFINDER00000026317 1/11 Cross Hyb Matching Probes None
SNAP00000033943 1/11 Cross Hyb Matching Probes None
GENEFINDER00000033946 1/11 Cross Hyb Matching Probes None
SNAP00000040433 1/11 Cross Hyb Matching Probes None
GENEFINDER00000040439 1/11 Cross Hyb Matching Probes None
SNAP00000013927 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013944 1/11 Cross Hyb Matching Probes None
SNAP00000017929 1/11 Cross Hyb Matching Probes None
SNAP00000017931 2/11 Cross Hyb Matching Probes None
GENEFINDER00000017933 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
SNAP00000009612 1/11 Cross Hyb Matching Probes None
GENEFINDER00000009623 1/11 Cross Hyb Matching Probes None
C53B4.5 1/11 Cross Hyb Matching Probes A 
T05A1.2 1/11 Cross Hyb Matching Probes A 
W01B6.7 1/11 Cross Hyb Matching Probes A 
C39E9.9 1/11 Cross Hyb Matching Probes A 
ZC513.8 1/11 Cross Hyb Matching Probes A 
F55C10.2 2/11 Cross Hyb Matching Probes A 
F55C10.3 1/11 Cross Hyb Matching Probes A 
T11F9.9 1/11 Cross Hyb Matching Probes R A 
C35B8.1 1/11 Cross Hyb Matching Probes A 
T10B10.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:14985612-14986720(-) 89.31 100.0
Public Domain and Genome References
Gene Title CUTICLE COLLAGEN 1
Gene Symbol dpy-4
Ensembl Y41E3.2
Entrez Gene 178414 Entrez gene
SwissProt O62432 EMBL-EBI
WormBase CE18370 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 CAB08999 Hypothetical protein Y41E3.2 [Caenorhabditis elegans] ref|NP_502808.1| DumPY : shorter than wild-type family member (dpy-4) [Caenorhabditis elegans] 3.0E-47
blast CAE68135 Hypothetical protein CBG13781 [Caenorhabditis briggsae] 9.0E-47
blast CAE68135 Hypothetical protein CBG13781 [Caenorhabditis briggsae] 1.0E-46
blast CAA92453 Hypothetical protein C53B4.5 [Caenorhabditis elegans] ref|NP_501561.1| C53B4.5 [Caenorhabditis elegans] 1.0E-26
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-18
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-15
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-18
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502808.1 1 12-34
Y41E3.2 1 12-34
SNAP00000001434 1 29-51
GENEFINDER00000001476 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:172809_X_AT
tgctgcttgccaggaccacaaggaccacagggaaccccaggaaagcctggaaagccagga
aagccaggagctccaggacaaccaggaactccaggacgtccaccacagcaaccatgtgag
ccaaccaccccaccaccatgccagccatgcccacaaggaccacccggaccaccaggacag
ccaggaattccaggagacaacggaccaccaggagagcaaggaccaaagggaccagacgcc
gcaccaggagagccaggaccaaagggaccgattggaccaccaggaccaccaggacaagcc
ggagccccaggagagccaggatcaccagccaagtctgagccagccgttccaggaccacca
ggaccaccaggacaggccggacaacaaggaccaccaggaccaccaggatccaacggaatc
gatggagctccaggagcaccaggagccaagggagaaccaggaactccaggagagccagga
aaggatggagagccaggaaagccaggaactccaggacaagacggaactccaggagagaag
ggaatctgtccaaagtactgcgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCTGCTTGCCAGGACCACAAGGAC 452 581 277 Antisense
GAAAGCCAGGAGCTCCAGGACAACC 325 359 335 Antisense
GACAACCAGGAACTCCAGGACGTCC 504 365 353 Antisense
GTCCACCACAGCAACCATGTGAGCC 335 477 374 Antisense
GGACCACCAGGACAGCCAGGAATTC 561 521 442 Antisense
GAGAGCCAGGACCAAAGGGACCGAT 61 395 524 Antisense
CCAGGATCACCAGCCAAGTCTGAGC 228 271 592 Antisense
GGACAGGCCGGACAACAAGGACCAC 560 523 646 Antisense
AGGACCACCAGGATCCAACGGAATC 235 55 672 Antisense
GCACCAGGAGCCAAGGGAGAACCAG 453 315 712 Antisense
GGGAATCTGTCCAAAGTACTGCGCT 630 493 816 Antisense
Sequence Source Affymetrix Proprietary Database